Publications by authors named "Qiang Cui"

241 Publications

O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism.

Proc Natl Acad Sci U S A 2021 Sep;118(39)

Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany;

Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in bacteriorhodopsin (bR) and its conversion back to the bR ground state. The computed free energy surface is consistent with available experimental data for the kinetics and thermodynamics of the O to bR transition. The simulation results highlight the importance of the proton release group (PRG, consisting of Glu194/204) and the conserved arginine 82 in modulating the hydration level of the protein cavity. In particular, in the O state, deprotonation of the PRG and downward rotation of Arg82 lead to elevated hydration level and a continuous water network that connects the PRG to the protonated Asp85. Proton exchange through this water network is shown by ∼0.1-μs semiempirical QM/MM free energy simulations to occur through the generation and propagation of a proton hole, which is relayed by Asp212 and stabilized by Arg82. This mechanism provides an explanation for the observation that the D85S mutant of bacteriorhodopsin pumps chloride ions. The electrostatics-hydration coupling mechanism and the involvement of all titration states of water are likely applicable to many biomolecules involved in bioenergetic transduction.
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http://dx.doi.org/10.1073/pnas.2024803118DOI Listing
September 2021

Pan-cancer Analysis of NEDD4L and Its Tumor Suppressor Effects in Clear Cell Renal Cell Carcinoma.

J Cancer 2021 28;12(20):6242-6253. Epub 2021 Aug 28.

Fujian Provincial Key Laboratory of Transplant Biology, Fuzong Clinical College, Fujian Medical University, Fuzhou 350025, China.

The expression level of NEDD4L, an E3 ubiquitin ligase, has changed significantly in human cancers. In this study, we aimed to study the expression of NEDD4L in pan-carcinoma and its function in malignant tumors. We analyzed the gene expression level of NEDD4L in pan-cancer from The Cancer Genome Atlas (TCGA) microarray data set, the correlation between gene expression and overall survival, disease-specific survival, and tumor immune microenvironment changes. NEDD4L expression changes in half of the cancer types. Low expression of NEDD4L gene predicts poor overall survival and disease-specific survival (DSS) in renal clear cell carcinoma (KIRC) and renal chromophobe cell carcinoma (KIRP). NEDD4L is negatively related to interstitial cell infiltration and immune cell infiltration in most common cancers. Furthermore, the low expression of NEDD4L was verified in our clear cell renal cell carcinoma (ccRCC) clinical tissues. In ccRCC cells, NEDD4L overexpression significantly reduced cell proliferation and migration. In the functional analysis, we proved that NEDD4L could inhibit ERBB3 and MAPK signaling pathways. When cells are deficient in nutrition, NEDD4L promoted the degradation of the autophagy regulatory protein ULK1. Our study provides novel insights into the role of NEDD4L in pan-cancer. NEDD4L may play a tumor suppressor effect in ccRCC, through tumor immune regulation and ubiquitination of key intracellular kinases.
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http://dx.doi.org/10.7150/jca.58004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8425189PMC
August 2021

Effect of two-step enzymatic hydrolysis on the antioxidant properties and proteomics of hydrolysates of milk protein concentrate.

Food Chem 2022 Jan 27;366:130711. Epub 2021 Jul 27.

College of Food Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Dairy Science of Ministry of Education, Northeast Agricultural University, Harbin 150030, China; Department of Nutrition and Food Sciences, College of Agriculture and Life Sciences, University of Vermont, Burlington 05405, United States. Electronic address:

Food protein and peptides are generally considered a source of dietary antioxidants. The antioxidant activity and peptide profiles of four extensive hydrolysates of milk protein concentrate (MPC) were examined using the two-step enzymatic method. The hydrolysis combinations were Alcalase-Flavourzyme (AE), Alcalase-ProteAXH (AH), Alcalase-Protamex (AX) and Alcalase-Protease A 2SD (AD). The results showed that highest degree of hydrolysis corresponded to the AE sample (20.41%). High-efficiency gel-filtration chromatography results indicated that the relative proportions of extensive hydrolysates with molecular weights < 3 kDa were 99.89%, 99.57%, 99.93%, and 99.89% for AX, AE, AD and AH, respectively. The hydrolysates of the MPC exhibited increased radical-scavenging capacity, as evidenced through an analysis with 1,1-diphenyl-2-pycryl-hydrazyl (DPPH), 2,2-azinobis (3-ethylbenzothiazo-line-6-sulfonic acid) diammonium salt (ABTS), reducing power and hydroxyl-radical scavenging activity testing. The main bioactive peptides were identified through EASY-nLC-orbitrap MS/MS and bioinformatics. The study may provide useful information regarding the antioxidant properties of extensive hydrolysates of MPC.
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http://dx.doi.org/10.1016/j.foodchem.2021.130711DOI Listing
January 2022

Conformational Features of Ras: Key Hydrogen-Bonding Interactions of Gln61 in the Intermediate State during GTP Hydrolysis.

J Phys Chem B 2021 Aug 29;125(31):8805-8813. Epub 2021 Jul 29.

Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Departments of Chemistry, Fudan University, Shanghai 200433, China.

The Ras protein is one of the most important drug targets for battling cancers. To effectively design novel drugs of Ras, we characterize here its conformational ensembles for the hydrolysis intermediate state RasGDP·Pi and the product state RasGDP by extensive replica-exchange molecular dynamics simulations. Several substates for RasGDP·Pi have been identified, while structural analyses have revealed an unrecognized hydrogen-bonding network that stabilizes the hydrolysis intermediate state. More interestingly, Gln61, which is involved in numerous oncogenic mutations, was found to be engaged in this hydrogen-bonding network, adopting a specific conformation that always points to Pi in contrast to that in the RasGTP state. The simulations also reveal that RasGDP has more than one substate, suggesting a conformational selection mechanism for the interaction between Ras and the guanine nucleotide exchange factors (GEFs). These findings offer new opportunities for the drug design of Ras by stabilizing the hydrolysis intermediate or disrupting its interaction with the GEFs.
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http://dx.doi.org/10.1021/acs.jpcb.1c04679DOI Listing
August 2021

Single-step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in Anaerobic Ergothioneine Biosynthesis.

ACS Catal 2020 Aug 16;10(16):8981-8994. Epub 2020 Jul 16.

Department of Chemistry, Boston University, Boston, MA 02215, USA.

Ergothioneine, a natural longevity vitamin and antioxidant, is a thiol-histidine derivative. Recently, two types of biosynthetic pathways were reported. In the aerobic ergothioneine biosynthesis, a non-heme iron enzyme incorporates a sulfoxide to an sp C-H bond in trimethyl-histidine (hercynine) through oxidation reactions. In contrast, in the anaerobic ergothioneine biosynthetic pathway in a green sulfur bacterium, , a rhodanese domain containing protein (EanB) directly replaces this unreactive hercynine C-H bond with a C-S bond. Herein, we demonstrate that polysulfide (HSSSR) is the direct sulfur-source in EanB-catalysis. After identifying EanB's substrates, X-ray crystallography of several intermediate states along with mass spectrometry results provide additional mechanistic details for this reaction. Further, quantum mechanics/molecular mechanics (QM/MM) calculations reveal that protonation of N of hercynine by Tyr353 with the assistance of Thr414 is a key activation step for the hercynine sp C-H bond in this trans-sulfuration reaction.
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http://dx.doi.org/10.1021/acscatal.0c01809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8302205PMC
August 2020

Protein-induced membrane curvature in coarse-grained simulations.

Biophys J 2021 08 29;120(15):3211-3221. Epub 2021 Jun 29.

Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, Boston, Massachusetts. Electronic address:

Using the endosomal sorting complex required for transport (ESCRT)-III membrane remodeling complex as an example, we analyze three popular coarse-grained models (the regular MARTINI, polarizable MARTINI (POL-MARTINI), and big multipole water MARTINI (BMW-MARTINI)) for the description of membrane curvature sensing and generation activities of peripheral proteins. Although the three variants of the MARTINI model provide consistent descriptions for the protein-protein interface in a linear filament model of ESCRT-III, they differ considerably in terms of protein-membrane interface and therefore membrane curvature sensing and generation behaviors. In particular, BMW-MARTINI provides the most consistent description of the protein-membrane interface as compared to all-atom simulations, whereas the regular MARTINI is most consistent with atomistic simulations in terms of the qualitative sign of membrane curvature sensing and generation. With POL-MARTINI, the ESCRT-III model interacts weakly with the membrane and therefore does not exhibit any curvature-sensitive activities. Analysis suggests that the incorrect membrane curvature activities predicted by BMW-MARTINI are due to overestimated insertion depth of an amphipathic helix and incorrect sign for the spontaneous curvature of anionic lipids. These results not only point to ways that coarse-grained models can be improved but also explicitly highlight local lipid composition and insertion depth of protein motifs as essential regulatory factors for membrane curvature sensing and generation.
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http://dx.doi.org/10.1016/j.bpj.2021.05.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8390925PMC
August 2021

Multicolor polymeric carbon dots: synthesis, separation and polyamide-supported molecular fluorescence.

Chem Sci 2020 Dec 22;12(7):2441-2455. Epub 2020 Dec 22.

Department of Chemistry, University of Minnesota-Twin Cities 207 Pleasant Street SE Minneapolis Minnesota 55455 USA

Multicolor carbon dots (CDs) have been developed recently and demonstrate great potential in bio-imaging, sensing, and LEDs. However, the fluorescence mechanism of their tunable colors is still under debate, and efficient separation methods are still challenging. Herein, we synthesized multicolor polymeric CDs through solvothermal treatment of citric acid and urea in formamide. Automated reversed-phase column separation was used to achieve fractions with distinct colors, including blue, cyan, green, yellow, orange and red. This work explores the physicochemical properties and fluorescence origins of the red, green, and blue fractions in depth with combined experimental and computational methods. Three dominant fluorescence mechanism hypotheses were evaluated by comparing time-dependent density functional theory and molecular dynamics calculation results to measured characteristics. We find that blue fluorescence likely comes from embedded small molecules trapped in carbonaceous cages, while pyrene analogs are the most likely origin for emission at other wavelengths, especially in the red. Also important, upon interaction with live cells, different CD color fractions are trafficked to different sub-cellular locations. Super-resolution imaging shows that the blue CDs were found in a variety of organelles, such as mitochondria and lysosomes, while the red CDs were primarily localized in lysosomes. These findings significantly advance our understanding of the photoluminescence mechanism of multicolor CDs and help to guide future design and applications of these promising nanomaterials.
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http://dx.doi.org/10.1039/d0sc05743fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8179321PMC
December 2020

Reverse Protonation of Buried Ion-Pairs in Staphylococcal Nuclease Mutants.

J Chem Theory Comput 2021 Jul 18;17(7):4550-4563. Epub 2021 Jun 18.

Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.

Although buried titratable residues in protein cavities are often of major functional importance, it is generally challenging to understand their properties such as the ionization state and factors of stabilization based on experimental studies alone. A specific set of examples involve buried Glu-Lys pairs in a series of variants of nuclease, for which recent structural and thermodynamic studies appeared to suggest that both the stability and the ionization state of the buried Glu-Lys pair are sensitive to its orientation (i.e., Glu23-Lys36 vs Lys23-Glu36). To further clarify the situation, especially ionization states of the buried Glu-Lys pairs, we have conducted extensive molecular dynamics simulations and free energy computations. Microsecond molecular dynamics simulations show that the hydration level of the cavity depends on the orientation of the buried ion-pair therein as well as its ionization state; free energy simulations recapitulate the relative stability of Glu23-Lys36 (EK) vs Lys23-Glu36 (KE) mutants measured experimentally, although the difference is similar in magnitude regardless of the ionization state of the Glu-Lys pair. A complementary set of free energy simulations strongly suggests that, in contrast to the original suggestion in the experimental analysis, the Glu and Lys residues prefer to adopt their charge-neutral rather than the ionized states. This result is consistent with the low dielectric constant computed for water in the cavity, which makes it difficult for the protein cavity to stabilize a pair of charged Glu-Lys residues, even with water penetration. The current study highlights the role of free energy simulations in understanding the ionization state of buried titratable residues and the relevant energetic contributions, forming the basis for the rational design of buried charge networks in proteins.
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http://dx.doi.org/10.1021/acs.jctc.1c00355DOI Listing
July 2021

Influence of Surface Ligand Molecular Structure on Phospholipid Membrane Disruption by Cationic Nanoparticles.

Langmuir 2021 06 11;37(24):7600-7610. Epub 2021 Jun 11.

Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.

Cationic nanoparticles are known to interact with biological membranes and often cause serious membrane damage. Therefore, it is important to understand the molecular mechanism for such interactions and the factors that impact the degree of membrane damage. Previously, we have demonstrated that spatial distribution of molecular charge at cationic nanoparticle surfaces plays an important role in determining the cellular uptake and membrane damage of these nanoparticles. In this work, using diamond nanoparticles (DNPs) functionalized with five different amine-based surface ligands and small phospholipid unilamellar vesicles (SUVs), we further investigate how chemical features and conformational flexibility of surface ligands impact nanoparticle/membrane interactions. P-NMR relaxation measurements quantify the mobility changes in lipid dynamics upon exposing the SUVs to functional DNPs, and coarse-grained molecular dynamics simulations further elucidate molecular details for the different modes of DNP-SUV interactions depending on the surface ligands. Collectively, our results show that the length of the hydrophobic segment and conformational flexibility of surface ligands are two key factors that dictate the degree of membrane damage by the DNP, while the amount of surface charge alone is not predictive of the strength of interaction.
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http://dx.doi.org/10.1021/acs.langmuir.1c01146DOI Listing
June 2021

Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.

Proc Natl Acad Sci U S A 2021 Jun;118(23)

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892;

DNA synthesis by polymerases is essential for life. Deprotonation of the nucleophile 3'-OH is thought to be the obligatory first step in the DNA synthesis reaction. We have examined each entity surrounding the nucleophile 3'-OH in the reaction catalyzed by human DNA polymerase (Pol) η and delineated the deprotonation process by combining mutagenesis with steady-state kinetics, high-resolution structures of in crystallo reactions, and molecular dynamics simulations. The conserved S113 residue, which forms a hydrogen bond with the primer 3'-OH in the ground state, stabilizes the primer end in the active site. Mutation of S113 to alanine destabilizes primer binding and reduces the catalytic efficiency. Displacement of a water molecule that is hydrogen bonded to the 3'-OH using the 2'-OH of a ribonucleotide or 2'-F has little effect on catalysis. Moreover, combining the S113A mutation with 2'-F replacement, which removes two potential hydrogen acceptors of the 3'-OH, does not reduce the catalytic efficiency. We conclude that the proton can leave the O3' via alternative paths, supporting the hypothesis that binding of the third Mg initiates the reaction by breaking the α-β phosphodiester bond of an incoming deoxyribonucleoside triphosphate (dNTP).
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http://dx.doi.org/10.1073/pnas.2103990118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201771PMC
June 2021

Substrate deformation regulates DRM2-mediated DNA methylation in plants.

Sci Adv 2021 Jun 2;7(23). Epub 2021 Jun 2.

Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA.

DNA methylation is a major epigenetic mechanism critical for gene expression and genome stability. In plants, domains rearranged methyltransferase 2 (DRM2) preferentially mediates CHH (H = C, T, or A) methylation, a substrate specificity distinct from that of mammalian DNA methyltransferases. However, the underlying mechanism is unknown. Here, we report structure-function characterization of DRM2-mediated methylation. An arginine finger from the catalytic loop intercalates into the nontarget strand of DNA through the minor groove, inducing large DNA deformation that affects the substrate preference of DRM2. The target recognition domain stabilizes the enlarged major groove via shape complementarity rather than base-specific interactions, permitting substrate diversity. The engineered DRM2 C397R mutation introduces base-specific contacts with the +2-flanking guanine, thereby shifting the substrate specificity of DRM2 toward CHG DNA. Together, this study uncovers DNA deformation as a mechanism in regulating the specificity of DRM2 toward diverse CHH substrates and illustrates methylome complexity in plants.
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http://dx.doi.org/10.1126/sciadv.abd9224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8172135PMC
June 2021

Recent advances in alleviating food allergenicity through fermentation.

Crit Rev Food Sci Nutr 2021 May 6:1-14. Epub 2021 May 6.

College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang, China.

The increasing prevalence of food allergies is a significant challenge to global food health and safety. Various strategies have been deployed to decrease the allergenicity of food for preventing and reducing related disorders. Compared to other methods, fermentation has unique advantages in reducing the allergenicity of food and may represent a new trend in preventing food-induced allergies. This review introduces the characteristics of allergens in various foods, including shellfish, soy, peanut, milk, tree nut, egg, wheat, and fish. The mechanism and pathological symptoms of allergic reactions are then summarized. Furthermore, the advantages of fermentation for reducing the allergenicity of these foods and preventing allergies are evaluated. Fermentation is an efficient approach for reducing or eliminating food allergenicity. Simultaneously, it improved the nutritional value and physicochemical properties of food materials. It is conceivable that a combination of mixed strain fermentation with additional processing, such as heat treatment, pulsed light, and ultrasonication, will efficiently reduce the allergenicity of various foods and preserve their unique taste and nutritional components, providing significance for patients with allergies.
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http://dx.doi.org/10.1080/10408398.2021.1913093DOI Listing
May 2021

DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation.

Nat Commun 2021 05 3;12(1):2490. Epub 2021 May 3.

Department of Biochemistry, University of California, Riverside, CA, USA.

DNA methylation and trimethylated histone H4 Lysine 20 (H4K20me3) constitute two important heterochromatin-enriched marks that frequently cooperate in silencing repetitive elements of the mammalian genome. However, it remains elusive how these two chromatin modifications crosstalk. Here, we report that DNA methyltransferase 1 (DNMT1) specifically 'recognizes' H4K20me3 via its first bromo-adjacent-homology domain (DNMT1). Engagement of DNMT1-H4K20me3 ensures heterochromatin targeting of DNMT1 and DNA methylation at LINE-1 retrotransposons, and cooperates with the previously reported readout of histone H3 tail modifications (i.e., H3K9me3 and H3 ubiquitylation) by the RFTS domain to allosterically regulate DNMT1's activity. Interplay between RFTS and BAH1 domains of DNMT1 profoundly impacts DNA methylation at both global and focal levels and genomic resistance to radiation-induced damage. Together, our study establishes a direct link between H4K20me3 and DNA methylation, providing a mechanism in which multivalent recognition of repressive histone modifications by DNMT1 ensures appropriate DNA methylation patterning and genomic stability.
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http://dx.doi.org/10.1038/s41467-021-22665-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8093215PMC
May 2021

Effect of temperature of preheated soy protein isolate on the structure and properties of soy protein isolate heated-vitamin D complex.

J Food Biochem 2021 06 23;45(6):e13733. Epub 2021 Apr 23.

School of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China.

In this paper, soy protein isolate (SPI) was preheated and combined with vitamin D (VD ) to study the protective effect of modified SPI on VD . The structure and properties of the SPI with heat treatment-VD (SPI(H)-VD ) complex were determined. The secondary and tertiary structure of SPI(H)-VD results showed that the content of α-helix decreased and the content of random coil increased, indicating that the rigid structure of the protein decreased, the flexibility increased, and the maximum fluorescence intensity wavelength was red shifted. When the heat treatment temperature was 85°C, the embedding rate of SPI(H)-VD composite was the highest. As the heat treatment temperature increased, the internal hydrophobic groups of SPI were exposed, and the average particle size decreased significantly. The light stability results showed that the content of VD in the SPI(H)-VD composite at a heat treatment temperature of 85°C was significantly increased compared with the unheated SPI. PRACTICAL APPLICATIONS: This article mainly discusses the structure and properties of modified soy protein isolates bound to VD by preheating soy protein isolates at different temperatures. It provides more possibilities for the application of VD in food.
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http://dx.doi.org/10.1111/jfbc.13733DOI Listing
June 2021

Modulation of Nanoparticle Diffusion by Surface Ligand Length and Charge: Analysis with Molecular Dynamics Simulations.

J Phys Chem B 2021 05 21;125(17):4555-4565. Epub 2021 Apr 21.

Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.

To help better interpret experimental measurement of nanoparticle size, it is important to understand how their diffusion depends on the physical and chemical features of surface ligands. In this study, explicit solvent molecular dynamics simulations are used to probe the effect of ligand charge and flexibility on the diffusion of small gold nanoparticles. The results suggest that despite a high bare charge (+18 ), cationic nanoparticles studied here have reduced diffusion constants compared to a hydrophobic gold nanoparticle by merely a modest amount. Increasing the ligand length by 10 CH units also has a limited impact on the diffusion constant. For the three particles studied here, the difference between estimated hydrodynamic radius and radius of gyration is on the order of one solvent layer (3-5 Å), confirming that the significant discrepancies found in the size of similar nanoparticles by recent transmission electron microscopy and dynamic light scattering measurements were due to aggregation under solution conditions. The limited impact of electrostatic friction on the diffusion of highly charged nanoparticles is found to be due to the strong anticorrelation between electrostatic and van der Waals forces between nanoparticle and environment, supporting the generality of recent observation for proteins by Matyushov and co-workers. Including the first shell of solvent molecules as part of the diffusing particle has a minor impact on the total force autocorrelation function but reduces the disparity in relaxation time between the total force and its electrostatic and van der Waals components.
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http://dx.doi.org/10.1021/acs.jpcb.1c01189DOI Listing
May 2021

Mapping temperature-dependent conformational change in the voltage-sensing domain of an engineered heat-activated K channel.

Proc Natl Acad Sci U S A 2021 Apr;118(14)

Graduate Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706;

Temperature-dependent regulation of ion channel activity is critical for a variety of physiological processes ranging from immune response to perception of noxious stimuli. Our understanding of the structural mechanisms that underlie temperature sensing remains limited, in part due to the difficulty of combining high-resolution structural analysis with temperature stimulus. Here, we use NMR to compare the temperature-dependent behavior of Shaker potassium channel voltage sensor domain (WT-VSD) to its engineered temperature sensitive (TS-VSD) variant. Further insight into the molecular basis for temperature-dependent behavior is obtained by analyzing the experimental results together with molecular dynamics simulations. Our studies reveal that the overall secondary structure of the engineered TS-VSD is identical to the wild-type channels except for local changes in backbone torsion angles near the site of substitution (V369S and F370S). Remarkably however, these structural differences result in increased hydration of the voltage-sensing arginines and the S4-S5 linker helix in the TS-VSD at higher temperatures, in contrast to the WT-VSD. These findings highlight how subtle differences in the primary structure can result in large-scale changes in solvation and thereby confer increased temperature-dependent activity beyond that predicted by linear summation of solvation energies of individual substituents.
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http://dx.doi.org/10.1073/pnas.2017280118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8040809PMC
April 2021

Interfacial Polarization and Ionic Structure at the Ionic Liquid-Metal Interface Studied by Vibrational Spectroscopy and Molecular Dynamics Simulations.

J Phys Chem B 2021 03 9;125(10):2741-2753. Epub 2021 Mar 9.

Department of Chemistry, University of Southern California, Los Angeles, California 90007, United States.

Ionic liquids (ILs) have both fundamental and practical value in interfacial science and electrochemistry. However, understanding their behavior near a surface is challenging because of strong Coulomb interactions and large and irregular ionic sizes, which affect both their structure and energetics. To understand this problem, we present a combined experimental and computational study using a vibrational probe molecule, 4-mercaptobenzonitrile, inserted at the junction between a metal and a variety of ILs. The vibrational frequency of the nitrile in the probe molecule reports on the local solvation environment and the electrostatic field at this junction. Within the ethylmethyl imidazolium (EMIM) cation family of ILs, we varied the anions over a range of sizes and types. Complementing our surface spectroscopy, we also ran molecular dynamics simulations of these interfaces to better understand the ionic structures that produced the measured fields. The magnitude of the frequency shifts, and thereby fields, shows a general correlation with the size of anions, with larger anions corresponding to smaller fields. We find that the source of this correlation is partial intercalation of smaller anions into the probe monolayer, resulting in tighter packing of ionic layers near the surface. Larger anions reduce the overall lateral ion packing density near the surface, which reduces the net charge per unit area and explains the smaller observed fields. The insight from this work is important for developing a fundamental picture of concentrated electrolytes near interfaces and can help with designing ILs to create tailored electric fields near an electrode.
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http://dx.doi.org/10.1021/acs.jpcb.0c11232DOI Listing
March 2021

Protective Role of Collectin 11 in a Mouse Model of Rheumatoid Arthritis.

Arthritis Rheumatol 2021 08 7;73(8):1430-1440. Epub 2021 Jul 7.

National Local Joint Engineering Research Centre of Biodiagnostics and Biotherapy, and The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China.

Objective: Collectin 11 (CL-11) is a soluble C-type lectin, a mediator of innate immunity. Its role in autoimmune disorders is unknown. We undertook this study to determine the role of CL-11 in a mouse model of rheumatoid arthritis (RA).

Methods: A murine collagen-induced arthritis (CIA) model was used and combined two approaches, including gene deletion of Colec11 and treatment with recombinant CL-11 (rCL-11). Joint inflammation and tissue destruction, circulating levels of inflammatory cytokines, and adaptive immune responses were assessed in mice with CIA. Splenic CD11c+ cells were used to examine the influence of CL-11 on antigen-presenting cell (APC) function. Serum CL-11 levels in RA patients were also examined.

Results: Colec11 mice developed more severe arthritis than wild-type mice, as determined by disease incidence, clinical arthritis scores, and histopathology (P < 0.05). Disease severity was associated with significantly enhanced APC activation, Th1/Th17 responses, pathogenic IgG2a production and joint inflammation, as well as elevated circulating levels of inflammatory cytokines. In vitro analysis of CD11c+ cells revealed that CL-11 is critical for suppression of APC activation and function. Pharmacologic treatment of mice with rCL-11 reduced the severity of CIA in mice. Analysis of human blood samples revealed that serum CL-11 levels were lower in RA patients (n = 51) compared to healthy controls (n = 53). Reduction in serum CL-11 was inversely associated with the Disease Activity Score in 28 joints, erythrocyte sedimentation rate, and C-reactive protein level (P < 0.05).

Conclusion: Our findings demonstrate a novel role of CL-11 in protection against RA, suggesting that the underlying mechanism involves suppression of APC activation and subsequent T cell responses.
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http://dx.doi.org/10.1002/art.41696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8324516PMC
August 2021

Effects of transglutaminase glycosylated soy protein isolate on its structure and interfacial properties.

J Sci Food Agric 2021 Sep 25;101(12):5097-5105. Epub 2021 Feb 25.

School of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, China.

Backgrounds: The structural and interfacial properties of soybean protein isolate (SPI) after glycosylation by the transglutaminase method were studied. It is hoped that preliminary explorations will find a new food ingredient and broader application of SPI in the food industry.

Results: The contents of free amino proves that transglutaminase can insert glucosamine into SPI through its transamination, and realize the enzymatic glycosylated SPI. The results of structure properties showed that a decrease in the content of the α-helical structure indicates that the rigid structure of the protein is opened and the flexibility is increased. The blue shift of the maximum fluorescence intensity of soy protein isolate-glucosamine with transglutaminase (SPI-G) indicates the formation of a new substance; scanning electron microscopy shows that the SPI-G powder can be seen at a magnification of 2000×, and the protein structure becomes soft. The results of interfacial properties found that enzymatic protein glycosylation exposes the internal hydrophobic groups of SPI, resulting in increased surface hydrophobicity, increased emulsification and emulsification stability, and reduced surface tension.

Conclusion: It shows that SPI-G effectively improves the interfacial properties of SPI, providing a theoretical basis for the application of enzymatic glycosylation of SPI in the food industry. © 2021 Society of Chemical Industry.
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http://dx.doi.org/10.1002/jsfa.11155DOI Listing
September 2021

Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

J Phys Chem B 2021 01 6;125(3):689-702. Epub 2021 Jan 6.

Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.

QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.
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http://dx.doi.org/10.1021/acs.jpcb.0c09898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8360698PMC
January 2021

Improvement of d-d interactions in density functional tight binding for transition metal ions with a ligand field model: assessment of a DFTB3+ model on nickel coordination compounds.

Phys Chem Chem Phys 2020 Dec;22(46):27084-27095

Institute of Physical Chemistry and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, D-76131 Karlsruhe, Germany.

To improve the description of interactions among the localized d, f electrons in transition metals, we have introduced a ligand-field motivated contribution into the Density Functional Tight Binding (DFTB) model. Referred to as DFTB3+U, the approach treats the d, f electron repulsions with rotationally invariant orbital-orbital interactions and a Hartree-Fock model; this represents a major conceptual improvement over the original DFTB3 approach, which treats the d, f-shell interactions in a highly averaged fashion without orbital level of description. The DFTB3+U approach is tested using a series of nickel compounds that feature Ni(ii) and Ni(iii) oxidation states. By using parameters developed with the original DFTB3 Hamiltonian and empirical +U parameters (F0/2/4 Slater integrals), we observe that the DFTB3+U model indeed provides substantial improvements over the original DFTB3 model for a number of properties of the nickel compounds, including the population and spin polarization of the d-shell, nature of the frontier orbitals, ligand field splitting and the energy different between low and high spin states at OPBE optimized structures. This proof-of-concept study suggests that with self-consistent parameterization of the electronic and +U parameters, the DFTB3+U model can develop into a promising model that can be used to efficiently study reactive events involving transition metals ion condensed phase systems. The methodology can be integrated with other approximate QM methods as well, such as the extended tight binding (xTB) approach.
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http://dx.doi.org/10.1039/d0cp04694aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7737908PMC
December 2020

Anionic nanoparticle-induced perturbation to phospholipid membranes affects ion channel function.

Proc Natl Acad Sci U S A 2020 11 26;117(45):27854-27861. Epub 2020 Oct 26.

Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706;

Understanding the mechanisms of nanoparticle interaction with cell membranes is essential for designing materials for applications such as bioimaging and drug delivery, as well as for assessing engineered nanomaterial safety. Much attention has focused on nanoparticles that bind strongly to biological membranes or induce membrane damage, leading to adverse impacts on cells. More subtle effects on membrane function mediated via changes in biophysical properties of the phospholipid bilayer have received little study. Here, we combine electrophysiology measurements, infrared spectroscopy, and molecular dynamics simulations to obtain insight into a mode of nanoparticle-mediated modulation of membrane protein function that was previously only hinted at in prior work. Electrophysiology measurements on gramicidin A (gA) ion channels embedded in planar suspended lipid bilayers demonstrate that anionic gold nanoparticles (AuNPs) reduce channel activity and extend channel lifetimes without disrupting membrane integrity, in a manner consistent with changes in membrane mechanical properties. Vibrational spectroscopy indicates that AuNP interaction with the bilayer does not perturb the conformation of membrane-embedded gA. Molecular dynamics simulations reinforce the experimental findings, showing that anionic AuNPs do not directly interact with embedded gA channels but perturb the local properties of lipid bilayers. Our results are most consistent with a mechanism in which anionic AuNPs disrupt ion channel function in an indirect manner by altering the mechanical properties of the surrounding bilayer. Alteration of membrane mechanical properties represents a potentially important mechanism by which nanoparticles induce biological effects, as the function of many embedded membrane proteins depends on phospholipid bilayer biophysical properties.
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http://dx.doi.org/10.1073/pnas.2004736117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668003PMC
November 2020

Differences in the Nature of the Phosphoryl Transfer Transition State in Protein Phosphatase 1 and Alkaline Phosphatase: Insights from QM Cluster Models.

Authors:
Rui Lai Qiang Cui

J Phys Chem B 2020 10 8;124(42):9371-9384. Epub 2020 Oct 8.

Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States.

Quantum mechanical (QM) cluster models are used to probe effects on the catalytic properties of protein phosphatase 1 (PP1) and alkaline phosphatase (AP) due to metal ions and active site residues. The calculations suggest that the phosphoryl transfer transition states in PP1 are synchronous in nature with a significant degree of P-O cleavage, while those in AP are tighter with a modest degree of P-O cleavage and a range of P-O formation. Similar to observations made in our recent work, a significant degree of cross talk between the forming and breaking P-O bonds complicates the interpretation of the Brønsted relation, especially in regard to AP for which the computed β/β value does not correlate with the degree of P-O cleavage regardless of the metal ions in the active site. By comparison, the correlation between β/β and the P-O bond order is more applicable to PP1, which generally exhibits less variation in the transition state than AP. Results for computational models with swapped metal ions between PP1 and AP suggest that the metal ions modulate both the nature of the transition state and the degrees of sensitivity of the transition state to the leaving group. In the reactant state, the degree of the scissile bond polarization is also different in the two enzymes, although this difference appears to be largely determined by the active site residues rather than the metal ions. Therefore, both the identity of the metal ion and the positioning of polar or charged residues in the active site contribute to the distinct catalytic characteristics of these enzymes. Several discrepancies observed between the QM cluster results and the available experimental data highlight the need for further QM/MM method developments for the quantitative analysis of metalloenzymes that contain open-shell transition metal ions.
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http://dx.doi.org/10.1021/acs.jpcb.0c07863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7647665PMC
October 2020

Functional plasticity and evolutionary adaptation of allosteric regulation.

Proc Natl Acad Sci U S A 2020 10 30;117(41):25445-25454. Epub 2020 Sep 30.

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706;

Allostery is a fundamental regulatory mechanism of protein function. Despite notable advances, understanding the molecular determinants of allostery remains an elusive goal. Our current knowledge of allostery is principally shaped by a structure-centric view, which makes it difficult to understand the decentralized character of allostery. We present a function-centric approach using deep mutational scanning to elucidate the molecular basis and underlying functional landscape of allostery. We show that allosteric signaling exhibits a high degree of functional plasticity and redundancy through myriad mutational pathways. Residues critical for allosteric signaling are surprisingly poorly conserved while those required for structural integrity are highly conserved, suggesting evolutionary pressure to preserve fold over function. Our results suggest multiple solutions to the thermodynamic conditions of cooperativity, in contrast to the common view of a finely tuned allosteric residue network maintained under selection.
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http://dx.doi.org/10.1073/pnas.2002613117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7568325PMC
October 2020

Interfacial water and ion distribution determine ζ potential and binding affinity of nanoparticles to biomolecules.

Nanoscale 2020 Sep 27;12(35):18106-18123. Epub 2020 Aug 27.

Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.

The molecular features that dictate interactions between functionalized nanoparticles and biomolecules are not well understood. This is in part because for highly charged nanoparticles in solution, establishing a clear connection between the molecular features of surface ligands and common experimental observables such as ζ potential requires going beyond the classical models based on continuum and mean field models. Motivated by these considerations, molecular dynamics simulations are used to probe the electrostatic properties of functionalized gold nanoparticles and their interaction with a charged peptide in salt solutions. Counterions are observed to screen the bare ligand charge to a significant degree even at the moderate salt concentration of 50 mM. As a result, the apparent charge density and ζ potential are largely insensitive to the bare ligand charge densities, which fall in the range of ligand densities typically measured experimentally for gold nanoparticles. While this screening effect was predicted by classical models such as the Manning condensation theory, the magnitudes of the apparent surface charge from microscopic simulations and mean-field models are significantly different. Moreover, our simulations found that the chemical features of the surface ligand (e.g., primary vs. quaternary amines, heterogeneous ligand lengths) modulate the interfacial ion and water distributions and therefore the interfacial potential. The importance of interfacial water is further highlighted by the observation that introducing a fraction of hydrophobic ligands enhances the strength of electrostatic binding of the charged peptide. Finally, the simulations highlight that the electric double layer is perturbed upon binding interactions. As a result, it is the bare charge density rather than the apparent charge density or ζ potential that better correlates with binding affinity of the nanoparticle to a charged peptide. Overall, our study highlights the importance of molecular features of the nanoparticle/water interface and underscores a set of design rules for the modulation of electrostatic driven interactions at nano/bio interfaces.
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http://dx.doi.org/10.1039/d0nr03792cDOI Listing
September 2020

Artificial Intracellular Filaments.

Cell Rep Phys Sci 2020 Jul 1;1(7). Epub 2020 Jul 1.

Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA.

Intracellular protein filaments are ubiquitous for cellular functions, but forming bona fide biomimetic intracellular filaments of small molecules in living cells remains elusive. Here, we report the formation of self-limiting intracellular filaments of a small peptide via enzymatic morphological transition of a phosphorylated and trimethylated heterochiral tetrapeptide. Enzymatic dephosphorylation reduces repulsive intermolecular electrostatic interactions and converts the peptidic nanoparticles into filaments, which exhibit distinct types of cross-β structures with either C7 or C2 symmetries, with the hydrophilic C-terminal residues at the periphery of the helix. Macromolecular crowding promotes the peptide filaments to form bundles, which extend from the plasma membrane to nuclear membrane and hardly interact with endogenous components, including cytoskeletons. Stereochemistry and post-translational modification (PTM) of peptides are critical for generating the intracellular bundles. This work may offer a way to gain lost functions or to provide molecular insights for understanding normal and aberrant intracellular filaments.
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http://dx.doi.org/10.1016/j.xcrp.2020.100085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7413147PMC
July 2020

Multi-level free energy simulation with a staged transformation approach.

J Chem Phys 2020 Jul;153(4):044115

Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.

Combining multiple levels of theory in free energy simulations to balance computational accuracy and efficiency is a promising approach for studying processes in the condensed phase. While the basic idea has been proposed and explored for quite some time, it remains challenging to achieve convergence for such multi-level free energy simulations as it requires a favorable distribution overlap between different levels of theory. Previous efforts focused on improving the distribution overlap by either altering the low-level of theory for the specific system of interest or ignoring certain degrees of freedom. Here, we propose an alternative strategy that first identifies the degrees of freedom that lead to gaps in the distributions of different levels of theory and then treats them separately with either constraints or restraints or by introducing an intermediate model that better connects the low and high levels of theory. As a result, the conversion from the low level to the high level model is done in a staged fashion that ensures a favorable distribution overlap along the way. Free energy components associated with different steps are mostly evaluated explicitly, and thus, the final result can be meaningfully compared to the rigorous free energy difference between the two levels of theory with limited and well-defined approximations. The additional free energy component calculations involve simulations at the low level of theory and therefore do not incur high computational costs. The approach is illustrated with two simple but non-trivial solution examples, and factors that dictate the reliability of the result are discussed.
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http://dx.doi.org/10.1063/5.0012494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7386948PMC
July 2020

Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation.

Proc Natl Acad Sci U S A 2020 08 16;117(31):18439-18447. Epub 2020 Jul 16.

Department of Biochemistry, University of California, Riverside, CA 92521;

In mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.
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http://dx.doi.org/10.1073/pnas.2009316117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7414182PMC
August 2020
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