Publications by authors named "Gillian C Lynch"

15 Publications

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The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry.

Biochim Biophys Acta Gen Subj 2020 04 17;1864(4):129538. Epub 2020 Jan 17.

Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston 77030, TX, USA; Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston 77555, TX, USA. Electronic address:

The Lac system of genes has been an important model system in understanding gene regulation. When the dimer lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The hinge region is disordered when binding to nonoperator sequences. This region of the protein must pay a conformational entropic penalty to order when it is bound to operator DNA. Structural studies show that this region is flexible. Previous simulations showed that this region is disordered when free in solution without the DNA binding domain present. Our simulations corroborate that this region is extremely flexible in solution, but we find that the presence of the DNA binding domain proximal to the hinge helix and salt make the ordered conformation more favorable even without DNA present.
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http://dx.doi.org/10.1016/j.bbagen.2020.129538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7366509PMC
April 2020

Allosteric discrimination at the NADH/ADP regulatory site of glutamate dehydrogenase.

Protein Sci 2019 12 1;28(12):2080-2088. Epub 2019 Nov 1.

Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas.

Glutamate dehydrogenase (GDH) is a target for treating insulin-related disorders, such as hyperinsulinism hyperammonemia syndrome. Modeling native ligand binding has shown promise in designing GDH inhibitors and activators. Our computational investigation of the nicotinamide adenine diphosphate hydride (NADH)/adenosine diphosphate (ADP) site presented in this paper provides insight into the opposite allosteric effects induced at a single site of binding inhibitor NADH versus activator ADP to GDH. The computed binding free-energy difference between NADH and ADP using thermodynamic integration is -0.3 kcal/mol, which is within the -0.275 and -1.7 kcal/mol experimental binding free-energy difference range. Our simulations show an interesting model of ADP with dissimilar binding conformations at each NADH/ADP site in the GDH trimer, which explains the poorly understood strong binding but weak activation shown in experimental studies. In contrast, NADH showed similar inhibitory binding conformations at each NADH/ADP site. The structural analysis of the important residues in the NADH/ADP binding site presented in this paper may provide potential targets for mutation studies for allosteric drug design.
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http://dx.doi.org/10.1002/pro.3748DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6863735PMC
December 2019

Peptide Solubility Limits: Backbone and Side-Chain Interactions.

J Phys Chem B 2018 04 13;122(13):3528-3539. Epub 2018 Feb 13.

Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology , University of Texas Medical Branch , 301 University Boulevard , Galveston , Texas 77555-0304 , United States.

We calculate the solubility limit of pentapeptides in water by simulating the phase separation in an oversaturated aqueous solution. The solubility limit order followed by our model peptides (GGRGG > GGDGG > GGGGG > GGVGG > GGQGG > GGNGG > GGFGG) is found to be the same as that reported for amino acid monomers from experiment (R > D > G > V > Q > N > F). Investigation of dynamical properties of peptides shows that the higher the solubility of a peptide is, the lower the time spent by the peptide in the aggregated cluster is. We also demonstrate that fluctuations in conformation and hydration number of peptide in monomeric form are correlated with the solubility of the peptide. We considered energetic mechanisms and dynamical properties of interbackbone CO-CO and CO···HN interactions. Our results confirm that CO-CO interactions more than the interbackbone H-bonds are important in peptide self-assembly and association. Further, we find that the stability of H-bonded peptide pairs arises mainly from coexisting CO-CO and CO···HN interactions.
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http://dx.doi.org/10.1021/acs.jpcb.7b10734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909690PMC
April 2018

Norovirus Escape from Broadly Neutralizing Antibodies Is Limited to Allostery-Like Mechanisms.

mSphere 2017 Sep-Oct;2(5). Epub 2017 Oct 18.

Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA.

Ideal antiviral vaccines elicit antibodies (Abs) with broad strain recognition that bind to regions that are difficult to mutate for escape. Using 10 murine norovirus (MNV) strains and 5 human norovirus (HuNoV) virus-like particles (VLPs), we identified monoclonal antibody (MAb) 2D3, which broadly neutralized all MNV strains tested. Importantly, escape mutants corresponding to this antibody were very slow to develop and were distal to those raised against our previously studied antibody, A6.2. To understand the atomic details of 2D3 neutralization, we determined the cryo-electron microscopy (cryo-EM) structure of the 2D3/MNV1 complex. Interestingly, 2D3 binds to the top of the P domain, very close to where A6.2 binds, but the only escape mutations identified to date fall well outside the contact regions of both 2D3 and A6.2. To determine how mutations in distal residues could block antibody binding, we used molecular dynamics flexible fitting simulations of the atomic structures placed into the density map to examine the 2D3/MNV1 complex and these mutations. Our findings suggest that the escape mutant, V339I, may stabilize a salt bridge network at the P-domain dimer interface that, in an allostery-like manner, affects the conformational relaxation of the P domain and the efficiency of binding. They further highlight the unusual antigenic surface bound by MAb 2D3, one which elicits cross-reactive antibodies but which the virus is unable to alter to escape neutralization. These results may be leveraged to generate norovirus (NoV) vaccines containing broadly neutralizing antibodies. The simplest and most common way for viruses to escape antibody neutralization is by mutating residues that are essential for antibody binding. Escape mutations are strongly selected for by their effect on viral fitness, which is most often related to issues of protein folding, particle assembly, and capsid function. The studies presented here demonstrated that a broadly neutralizing antibody to mouse norovirus binds to an exposed surface but that the only escape mutants that arose were distal to the antibody binding surface. To understand this finding, we performed an analysis that suggested that those escape mutations blocked antibody binding by affecting structural plasticity. This kind of antigenic region-one that gives rise to broadly neutralizing antibodies but that the virus finds difficult to escape from-is therefore ideal for vaccine development.
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http://dx.doi.org/10.1128/mSphere.00334-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5646240PMC
October 2017

Systematic identification of single amino acid variants in glioma stem-cell-derived chromosome 19 proteins.

J Proteome Res 2015 Feb 25;14(2):778-86. Epub 2014 Nov 25.

Department of Pharmacology and Toxicology and ‡Biochemistry and Molecular Biology, UTMB Cancer Center, University of Texas Medical Branch , Galveston, Texas 77555, United States.

Novel proteoforms with single amino acid variations represent proteins that often have altered biological functions but are less explored in the human proteome. We have developed an approach, searching high quality shotgun proteomic data against an extended protein database, to identify expressed mutant proteoforms in glioma stem cell (GSC) lines. The systematic search of MS/MS spectra using PEAKS 7.0 as the search engine has recognized 17 chromosome 19 proteins in GSCs with altered amino acid sequences. The results were further verified by manual spectral examination, validating 19 proteoforms. One of the novel findings, a mutant form of branched-chain aminotransferase 2 (p.Thr186Arg), was verified at the transcript level and by targeted proteomics in several glioma stem cell lines. The structure of this proteoform was examined by molecular modeling in order to estimate conformational changes due to mutation that might lead to functional modifications potentially linked to glioma. Based on our initial findings, we believe that our approach presented could contribute to construct a more complete map of the human functional proteome.
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http://dx.doi.org/10.1021/pr500810gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4324435PMC
February 2015

Solvation and cavity occupation in biomolecules.

Biochim Biophys Acta 2015 May 28;1850(5):923-931. Epub 2014 Sep 28.

Sealy Center for Structural Biology and Molecular Biophysics, Departments of Biochemistry and Molecular Biology and Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-0304, USA. Electronic address:

Background: Solvation density locations are important for protein dynamics and structure. Knowledge of the preferred hydration sites at biomolecular interfaces and those in the interior of cavities can enhance understanding of structure and function. While advanced X-ray diffraction methods can provide accurate atomic structures for proteins, that technique is challenged when it comes to providing accurate hydration structures, especially for interfacial and cavity bound solvent molecules.

Methods: Advances in integral equation theories which include more accurate methods for calculating the long-ranged Coulomb interaction contributions to the three-dimensional distribution functions make it possible to calculate angle dependent average solvent structure, accurately, around and inside irregular molecular conformations. The proximal radial distribution method provides another approximate method to determine average solvent structures for biomolecular systems based on a proximal or near neighbor solvent distribution that can be constructed from previously collected solvent distributions. These two approximate methods, along with all-atom molecular dynamics simulations are used to determine the solvent density inside the myoglobin heme cavity.

Discussion And Results: Myoglobin is a good test system for these methods because the cavities are many and one is large, tens of Å(3), but is shown to have only four hydration sites. These sites are not near neighbors which implies that the large cavity must have more than one way in and out.

Conclusions: Our results show that main solvation sites are well reproduced by all three methods. The techniques also produce a clearly identifiable solvent pathway into the interior of the protein.

General Significance: The agreement between molecular dynamics and less computationally demanding approximate methods is encouraging. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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http://dx.doi.org/10.1016/j.bbagen.2014.09.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339624PMC
May 2015

Domain organization of membrane-bound factor VIII.

Biopolymers 2013 Jul;99(7):448-59

Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA.

Factor VIII (FVIII) is the blood coagulation protein which when defective or deficient causes for hemophilia A, a severe hereditary bleeding disorder. Activated FVIII (FVIIIa) is the cofactor to the serine protease factor IXa (FIXa) within the membrane-bound Tenase complex, responsible for amplifying its proteolytic activity more than 100,000 times, necessary for normal clot formation. FVIII is composed of two noncovalently linked peptide chains: a light chain (LC) holding the membrane interaction sites and a heavy chain (HC) holding the main FIXa interaction sites. The interplay between the light and heavy chains (HCs) in the membrane-bound state is critical for the biological efficiency of FVIII. Here, we present our cryo-electron microscopy (EM) and structure analysis studies of human FVIII-LC, when helically assembled onto negatively charged single lipid bilayer nanotubes. The resolved FVIII-LC membrane-bound structure supports aspects of our previously proposed FVIII structure from membrane-bound two-dimensional (2D) crystals, such as only the C2 domain interacts directly with the membrane. The LC is oriented differently in the FVIII membrane-bound helical and 2D crystal structures based on EM data, and the existing X-ray structures. This flexibility of the FVIII-LC domain organization in different states is discussed in the light of the FVIIIa-FIXa complex assembly and function.
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http://dx.doi.org/10.1002/bip.22199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090243PMC
July 2013

Ion and solvent density distributions around canonical B-DNA from integral equations.

J Phys Chem B 2011 Jan 29;115(3):547-56. Epub 2010 Dec 29.

Department of Chemistry, University of Houston, Houston, Texas 77204-5003, USA.

We calculate the water and ion spatial distributions around charged oligonucleotides using a renormalized three-dimensional reference interaction site theory coupled with the HNC closure. Our goal is to understand the balance between inter-DNA strand forces and solvation forces as a function of oligonucleotide length in the short strand limit. The DNA is considered in aqueous electrolyte solutions of 1 M KCl, 0.1 M KCl, or 0.1 M NaCl. The current theoretical results are compared to molecular dynamics (MD) simulations and experiments. It is found that the integral equation (IE) theory replicates the MD and the experimental results for the base-specific hydration patterns in both the major and the minor grooves. We are also able to discern characteristic structural pattern differences between Na(+) and K(+) ions. When compared to Poisson-Boltzmann methods, the IE theory, like simulation, predicts a richly structured ion environment, which is better described as multilayer rather than double layer.
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http://dx.doi.org/10.1021/jp107383sDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025534PMC
January 2011

Backbone additivity in the transfer model of protein solvation.

Protein Sci 2010 May;19(5):1011-22

Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.

The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (DeltaG(tr)) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and DeltaG(tr) values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of -54 cal/mol/M compares quite favorably with -43 cal/mol/M determined experimentally.
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http://dx.doi.org/10.1002/pro.378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2868243PMC
May 2010

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories.

J Chem Phys 2010 Feb;132(6):064106

Department of Chemistry, University of Houston, Houston, Texas 77204-5003, USA.

Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories make it possible to calculate the angle dependent average solvent structure around an irregular molecular solution. We consider two methodological problems here: the treatment of long-ranged forces without the use of artificial periodicity or truncations and the effect of closures. We derive a method for calculating the long-ranged Coulomb interaction contributions to three-dimensional distribution functions involving only a rewriting of the system of integral equations and introducing no new formal approximations. We show the comparison of the exact forms with those implied by the supercell method. The supercell method is shown to be a good approximation for neutral solutes whereas the new method does not exhibit the known problems of the supercell method for charged solutes. Our method appears more numerically stable with respect to thermodynamic starting state. We also compare closures including the Kovalenko-Hirata closure, the hypernetted-chain (HNC) and an approximate three-dimensional bridge function combined with the HNC closure. Comparisons to molecular dynamics results are made for water as well as for the protein solute bovine pancreatic trypsin inhibitor. The proposed equations have less severe approximations and often provide results which compare favorably to molecular dynamics simulation where other methods fail.
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http://dx.doi.org/10.1063/1.3299277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833187PMC
February 2010

THE MELTING MECHANISM OF DNA TETHERED TO A SURFACE.

Int J Numer Anal Model 2009 Mar;6(3):474-488

Department of Chemistry and Institute for Molecular Design, University of Houston, Houston, TX 77204-5003, USA.

The details of melting of DNA immobilized on a chip or nanoparticle determines the sensitivity and operating characteristics of many analytical and synthetic biotechnological devices. Yet, little is known about the differences in how the DNA melting occurs between a homogeneous solution and that on a chip. We used molecular dynamics simulations to explore possible pathways for DNA melting on a chip. Simulation conditions were chosen to ensure that melting occurred in a submicrosecond timescale. The temperature was set to 400 K and the NaCl concentration was set to 0.1 M. We found less symmetry than in the solution case where for oligomeric double-stranded nucleic acids both ends melted with roughly equal probability. On a prepared silica surface we found melting is dominated by fraying from the end away from the surface. Strand separation was hindered by nonspecific surface adsorption at this temperature. At elevated temperatures the melted DNA was attracted to even uncharged organically coated surfaces demonstrating surface fouling. While hybridization is not the simple reverse of melting, this simulation has implications for the kinetics of hybridization.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755589PMC
March 2009

Trimethylamine N-oxide influence on the backbone of proteins: an oligoglycine model.

Proteins 2010 Feb;78(3):695-704

Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, USA.

The study of organic osmolytes has been pivotal in demonstrating the role of solvent effects on the protein backbone in the folding process. Although a thermodynamic description of the interactions between the protein backbone and osmolyte has been well defined, the structural analysis of the effect of osmolyte on the protein backbone has been incomplete. Therefore, we have performed simulations of a peptide backbone model, glycine(15), in protecting osmolyte trimethylamine N-oxide (TMAO) solution, in order to determine the effect of the solution structure on the conformation of the peptide backbone. We show that the models chosen show that the ensemble of backbone structures shifts toward a more collapsed state in TMAO solution as compared with pure water solution. The collapse is consistent with preferential exclusion of the osmolyte caused by unfavorable interactions between osmolyte and peptide backbone. The exclusion is caused by strong triplet correlations of osmolyte, water, and peptide backbone. This provides a clear mechanism showing that even a modest concentration of TMAO forces the protein backbone to adopt a more collapsed structure in the absence of side chain effects.
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http://dx.doi.org/10.1002/prot.22598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805780PMC
February 2010

Salt effects on surface-tethered peptides in solution.

J Phys Chem B 2009 Jul;113(28):9472-8

Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.

The capability to manipulate proteins/peptide fragments at liquid-solid interfaces has led to tremendous applications in detectors and biotechnology. Therefore, understanding the detailed molecular behavior of proteins and peptides tethered on a hard material surface is an interesting and important topic. The inhomogeneity presented by surfaces as well as ions in the solution plays an important role in the thermodynamics and kinetics of the tethered proteins. In this study, we perform a series of molecular dynamics simulations of a pentapeptide RHSVV, a p53 epitope, tethered on a prepared microarray surface in various salt concentrations (0, 0.14, 0.5, and 1 M NaCl), as well as free in ionic solution (0, 0.5, and 1 M). The conformational space the tethered peptide visits largely overlaps with the free peptide in solution. However, surface tethering as well as the salt concentration changes both the thermodynamics and kinetics of the peptide. Frequent conformational changes are observed during the simulations and tend to be slowed down by both increasing the salt concentration and surface tethering. The local composition of ions at different salt concentrations is also compared between the tethered and free peptide.
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http://dx.doi.org/10.1021/jp902537fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726803PMC
July 2009

Peptide conformations for a microarray surface-tethered epitope of the tumor suppressor p53.

J Phys Chem B 2007 Dec 16;111(49):13797-806. Epub 2007 Nov 16.

Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.

Peptides or proteins near surfaces exhibit different structural properties from those present in a homogeneous solution, and these differences give rise to varied biological activity. Therefore, understanding the detailed molecular structure of these molecules tethered to a surface is important for interpreting the performance of the various microarrays based on the activities of the immobilized peptides or proteins. We performed molecular dynamics simulations of a pentapeptide, RHSVV, an epitope of the tumor suppressor protein p53, tethered via a spacer on a functionalized silica surface and free in solution, to study their structural and conformational differences. These calculations allowed analyses of the peptide-surface interactions, the sequence orientations, and the translational motions of the peptide on the surface to be performed. Conformational similarities are found among dominant structures of the tethered and free peptide. In the peptide microarray simulations, the peptide fluctuates between a parallel and tilted orientation driven in part by the hydrophobic interactions between the nonpolar peptide residues and the methyl-terminated silica surface. The perpendicular movement of the peptide relative to the surface is also restricted due to the hydrophobic nature of the microarray surface. With regard to structures available for recognition and binding, we find that similar conformations to those found in solution are available to the peptide tethered to the surface, but with a shifted equilibrium constant. Comparisons with experimental results show important implications of this for peptide microarray design and assays.
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http://dx.doi.org/10.1021/jp075051yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538448PMC
December 2007

Molecular dynamics simulations of Trichomonas vaginalis ferredoxin show a loop-cap transition.

Biophys J 2007 May 26;92(10):3337-45. Epub 2007 Feb 26.

Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.

The crystal structure of the oxidized Trichomonas vaginalis ferredoxin (Tvfd) showed a unique crevice that exposed the redox center. Here we have examined the dynamics and solvation of the active site of Tvfd using molecular dynamics simulations of both the reduced and oxidized states. The oxidized simulation stays true to the crystal form with a heavy atom root mean-squared deviation of 2 A. However, within the reduced simulation of Tvfd a profound loop-cap transition into the redox center occurred within 6-ns of the start of the simulation and remained open throughout the rest of the 20-ns simulation. This large opening seen in the simulations supports the hypothesis that the exceptionally fast electron transfer rate between Tvfd and the drug metronidazole is due to the increased access of the antibiotic to the redox center of the protein and not due to the reduction potential.
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http://dx.doi.org/10.1529/biophysj.106.088096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853131PMC
May 2007