3,283 results match your criteria characterize conformational


Effects of different alcohol and ultrasonic treatments on thermal and structural properties of zein-starch sodium octenyl succinate composite nanoparticles.

J Food Sci 2021 Jul 19. Epub 2021 Jul 19.

School of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, P. R. China.

The objective of this study is to prepare zein/starch sodium octenyl succinate composite nanoparticles (ZSPs) via anti-solvent precipitation technology and characterize their colloidal properties. The effects of polar solvents, ultrasonic treatment time, and concentrations of starch sodium octenyl succinate were investigated. We measured the particle size distribution, hydrophobicity, and apparent structures of the composite nanoparticles. Read More

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Combining Well-Tempered Metadynamics Simulation and SPR Assays to Characterize the Binding Mechanism of the Universal T-Lymphocyte Tetanus Toxin Epitope TT830-843.

Biomed Res Int 2021 4;2021:5568980. Epub 2021 Jul 4.

Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.

Peptide TT830-843 from the tetanus toxin is a universal T-cell epitope. It helps in vaccination and induces T-cell activation. However, the fine molecular interaction between this antigen and the major histocompatibility complex (MHC) remains unknown. Read More

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Evaluation of guanidine-based multimodal anion exchangers for protein selectivity and orthogonality.

J Chromatogr A 2021 Jul 9;1653:462398. Epub 2021 Jul 9.

Department of Chemical and Biological Engineering and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States. Electronic address:

In this paper, we examined the chromatographic behavior of a new class of guanidine-based multimodal anion exchange resins. The selectivities and protein recoveries on these resins were first evaluated using linear gradient chromatography with a model acidic protein library at pH 5, 6 and 7. While a single-guanidine based resin exhibited significant recovery issues at high ligand density, a bis-guanidine based resin showed high recoveries of all but two of the proteins evaluated in the study. Read More

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Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.

J Gen Physiol 2021 Aug 13;153(8). Epub 2021 Jul 13.

Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY.

YiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. Read More

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Formation and Evolution of Nanoscale Calcium Phosphate Precursors under Biomimetic Conditions.

Anal Chem 2021 Jul 12. Epub 2021 Jul 12.

Faculty of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger Str. 38, 1090 Vienna, Austria.

Simulated body fluids (SBFs) that mimic human blood plasma are widely used media for studies in an extensive array of research fields, from biomineralization to surface and corrosion sciences. We show that these solutions undergo dynamic nanoscopic conformational rearrangements on the timescale of minutes to hours, even though they are commonly considered stable or metastable. In particular, we find and characterize nanoscale inhomogeneities made of calcium phosphate (CaP) aggregates that emerge from homogeneous SBFs within a few hours and evolve into prenucleation species (PNS) that act as precursors in CaP crystallization processes. Read More

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The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication.

J Biol Chem 2021 Jan-Jun;296:100522. Epub 2021 Apr 7.

Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA; The Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA. Electronic address:

My personal and professional journeys have been far from predictable based on my early childhood. Owing to a range of serendipitous influences, I miraculously transitioned from a rebellious, apathetic teenage street urchin who did poorly in school to a highly motivated, disciplined, and ambitious academic honors student. I was the proverbial "late bloomer. Read More

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Dependence of phase transition uniformity on crystal sizes characterized using birefringence.

Struct Dyn 2021 May 30;8(3):034301. Epub 2021 Jun 30.

Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA.

Solid-solid phase transitions (SSPTs) have been widely observed in crystals of organic or inorganic small-molecules. Although SSPTs in macromolecular crystals have been reported, the majority involve local atomic changes, such as those induced by changes in hydration. SSPTs driven by large conformational changes, however, can be more difficult to characterize since they often significantly disrupt lattice packing interactions. Read More

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Guanidine-II aptamer conformations and ligand binding modes through the lens of molecular simulation.

Nucleic Acids Res 2021 Jul 7. Epub 2021 Jul 7.

Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.

Regulation of gene expression via riboswitches is a widespread mechanism in bacteria. Here, we investigate ligand binding of a member of the guanidine sensing riboswitch family, the guanidine-II riboswitch (Gd-II). It consists of two stem-loops forming a dimer upon ligand binding. Read More

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Conformational and Structural characterization of carbohydrates and their interactions studied by NMR.

Curr Med Chem 2021 Jul 5. Epub 2021 Jul 5.

Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain.

Carbohydrates, either free or as glycans conjugated with other biomolecules, participate in many essential biological processes. Their apparent simplicity in terms of chemical functionality hides an extraordinary diversity and structural complexity. Deeply deciphering at the atomic level their structures is essential to understand their biological function and activities, but it is still a challenging task in need of complementary approaches and no generalized procedures are available to address the study of such complex, natural glycans. Read More

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IgE Epitopes of the House Dust Mite Allergen Der p 7 Are Mainly Discontinuous and Conformational.

Front Immunol 2021 15;12:687294. Epub 2021 Jun 15.

Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.

Background: Several studies indicate that Der p 7 is an important and clinically relevant allergen of which should be included in vaccines for treatment of house dust mite (HDM) allergy. Aim of this study was to characterize the IgE epitopes of Der p 7.

Methods: Recombinant Der p 7 was expressed and purified, analyzed for fold by circular dichroism and tested for its allergenic activity by basophil activation. Read More

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Membrane-dependent heterogeneity of LHCII characterized using single-molecule spectroscopy.

Biophys J 2021 Jun 30. Epub 2021 Jun 30.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts. Electronic address:

In green plants, light harvesting complex of Photosystem II (LHCII) absorbs and transports excitation energy toward the photosynthetic reaction centers and serves as a site for energy-dependent nonphotochemical quenching (qE), the photoprotective dissipation of energy as heat. LHCII is thought to activate dissipation through conformational changes that change the photophysical behaviors. Understanding this balance requires a characterization of how the conformations of LHCII, and thus its photophysics, are influenced by individual factors within the membrane environment. Read More

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Peptide Triazole Thiol Irreversibly Inactivates Metastable HIV-1 Env by Accessing Conformational Triggers Intrinsic to Virus-Cell Entry.

Microorganisms 2021 Jun 12;9(6). Epub 2021 Jun 12.

Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, PA 19102, USA.

KR13, a peptide triazole thiol previously established to inhibit HIV-1 infection and cause virus lysis, was evaluated by flow cytometry against JRFL Env-presenting cells to characterize induced Env and membrane transformations leading to irreversible inactivation. Transiently transfected HEK293T cells were preloaded with calcein dye, treated with KR13 or its thiol-blocked analogue KR13b, fixed, and stained for gp120 (35O22), MPER (10E8), 6-helix-bundle (NC-1), immunodominant loop (50-69), and fusion peptide (VRC34.01). Read More

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Stability of p53 oligomers: Tetramerization of p53 impinges on its stability.

Biochimie 2021 Jun 28;189:99-107. Epub 2021 Jun 28.

School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, 695551, Kerala, India. Electronic address:

The p53 protein has been known to exist structurally in three different forms inside the cells. Earlier studies have reported the predominance of the lower oligomeric forms of p53 over its tetrameric form inside the cells, although only the tetrameric p53 contributes to its transcriptional activity. However, it remains unclear the functional relevance of the existence of other p53 oligomers inside the cells. Read More

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The PRKAR1B p.R115K Variant is Associated with Lipoprotein Profile in African American Youth with Metabolic Challenges.

J Endocr Soc 2021 Aug 16;5(8):bvab071. Epub 2021 Apr 16.

Section on Endocrinology & Genetics, Program on Developmental Endocrinology & Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA.

Context: High childhood obesity rates coincide with increased incidence of nonalcoholic fatty liver disease (NAFLD) and other comorbidities. Understanding the genetics of susceptibility to obesity and its comorbidities could guide intervention. The cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) signaling pathway regulates energy balance, glucose homeostasis, and lipid metabolism. Read More

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A combined approach to characterize ligand-induced solid-solid phase transitions in biomacromolecular crystals.

J Appl Crystallogr 2021 Jun 9;54(Pt 3):787-796. Epub 2021 May 9.

Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.

Solid-solid phase transitions (SSPTs) are widespread naturally occurring phenomena. Understanding the molecular mechanisms and kinetics of SSPTs in various crystalline materials, however, has been challenging due to technical limitations. In particular, SSPTs in biomacromolecular crystals, which may involve large-scale changes and particularly complex sets of interactions, are largely unexplored, yet may have important implications for time-resolved crystallography and for developing synthetic biomaterials. Read More

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A novel approach for studying receptor-ligand interactions on living cells surface by using NUS/T1ρ-NMR methodologies combined with computational techniques: The RGDechi15D-αβ integrin complex.

Comput Struct Biotechnol J 2021 29;19:3303-3318. Epub 2021 May 29.

Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy.

Structural investigations of receptor-ligand interactions on living cells surface by high-resolution Nuclear Magnetic Resonance (NMR) are problematic due to their short lifetime, which often prevents the acquisition of experiments longer than few hours. To overcome these limitations, we developed an on-cell NMR-based approach for exploring the molecular determinants driving the receptor-ligand recognition mechanism under native conditions. Our method relies on the combination of high-resolution structural and dynamics NMR data with Molecular Dynamics simulations and Molecular Docking studies. Read More

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Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy.

J Comput Aided Mol Des 2021 Jun 28. Epub 2021 Jun 28.

Laboratório de Bioinformática e Modelagem Molecular, Faculdade de Farmácia da Universidade Federal da Bahia, Av. Barão de Jeremoabo s/n Ondina, BA, 40170-115, Salvador, Brasil.

Assessment of target druggability guided by search and characterization of hot spots is a pivotal step in early stages of drug-discovery. The raw output of FTMap provides the data to perform this task, but it relies on manual intervention to properly combine different sets of consensus sites, therefore allowing identification of hot spots and evaluation of strength, shape and distance among them. Thus, the user's previous experience on the target and the software has a direct impact on how data generated by FTMap server can be explored. Read More

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Capillary Electrophoresis-based Hydrogen/Deuterium Exchange for Conformational Characterization of Proteins with Top-down Mass Spectrometry.

J Vis Exp 2021 Jun 8(172). Epub 2021 Jun 8.

School of Chemistry and Materials Science, Nanjing Normal University;

Resolving conformational heterogeneity of multiple protein states that coexist in solution remains one of the main obstacles in the characterization of protein therapeutics and the determination of the conformational transition pathways critical for biological functions, ranging from molecular recognition to enzymatic catalysis. Hydrogen/deuterium exchange (HDX) reaction coupled with top-down mass spectrometric (MS) analysis provides a means to characterize protein higher-order structures and dynamics in a conformer-specific manner. The conformational resolving power of this technique is highly dependent on the efficiencies of separating protein states at the intact protein level and minimizing the residual non-deuterated protic content during the HDX reactions. Read More

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A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.

J Mol Biol 2021 Jun 24;433(18):167118. Epub 2021 Jun 24.

Institute of Physics of Sao Carlos, University of Sao Paulo, Av. Joao Dagnone, 1100, Jardim Santa Angelina, Sao Carlos 13563-120, Brazil. Electronic address:

SARS-CoV-2 is the causative agent of COVID-19. The dimeric form of the viral M is responsible for the cleavage of the viral polyprotein in 11 sites, including its own N and C-terminus. The lack of structural information for intermediary forms of M is a setback for the understanding its self-maturation process. Read More

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Conformational editing of intrinsically disordered protein by α-methylation.

Chem Sci 2020 Nov 4;12(3):1080-1089. Epub 2020 Nov 4.

Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS, UMR 7006 Strasbourg France

Intrinsically disordered proteins (IDPs) constitute a large portion of "Dark Proteome" - difficult to characterize or yet to be discovered protein structures. Here we used conformationally constrained α-methylated amino acids to bias the conformational ensemble in the free unstructured activation domain of transcriptional coactivator ACTR. Different sites and patterns of substitutions were enabled by chemical protein synthesis and led to distinct populations of α-helices. Read More

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November 2020

Automatic Bayesian Weighting for SAXS Data.

Front Mol Biosci 2021 4;8:671011. Epub 2021 Jun 4.

Department of Structural Biology and Chemistry, Structural Bioinformatics Unit, CNRS UMR 3528, Institute Pasteur, Paris, France.

Small-angle X-ray scattering (SAXS) experiments are important in structural biology because they are solution methods, and do not require crystallization of protein complexes. Structure determination from SAXS data, however, poses some difficulties. Computation of a SAXS profile from a protein model is expensive in CPU time. Read More

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Exploring the Binding Interaction of Raf Kinase Inhibitory Protein With the N-Terminal of C-Raf Through Molecular Docking and Molecular Dynamics Simulation.

Front Mol Biosci 2021 28;8:655035. Epub 2021 May 28.

Division of Life Sciences, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Department of Bio and Medical Big Data (BK21 Four Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Korea.

Protein-protein interactions are indispensable physiological processes regulating several biological functions. Despite the availability of structural information on protein-protein complexes, deciphering their complex topology remains an outstanding challenge. Raf kinase inhibitory protein (RKIP) has gained substantial attention as a favorable molecular target for numerous pathologies including cancer and Alzheimer's disease. Read More

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Elusive structural changes of New Delhi metallo-β-lactamase revealed by ultraviolet photodissociation mass spectrometry.

Chem Sci 2020 Aug 11;11(33):8999-9010. Epub 2020 Aug 11.

Department of Chemistry, University of Texas at Austin Austin TX 78712 USA

We use mass spectrometry (MS), under denaturing and non-denaturing solution conditions, along with ultraviolet photodissociation (UVPD) to characterize structural variations in New Delhi metallo-β-lactamase (NDM) upon perturbation by ligands or mutation. Mapping changes in the abundances and distributions of fragment ions enables sensitive detection of structural alterations throughout the protein. Binding of three covalent inhibitors was characterized: a pentafluorphenyl ester, an -aryloxycarbonyl hydroxamate, and ebselen. Read More

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Mechanisms of typhoid toxin neutralization by antibodies targeting glycan receptor binding and nuclease subunits.

iScience 2021 May 20;24(5):102454. Epub 2021 Apr 20.

Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.

Nearly all clinical isolates of Typhi, the cause of typhoid fever, are antibiotic resistant. All Typhi isolates secrete an AB exotoxin called typhoid toxin to benefit the pathogen during infection. Here, we demonstrate that antibiotic-resistant Typhi secretes typhoid toxin continuously during infection regardless of antibiotic treatment. Read More

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Tying up the Loose Ends: A Mathematically Knotted Protein.

Front Chem 2021 24;9:663241. Epub 2021 May 24.

Institute of Biotechnology, University of Helsinki, Helsinki, Finland.

Knots have attracted scientists in mathematics, physics, biology, and engineering. Long flexible thin strings easily knot and tangle as experienced in our daily life. Similarly, long polymer chains inevitably tend to get trapped into knots. Read More

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Structure and Sequence-based Computational Approaches to Allosteric Signal Transduction: Application to Electromechanical Coupling in Voltage-gated Ion Channels.

J Mol Biol 2021 Jun 6:167095. Epub 2021 Jun 6.

KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden. Electronic address:

Allosteric signaling underlies the function of many biomolecules, including membrane proteins such as ion channels. Experimental methods have enabled specific quantitative insights into the coupling between the voltage sensing domain (VSD) and the pore gate of voltage-gated ion channels, located tens of Ångström apart from one another, as well as pinpointed specific residues and domains that participate in electromechanical signal transmission. Nevertheless, an overall atomic-level resolution picture is difficult to obtain from these methods alone. Read More

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Integrin intra-heterodimer affinity inversely correlates with integrin activatability.

Cell Rep 2021 Jun;35(10):109230

Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, CT 06520, USA. Electronic address:

Integrins are heterodimeric cell surface receptors composed of an α and β subunit that mediate cell adhesion to extracellular matrix proteins such as fibronectin. We previously studied integrin α5β1 activation during zebrafish somitogenesis, and in the present study, we characterize the integrin αV fibronectin receptors. Integrins are activated via a conformational change, and we perform single-molecule biophysical measurements of both integrin activation via fluorescence resonance energy transfer (FRET)-fluorescence lifetime imaging microscopy (FLIM) and integrin intra-heterodimer stability via fluorescence cross-correlation spectroscopy (FCCS) in living embryos. Read More

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A High-Resolution Ternary Model Demonstrates How PEGylated 2D Nanomaterial Stimulates Integrin α β on Cell Membrane.

Adv Sci (Weinh) 2021 06 23;8(11):e2004506. Epub 2021 Mar 23.

State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, No. 1 Bei-Er-Tiao, Zhong-Guan-Cun, Haidian District, Beijing, 100190, P. R. China.

Bio-nano interfaces are integral to all applications of nanomaterials in biomedicine. In addition to peptide-ligand-functionalized nanomaterials, passivation on 2D nanomaterials has emerged as a new regulatory factor for integrin activation. However, the mechanisms underlying such ligand-independent processes are poorly understood. Read More

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Phenotyping Angiotensin-Converting Enzyme in Blood: A Necessary Approach for Precision Medicine.

J Appl Lab Med 2021 Jun 7. Epub 2021 Jun 7.

Medical Center, Moscow University, Moscow, Russia.

Background: Angiotensin-converting enzyme (ACE) metabolizes a number of important peptides participating in blood pressure regulation and vascular remodeling. Elevated ACE expression in tissues (which is generally reflected by ACE in blood) is associated with increased risk of cardiovascular diseases. Elevated ACE in blood is also a marker for granulomatous diseases. Read More

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Photoisomerization of dicyanorhodanine-functionalized thiophenes.

Chem Sci 2020 Sep 9;11(37):10190-10197. Epub 2020 Sep 9.

Department of Chemistry, University of Florida PO Box 117200 Gainesville FL 32611 USA

π-Conjugated oligomers functionalized with the popular dicyanorhodanine (RCN) electron acceptor are shown to be susceptible to photo-induced / isomerization. The stereochemistry of two model RCN-functionalized thiophenes is confirmed by single crystal X-ray analysis and 2D NMR, and shown to be the thermodynamically stable form. Relative energies, / configurations, and conformational preferences are modelled using density functional theory (DFT). Read More

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September 2020