Peter J. Steinbach
NIH, CIT, CMM
Bldg 12A, Room 2051
12 South Drive MSC 5624
Bethesda, MD 20892-5624
steinbac@helix.nih.gov

Selected Publications

Molecular Modeling, Structure Prediction, & Dynamics Simulation: Collaboration with Experimentalists

M.L. Herman, S. Farasat, P.J. Steinbach, M.-H. Wei, O. Toure, P. Fleckman, P. Blake, S.J. Bale, J.R. Toro, Transglutaminase-1 (TGM1) Gene Mutations in Autosomal Recessive Congenital Ichthyosis: Summary of Mutations (Including 23 Novel) and Modeling of TGase-1. (2009) Human Mutation, in press.

A. Balla, G. Tuymetova, B. Toth, Z. Szentpetery, X. Zhao, Z.A. Knight, K. Shokat, P.J. Steinbach, & T. Balla, Design of Drug-Resistant Alleles of Type-III Phosphatidylinositol 4-Kinases using Mutagenesis and Molecular Modeling. (2008) Biochemistry 47, 1599-1607.

Z. Xiang, P.J. Steinbach, M.P. Jacobson, R.A. Friesner, & B. Honig, Prediction of Side-Chain Conformations on Protein Surfaces. (2007) Proteins Struct. Funct. Bioinform. 66, 814-823.

M.Y.-K. Leung, P.J. Steinbach, D. Bear, V. Baxendale, P.Y. Fechner, O.M. Rennert, & W.-Y. Chan, Biological Effect of a Novel Mutation in the Third Leucine-Rich Repeat of Human Luteinizing Hormone Receptor. (2006) Mol. Endocrinol. 20, 2493-2503.

M. Pithukpakorn, M.-H. Wei, O. Toure, P.J. Steinbach, G.M. Glenn, B. Zbar, W.M. Linehan, & J.R. Toro, Fumarate Hydratase Enzyme Activity in Lymphoblastoid Cells and Fibroblasts of Individuals in Families with Hereditary Leiomyomatosis and Renal Cell Cancer. (2006) J. Med. Genet. 43, 755-762.

S.A. Gaidamakov, I.I. Gorshkova, P. Schuck, P.J. Steinbach, H. Yamada, S.M. Cerritelli, & R.J. Crouch, Eucharyotic Ribonucleases H1 Act Processively by Interactions through the Duplex RNA-binding Domain. (2005) Nucl. Acids Res. 33, 2166-2175.

B. Schuler, E.A. Lipman, P.J. Steinbach, M. Kumke, & W.A. Eaton, Polyproline and the `Spectroscopic Ruler' Revisited with Single-Molecule Fluorescence. (2005) Proc. Natl. Acad. Sci. USA 102, 2754-2759.

P.J. Steinbach, Exploring Peptide Energy Landscapes: A Test of Force Fields and Implicit Solvent Models. (2004) Proteins Struct. Funct. Bioinform. 57, 665-677.

J. Tang, S. Stern-Nezer, P.-C. Liu, L. Matyakhina, M. Riordan, N.L.C. Luban, P.J. Steinbach & S.G. Kaler, Mutation in the Leucine-rich Repeat C-flanking Region of Platelet Glycoprotein Ib-beta Impairs Assembly of von Willebrand Factor Receptor. (2004) Thromb. Haemost. 92, 75-88.

L.J. Lapidus, P.J. Steinbach, W.A. Eaton, A. Szabo, & J. Hofrichter, Effects of Chain Stiffness on the Dynamics of Loop Formation in Polypeptides. (2002) J. Phys. Chem. B 106, 11628-11640.

R. Chu, J. Takei, J.R. Knowlton, M. Andrykovitch, W. Pei, A.V. Kajava, P.J. Steinbach, X. Ji, & Y. Bai, Redesign of a Four-helix Bundle Protein by Phage Display Coupled with Proteolysis and Structural Characterization by NMR and X-ray Crystallography. (2002) J. Mol. Biol. 323, 253-62.

S. Dhanvantari, I. Arnaoutova, C.R. Snell, P.J. Steinbach, K. Hammond, G.A. Caputo, E. London, & Y.P. Loh, Carboxypeptidase E, a Prohormone Sorting Receptor, is Anchored to Secretory Granules via a C-terminal Transmembrane Insertion. (2002) Biochemistry 41, 52-60.

S. Ganguly, P. Mummaneni, P.J. Steinbach, D.C. Klein, & S.L.Coon, Characterization of the Saccharomyces cerevisiae Homolog of the Melatonin Rhythm Enzyme Arylalkylamine N-acetyltransferase (AANAT, EC 2.3.1.87). (2001) J. Biol. Chem. 276, 47239-47247.

J. Piatigorsky, B. Norman, L.J. Dishaw, L. Kos, J. Horwitz, P.J. Steinbach, & Z. Kozmik, J3-Crystallin of the Jellyfish Lens: Homology to Saposins. (2001) Proc. Natl. Acad. Sci. USA 98, 12362-12367.

G. Reyes-Cruz, J. Hu, P.K. Goldsmith, P.J. Steinbach, & A.M. Spiegel, Human Ca Receptor Extracellular Domain: Analysis of Function of Lobe I Loop Deletion Mutants. (2001) J. Biol. Chem. 276, 32145-32151.

J. Piatigorsky, Z. Kozmik, J. Horwitz, L. Ding, E. Carosa, W.G. Robison, Jr., P.J. Steinbach, & E.R. Tamm, Omega-Crystallin of the Scallop Lens: A Dimeric Aldehyde Dehydrogenase Class 1/2 Enzyme-Crystallin. (2000) J. Biol. Chem. 275, 41064-41073.

J.J. Balbach, J. Yang, D.P. Weliky, P.J. Steinbach, V. Turganov, J. Anglister, & R. Tycko, Probing Hydrogen Bonds in the Antibody-Bound HIV-1 gp120 V3 Loop by Solid State NMR REDOR Measurements. (2000) J. Biomol. NMR 16, 313-327.

K. Ray, B.C. Hauschild, P.J. Steinbach, P.K. Goldsmith, O. Hauache, & A.M. Spiegel, Identification of the Cysteine Residues in the Amino-Terminal Extracellular Domain of the Human Ca Receptor Critical for Dimerization: Implications for Function of Monomeric Ca Receptor. (1999) J. Biol. Chem. 274, 27642-27650.

P. Sharma, P.J. Steinbach, M. Sharma, N.D. Amin, J.J. Barchi, Jr., & H.C. Pant, Identification of Substrate Binding Site of Cyclin-Dependent Kinase 5. (1999) J. Biol. Chem. 274, 9600-9606.

D.P. Weliky, A.E. Bennett, A. Zvi, J. Anglister, P.J. Steinbach, & R. Tycko, Solid-State NMR Evidence for an Antibody-Dependent Conformation of the V3 Loop of HIV-1 gp120. (1999) Nature Struct. Biol. 6, 141-145.

E. Leroy, R. Boyer, G. Auburger, B. Leube, G. Ulm, E. Mezey, G. Harta, M.J. Brownstein, S. Jonnalagada, T. Chernova, A. Dehejia, C. Lavedan, T. Gasser, P.J. Steinbach, K.D. Wilkinson, & M.H. Polymeropoulos, The Ubiquitin Pathway in Parkinson's Disease. (1998) Nature 395, 451-452.

Molecular Dynamics Simulation

P.J. Steinbach & B.R. Brooks, Hydrated Myoglobin's Anharmonic Fluctuations are Not Primarily Due to Dihedral Transitions, (1996) Proc. Natl. Acad. Sci. USA 93, 55-59.

P.J. Steinbach & B.R. Brooks, Protein Simulation Below the Glass-Transition Temperature: Dependence on Cooling Protocol, (1994) Chem. Phys. Letters 226, 447-452.

P.J. Steinbach & B.R. Brooks, New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation, (1994) J. Comp. Chem. 15, 667-683.

P.J. Steinbach & B.R. Brooks, Protein Hydration Elucidated by Molecular Dynamics Simulation, (1993) Proc. Natl. Acad. Sci. USA 90, 9135-9139.

Y. Osawa, J.F. Darbyshire, P.J. Steinbach, & B.R. Brooks, Metabolism-Based Transformation of Myoglobin to an Oxidase by BrCCl and Molecular Modeling of the Oxidase Form, (1993) J. Biol. Chem. 268, 2953-2959.

P.J. Steinbach, R.J. Loncharich, & B.R. Brooks, The Effects of Environment and Hydration on Protein Dynamics: a Simulation Study of Myoglobin, (1991) Chem. Phys. 158, 383-394.

Ligand Rebinding Kinetics & Analysis of Kinetics Data via Maximum Entropy and other Techniques

P.J. Steinbach, Inferring Lifetime Distributions from Kinetics by Maximizing Entropy Using a Bootstrapped Model, (2002) J. Chem. Inf. Comput. Sci. 42, 1476-1478.

P.J. Steinbach, R. Ionescu, & C.R. Matthews, Analysis of Kinetics using a Hybrid Maximum-Entropy / Nonlinear-Least-Squares Method: Application to Protein Folding, (2002) Biophys. J. 82, 2244-2255. Download software.

P.J. Steinbach, Two-Dimensional Distributions of Activation Enthalpy and Entropy from Kinetics by the Maximum Entropy Method, (1996) Biophys. J. 70, 1521-1528.

P.J. Steinbach, K. Chu, H. Frauenfelder, J.B. Johnson, D.C. Lamb, G.U. Nienhaus, T.B. Sauke, & R.D. Young, Determination of Rate Distributions from Kinetic Experiments, (1992) Biophys. J. 61, 235-245.

P.J. Steinbach, A. Ansari, J. Berendzen, D. Braunstein, K. Chu, B.R. Cowen, D. Ehrenstein, H. Frauenfelder, J.B. Johnson, D.C. Lamb, S. Luck, J.R. Mourant, G.U. Nienhaus, P. Ormos, R. Philipp, A. Xie, & R.D. Young, Ligand Binding to Heme Proteins: Connection between Dynamics and Function, (1991) Biochemistry 30, 3988-4001.

Book Chapter

S.A. Hassan, L. Gracia, G. Vasudevan, & P.J. Steinbach, Computer Simulation of Protein-Ligand Interactions: Challenges and Applications, in Protein-Ligand Interactions: Methods and Applications, G.U. Nienhaus, editor. (2005) Humana Press, Totowa, NJ.

Original Tutorials

Introduction to Macromolecular Simulation, included in the Biophysical Society's Biophysics Textbook Online

Introduction to the Maximum Entropy Method

Downloadable Software

MemExp: Analysis of kinetics in terms of lifetime distributions and discrete exponentials.