Department of Biochemistry and Molecular Biology (BMB)
6/1990 - present
Sealy Center for Structural Biology and Molecular Biophysics
University of Texas Medical Branch
301 University Blvd
Galveston, TX 77555-0304
5.216 Research Bldg 6 jsperkyn@utmb.edu
409.772.0722 (Office)
409.772.0725 (Fax)
Education
University of British Columbia, Vancouver, Canada, Ph.D., 1990 in Physical (Theoretical) Chemistry
University of British Columbia, Vancouver, Canada, M.Sc., 1985
Dalhousie University, Halifax, Nova Scotia, Canada, B.Sc., 1983; B.A., 1981
Selected Recent Publications
Dyer KM, Perkyns JS, Pettitt BM. Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries. J Phys Chem B., 119 (29), 9450-9459 (2015)
Lynch GC, Perkyns JS, Nguyen BL, Pettitt BM. Solvation and cavity occupation in biomolecules. Biochim Biophys Acta., 1850(5), 923-31 (2015)
Howard JJ, Perkyns JS, Pettitt BM. The behavior of ions near a charged wall-dependence on ion size, concentration, and surface charge. J Phys Chem B, 114, 6074-6083 (2010)
Perkyns JS, Lynch GC, Howard JJ, Pettitt BM. Protein solvation from theory and simulation: exact treatment of coulomb interactions in three-dimensional theories. J Chemi Phys, 132, 064106 (2010)
Dyer KM, Perkyns JS, Stell G, Pettitt BM. Site-renormalised molecular fluid theory: on the utility of a two-site model of water. Mol Phys, 107, 423-431 (2009)
Howard JJ, Perkyns JS, Choudhury N, Pettitt BM. An integral equation study of the hydrophobic interaction between graphene plates. J Chem Theo Comput, 4, 1928-1939 (2008)
Dyer KM, Perkyns JS, Stell G, Pettitt BM. A molecular site-site integral equation that yields the dielectric constant. J Chem Phys, 129, 104512 (2008)
Dyer KM, Perkyns JS, Pettitt BM. A site-renormalized molecular fluid theory. Condensed Matter Physics, 10, 331-342 (2007)
Department of Biochemistry and Molecular Biology (BMB) 9/1993 - present Sealy Center for Structural Biology and Molecular Biophysics University of Texas Medical
Branch 301 University Blvd Galveston, TX 77555-0304
5.419 Research Bldg 6 gclynch@utmb.edu 409.772.0721 (Office) 409.772.0725 (Fax)
Education
University of Minnesota, Minneapolis, MN Ph.D. 1993 Physical (Theoretical) Chemistry Oklahoma State University, Stillwater, OK B.Sc. 1986 Chemistry
Selected Publications
Yousefi R, Lynch GC, Galbraith M, Pettitt BM. Contributions of higher-order proximal distribution functions to solvent structure around proteins.J Chem Phys. 155(10), 104110 (2021)
Seckfort D, Lynch GC, Pettitt BM. The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry. Biochim Biophys Acta Gen Subj. 1864 (4), 129538 (2020)
Sarma R, Wong KY, Lynch GC, Pettitt BM. Peptide Solubility Limits: Backbone and Side-Chain Interactions.J Phys Chem B. 122(13), 3528-3539 (2018)
Lynch GC, Perkyns JS, Nguyen BL, Pettitt BM. Solvation and cavity occupation in biomolecules. Biochim Biophys Acta., 1850(5), 923-31 (2015)
Lichti CF, Mostovenko E, Wadsworth PA, Lynch GC, Pettitt BM, Sulman EP, Wang Q, Lang FF, Rezeli M, Marko-Varga G, Végvári A, Nilsson CL. Systematic identification of single amino acid variants in glioma stem-cell-derived chromosome 19 proteins.
J Proteome Res., 14(2), 778-86 (2015)
Stoilova-McPhie S, Lynch GC, Ludtke S, Pettitt BM. Domain organization of membrane-bound factor VIII. Biopolymers, 99, 448-459 (2013)
Feng J, Lynch GC, Pettitt BM. Studying proteins and peptides at material surface. in Innovations in Biomolecular Modeling and Simulations; Tamar Schlick (eds.); The Royal Society of Chemistry, 293-320 (2012)
Howard JJ, Lynch GC, Pettitt BM. Ion and solvent density distributions around canonical B-DNA from integral equations. J. Phys. Chem. B, 115, 547-556 (2011)
Perkyns JS, Lynch GC, Howard JJ, Pettitt BM. Protein solvation from theory and simulation: exact treatment of coulomb interactions in three-dimensional theories. J. Chem. Phys., 132, 064106 (2010)
Hu CY, Lynch GC, Kokubo H, Pettitt BM. Trimethylamine N-oxide influence on the backbone of proteins: an oligoglycine model. Proteins: Structure, Function, and Bioinformatics, 78, 695-704 (2010)
Department of Biochemistry and Molecular Biology (BMB) 5/1998 - present Sealy Center for Structural Biology and Molecular Biophysics University of Texas Medical
Branch 301 University Blvd Galveston, TX 77555-0304
5.420 Research Bldg 6 kayiu.wong@utmb.edu 409.772.0733 (Office) 409.772.0725 (Fax)
Education
Texas A&M University, College Station, Ph.D. The Chinese University of Hong Kong, Hong Kong, B.Sc.
Research Interests
Modeling of nucleic acids in salt solutions.
Selected Publications
Nassar OM, Wong KY, Lynch GC, Smith TJ, Pettitt BM. Allosteric discrimination at the NADH/ADP regulatory site of glutamate dehydrogenase.Protein Sci. 12, 2080-2088 (2019)
Sarma R, Wong KY, Lynch GC, Pettitt BM. Peptide Solubility Limits: Backbone and Side-Chain Interactions.J Phys Chem B. 122(13), 3528-3539 (2018)
Karandur D, Wong KY, Pettitt BM. Solubility and aggregation of Gly(5) in water. J Phys Chem B, 118(32), 9565-72 (2014)
Lin B, Wong KY, Hu C, Kokubo H, Pettitt BM. Correction to "Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions". The Journal of Physical Chemistry Letters,
3, 69-69 (2012)
Lin B, Wong KY, Hu C, Kokubo H, Pettitt BM. Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions. The Journal of Physical Chemistry Letters,
2, 1626-1632 (2011)
Feng J, Wong KY, Dyer K, PettittBM. Transport Properties of Water at Functionalized Molecular Interfaces. J. Chem. Phys., 131:125102 (2009)
Qamhieh K, Wong KY, Lynch GC, Pettitt BM. The melting mechanism of DNA tethered to a surface. International Journal of Numerical Analysis and Modeling, 6, 474-488 (2009)
Feng J, Wong KY, Lynch GC, Gao X, Pettitt BM. Salt effects on surface-tethered peptides in solution. J Phys. Chem. B, 113, 9472-9478 (2009)
Wong KY, Pettitt BM. The pathway of oligomeric DNA melting investigated by molecular dynamics simulations. Biophys J, 95, 5618-5626 (2008)
Feng J, Wong KY, Lynch GC, Gao X, Pettitt BM. Peptide conformations for a microarray surface-tethered epitope of the tumor suppressor p53. J Phys Chem B, 111, 13797-13806 (2007)
Pettitt BM, Vainrub A, Wong KY. DNA saline solutions near surfaces - A few ideas towards design parameters of DNA arrays. In Ionic Soft Matter: Modern Trends in Theory and Applications; NATO Science Series; Douglas Henderson,
Myroslav Holovko, Andrij Trokhymchuk (eds.); Springer, 381-393 (2005)
Wong KY, Pettitt BM. Orientation of DNA on a surface from simulation. Biopolymers, 73, 570-578 (2004)
Wong KY, Vainrub A, Powdrill T, Hogan M, Pettitt BM. A non-Watson-Crick motif of base-pairing on surfaces for untethered oligonucleotides. Molecular Simulation, 30, 121-129 (2004)
Department of Biochemistry and Molecular Biology (BMB) 8/2003 - present Sealy Center for Structural Biology and Molecular Biophysics University of Texas Medical
Branch 301 University Blvd Galveston, TX 77555-0304
5.421 Research Bldg 6 ch2chen@utmb.edu 409.772.0718 (Office) 409.772.0725 (Fax)
Education
Georgia State University, Ph.D., 2003 in Biophysical Chemistry Lanzhou University, China, M.Sc., 1998 in Physical Chemistry Lanzhou University, China, B.Sc., 1995 in Physical Chemistry
Research Interests
In all biological processes, molecular recognition plays a central role in the assembly of biological structures and cellular events. A better understanding of molecular recognition is essential to the development of new drugs and biomaterials and
of the design of novel molecular devices for catalysts and drug delivery. Currently I work on the topics of molecular recognition and solvation effects on biological processes using molecular modeling and simulation. I try to gain molecular descriptions
of the free energy surface that govern these interactions and the corresponding mechanism that are consistent with known biological, thermodynamic, kinetic, and structural data.
Selected Publications
Chen C, Pettitt BM. The Effects of Flexibility on dsDNA–dsDNA Interactions. Life (Basel) 12(5), 699 (2022)
Lai CL, Chen C, Ou SC, Prentiss M, Pettitt BM. Interactions between identical DNA double helices. Physical Review E 101, 032414 (2020) (Featured in Editors' Suggestion)
Esadze A, Chen C, Zandarashvili L, Roy S, Pettitt BM, Iwahara J. Changes in conformational dynamics of basic side chains upon protein-DNA association. Nucl. Acids Res., 44(14), 6961-70 (2016).
Chen C, Pettitt BM. DNA shape versus sequence variations in the protein binding process. Biophys. J., 110(3), 534-44 (2016)
Chen C, Esadze A, Zandarashvili L, Nguyen D, Pettitt BM, Iwahara J. Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes. J Phys Chem Lett., 6(14), 2733-2737 (2015)
Chen C, Pettitt BM. The binding process of a nonspecific enzyme with DNA. Biophys. J., 101, 1139-1147 (2011)
Chen C, Krause K, Pettitt BM. Advantage of being a dimer for Serratia marcescens endonuclease?J. Phys. Chem. B., 113, 395-588 (2009). (Figure featured on journal cover)
Chen C, Beck BW, Krause K, Warth T E, Pettitt BM. The effects of dimerization of Serratia marcescens endonuclease on water dynamics. Biopolymers, 85, 241-252 (2007). (Figure featured on journal cover)
Chen C, Beck BW, Krause K, Pettitt BM. Solvent participation in Serratia marcescens endonuclease complexes with DNA. Proteins: Structure, Function and Bioinformatics, 62, 982-995 (2006). (Figure featured on journal cover)
Department of Biochemistry and Molecular Biology (BMB)
8/2018 - present
Sealy Center for Structural Biology and Molecular Biophysics
University of Texas Medical Branch
301 University Blvd
Galveston, TX 77555-0304
5.416 Research Bldg 6 riworkma@utmb.edu
409.772.0731 (Office)
409.772.0725 (Fax)