Bernard Pettitt, PhD

Director, Sealy Center for Structural Biology

  • 12140 Citations
  • 62 h-Index
1978 …2021

Research output per year

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Research Output

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Article
2020

Structure and the role of filling rate on model dsDNA packed in a phage capsid

Bores, C. & Pettitt, B. M., Jan 13 2020, In : Physical Review E. 101, 1, 012406.

Research output: Contribution to journalArticle

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

Seckfort, D., Lynch, G. C. & Pettitt, B. M., Apr 2020, In : Biochimica et Biophysica Acta - General Subjects. 1864, 4, 129538.

Research output: Contribution to journalArticle

2019

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

Nassar, O. M., Wong, K. Y., Lynch, G. C., Smith, T. J. & Pettitt, B. M., Dec 1 2019, In : Protein Science. 28, 12, p. 2080-2088 9 p.

Research output: Contribution to journalArticle

Mobility of Histidine Side Chains Analyzed with 15 N NMR Relaxation and Cross-Correlation Data: Insight into Zinc-Finger-DNA Interactions

Kemme, C. A., Luu, R. H., Chen, C., Pletka, C. C., Pettitt, B. & Iwahara, J., May 2 2019, In : Journal of Physical Chemistry B. 123, 17, p. 3706-3710 5 p.

Research output: Contribution to journalArticle

Price of disorder in the lac repressor hinge helix

Seckfort, D. & Pettitt, B., Jan 1 2019, In : Biopolymers. 110, 1, e23239.

Research output: Contribution to journalArticle

1 Scopus citations
2018
2 Scopus citations
1 Scopus citations

Peptide Solubility Limits: Backbone and Side-Chain Interactions

Sarma, R., Wong, K. Y., Lynch, G. C. & Pettitt, B., Apr 5 2018, In : Journal of Physical Chemistry B. 122, 13, p. 3528-3539 12 p.

Research output: Contribution to journalArticle

Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model

Drake, J. A. & Pettitt, B., Jun 19 2018, In : Biophysical Journal. 114, 12, p. 2799-2810 12 p.

Research output: Contribution to journalArticle

4 Scopus citations

Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography

Dai, W., Chen, M., Myers, C., Ludtke, S. J., Pettitt, B., King, J. A., Schmid, M. F. & Chiu, W., Jan 1 2018, (Accepted/In press) In : Journal of Molecular Biology.

Research output: Contribution to journalArticle

3 Scopus citations
2017

Influence of DNA sequence on the structure of minicircles under torsional stress

Wang, Q., Irobalieva, R. N., Chiu, W., Schmid, M. F., Fogg, J. M., Zechiedrich, L. & Pettitt, B., Jul 1 2017, In : Nucleic Acids Research. 45, 13, p. 7633-7642 10 p.

Research output: Contribution to journalArticle

9 Scopus citations

Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15

Asthagiri, D., Karandur, D., Tomar, D. S. & Pettitt, B., Aug 31 2017, In : Journal of Physical Chemistry B. 121, 34, p. 8078-8084 7 p.

Research output: Contribution to journalArticle

12 Scopus citations

Nonpolar Solvation Free Energy from Proximal Distribution Functions

Ou, S. C., Drake, J. A. & Pettitt, B., Apr 20 2017, In : Journal of Physical Chemistry B. 121, 15, p. 3555-3564 10 p.

Research output: Contribution to journalArticle

4 Scopus citations

Norovirus escape from broadly neutralizing antibodies is limited to allostery-like mechanisms

Kolawole, A. O., Smith, H. Q., Svoboda, S. A., Lewis, M. S., Sherman, M., Lynch, G. C., Pettitt, B., Smith, T. & Wobus, C. E., Sep 1 2017, In : mSphere. 2, 5, e00334-17.

Research output: Contribution to journalArticle

13 Scopus citations

Optimal updating magnitude in adaptive flat-distribution sampling

Zhang, C., Drake, J. A., Ma, J. & Pettitt, B., Nov 7 2017, In : Journal of Chemical Physics. 147, 17, 174105.

Research output: Contribution to journalArticle

Phage-like packing structures with mean field sequence dependence

Myers, C. G. & Pettitt, B., 2017, (Accepted/In press) In : Journal of Computational Chemistry.

Research output: Contribution to journalArticle

5 Scopus citations
2016

Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace

Zhang, C., Lai, C. L. & Pettitt, B., Sep 1 2016, In : Molecular Simulation. 42, 13, p. 1079-1089 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

Changes in conformational dynamics of basic side chains upon protein-DNA association

Esadze, A., Chen, C., Zandarashvili, L., Roy, S., Pettitt, B. & Iwahara, J., Aug 19 2016, In : Nucleic Acids Research. 44, 14, p. 6961-6970 10 p.

Research output: Contribution to journalArticle

33 Scopus citations

Dielectric behavior for saline solutions from renormalized diagrammatically proper interaction site model theory

Dyer, K. M., Perkyns, J. S. & Pettitt, B., Aug 22 2016, In : Journal of Physics Condensed Matter. 28, 41, 414006.

Research output: Contribution to journalArticle

1 Scopus citations

DNA Shape versus Sequence Variations in the Protein Binding Process

Chen, C. & Pettitt, B., Feb 2 2016, In : Biophysical Journal. 110, 3, p. 534-544 11 p.

Research output: Contribution to journalArticle

3 Scopus citations
15 Scopus citations

Protein collapse driven against solvation free energy without H-bonds

Karandur, D., Harris, R. C. & Pettitt, B., Jan 1 2016, In : Protein Science. 25, 1, p. 103-110 8 p.

Research output: Contribution to journalArticle

10 Scopus citations

Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins

Harris, R. C. & Pettitt, B., Feb 2 2016, In : Journal of Physics Condensed Matter. 28, 8, 083003.

Research output: Contribution to journalArticle

11 Scopus citations

Sequence Affects the Cyclization of DNA Minicircles

Wang, Q. & Pettitt, B., Mar 17 2016, In : Journal of Physical Chemistry Letters. 7, 6, p. 1045-1046 2 p.

Research output: Contribution to journalArticle

6 Scopus citations

Solute-Solvent Energetics Based on Proximal Distribution Functions

Ou, S. C. & Pettitt, B., Aug 25 2016, In : Journal of Physical Chemistry B. 120, 33, p. 8230-8237 8 p.

Research output: Contribution to journalArticle

7 Scopus citations

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility

Drake, J. A., Harris, R. C. & Pettitt, B., Aug 23 2016, In : Biophysical Journal. 111, 4, p. 756-767 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

The contribution of electrostatic interactions to the collapse of oligoglycine in water

Karandur, D. & Pettitt, B., 2016, In : Condensed Matter Physics. 19, 2, 23802.

Research output: Contribution to journalArticle

1 Scopus citations
2015

Computation of virial coefficients from integral equations

Zhang, C., Lai, C. L. & Pettitt, B., Jun 5 2015, In : Journal of Chemical Physics. 142, 21, 214110.

Research output: Contribution to journalArticle

2 Scopus citations

Dynamic equilibria of short-range electrostatic interactions at molecular interfaces of protein-DNA complexes

Chen, C., Esadze, A., Zandarashvili, L., Nguyen, D., Pettitt, B. & Iwahara, J., Jul 16 2015, In : Journal of Physical Chemistry Letters. 6, 14, p. 2733-2737 5 p.

Research output: Contribution to journalArticle

25 Scopus citations

Effects of acids, bases, and heteroatoms on proximal radial distribution functions for proteins

Nguyen, B. L. & Pettitt, B., Apr 14 2015, In : Journal of Chemical Theory and Computation. 11, 4, p. 1399-1409 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

Examining the Assumptions Underlying Continuum-Solvent Models

Harris, R. C. & Pettitt, B., Sep 1 2015, In : Journal of Chemical Theory and Computation. 11, 10, p. 4593-4600 8 p.

Research output: Contribution to journalArticle

14 Scopus citations

Force field-dependent solution properties of glycine oligomers

Drake, J. A. & Pettitt, B., Jun 1 2015, In : Journal of Computational Chemistry. 36, 17, p. 1275-1285 11 p.

Research output: Contribution to journalArticle

18 Scopus citations
2 Scopus citations

Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries

Dyer, K. M., Perkyns, J. S. & Pettitt, B., Jul 23 2015, In : Journal of Physical Chemistry B. 119, 29, p. 9450-9459 10 p.

Research output: Contribution to journalArticle

1 Scopus citations

Solvation and cavity occupation in biomolecules

Lynch, G. C., Perkyns, J. S., Nguyen, B. L. & Pettitt, B., 2015, In : Biochimica et Biophysica Acta - General Subjects. 1850, 5, p. 923-931 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

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

Lichti, C. F., Mostovenko, E., Wadsworth, P. A., Lynch, G. C., Pettitt, B., Sulman, E. P., Wang, Q., Lang, F. F., Rezeli, M., Marko-Varga, G., Végvári, Á. & Nilsson, C. L., Feb 6 2015, In : Journal of Proteome Research. 14, 2, p. 778-786 9 p.

Research output: Contribution to journalArticle

15 Scopus citations

Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density

Wang, Q., Myers, C. G. & Pettitt, B., Apr 16 2015, In : Journal of Physical Chemistry B. 119, 15, p. 4937-4943 7 p.

Research output: Contribution to journalArticle

4 Scopus citations
2014

A cavity corrected 3D-RISM functional for accurate solvation free energies

Truchon, J. F., Pettitt, B. & Labute, P., Mar 11 2014, In : Journal of Chemical Theory and Computation. 10, 3, p. 934-941 8 p.

Research output: Contribution to journalArticle

81 Scopus citations

Computation of high-order virial coefficients in high-dimensional hard-sphere fluids by Mayer sampling

Zhang, C. & Pettitt, B., May 19 2014, In : Molecular Physics. 112, 9-10, p. 1427-1447 21 p.

Research output: Contribution to journalArticle

18 Scopus citations

Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model

Tomar, D. S., Weber, V., Pettitt, B. & Asthagiri, D., Apr 17 2014, In : Journal of Physical Chemistry B. 118, 15, p. 4080-4087 8 p.

Research output: Contribution to journalArticle

9 Scopus citations

Effects of geometry and chemistry on hydrophobic salvation

Harris, R. C., Pettitt, B. & Debenedetti, P. G., Oct 14 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 41, p. 14681-14686 6 p.

Research output: Contribution to journalArticle

39 Scopus citations

Modeling DNA thermodynamics under torsional stress

Wang, Q. & Pettitt, B., Mar 4 2014, In : Biophysical Journal. 106, 5, p. 1182-1193 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

Multibody correlations in the hydrophobic solvation of glycine peptides

Harris, R. C., Drake, J. A. & Pettitt, B., Dec 14 2014, In : Journal of Chemical Physics. 141, 22, 22D525.

Research output: Contribution to journalArticle

10 Scopus citations

Solubility and aggregation of Gly5 in water

Karandur, D., Wong, K. Y. & Pettitt, B., Aug 14 2014, In : Journal of Physical Chemistry B. 118, 32, p. 9565-9572 8 p.

Research output: Contribution to journalArticle

19 Scopus citations
2013

Communication: Origin of the contributions to DNA structure in phages

Myers, C. G. & Pettitt, B., Feb 21 2013, In : Journal of Chemical Physics. 138, 7, 071103.

Research output: Contribution to journalArticle

5 Scopus citations

Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence

Theruvathu, J. A., Yin, Y., Pettitt, B. & Sowers, L., Nov 26 2013, In : Biochemistry. 52, 47, p. 8590-8598 9 p.

Research output: Contribution to journalArticle

7 Scopus citations

Domain organization of membrane-bound factor VIII

Stoilova-Mcphie, S., Lynch, G. C., Ludtke, S. & Pettitt, B., Jul 2013, In : Biopolymers. 99, 7, p. 448-459 12 p.

Research output: Contribution to journalArticle

18 Scopus citations

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Harrison, A., Binder, H., Buhot, A., Burden, C. J., Carlon, E., Gibas, C., Gamble, L. J., Halperin, A., Hooyberghs, J., Kreil, D. P., Levicky, R., Noble, P. A., Ott, A., Pettitt, B., Tautz, D. & Pozhitkov, A. E., Mar 2013, In : Nucleic Acids Research. 41, 5, p. 2779-2796 18 p.

Research output: Contribution to journalArticle

43 Scopus citations