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