Publications

Selected Publications

2011+ @ResearchGate

2006-2010
Komatsu, H., E. Feingold-Link, K. Sharp, R. Tanvi and P. H. Axelsen (2010). "Intrinsic linear heterogeneity of amyloid beta protein fibrils revealed by higher resolution mass-per-length determinations."
J. Biol. Chem. http://www.jbc.org/cgi/doi/10.1074/jbc.M110.165068
Sharp KA., Vanderkooi, JM. 2010. Water in the Half Shell: Structure of water, focusing on angular structure and solvation
Accounts of Chemical Research 43:231-239
Ward, P. S. et al. 2010. The common feature of leukemia asociated IDH1 and IDH2 mutations is a neomorphic ensymatic activity that converts alph-ketogluterate to 2-hydroxygluterate.
Cancer Cell 17:225-234
Zelent B, Bryan, M, Sharp KA., Vanderkooi, JM. 2010. Influence of surface groups of proteins on water studied by freezing/thawing hysteresis and infrared spectroscopy.
Biophys. Chem. 141:222-230
Coleman, R. G., K. A. Sharp. 2010. Protein Pockets: Inventory, Shape, and Comparison
J Chem Inf Model 50:589-603
Daber, R., K. A. Sharp and M. Lewis. 2009. One is not enough.
J. Mol. Biol. 392:1133-1144.
Coleman, R. G., K. A. Sharp. 2009. Shape and evolution of thermostable protein structure
Proteins 78:420-433.
Coleman, R. G., K. A. Sharp. 2009. Finding and characterizing tunnels in macromolecules with application to ion channels and pores.
Biophys. J. 96:632-645.
Frederick, K. K., Sharp, K. A., Warischalk, N., Wand, A. J. 2008. Re-evaluation of the model free analysis of fast internal motion in proteins using NMR relaxation.
J. Phys. Chem. B 112:12095-12103.
Yang, Q., Sharp, K. A. 2008. Building alternate protein structures using the elastic network model.
Proteins, 74:682-700.
Prabhu, N., M. Panda, Q. Yang, and K. Sharp. 2008. Explicit ion, Implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules.
J Comp Chem 29:1113-1130. PMID: 18074338
Ma, Z., K. A. Sharp, P. A. Janmey, and T. H. Finkel. 2008. Surface-anchored monomeric agonist pMHCs alone trigger TCR with high sensitivity.
PLoS Biology 6:328-342. PMID: 18303949
Domene, C., S. Vemparala, S. Furini, K. Sharp, and M. L. Klein. 2008. The Role of Conformation in Ion Permeation in a K+ Channel.
JACS 130:3389-3398.
Yang Q, Sharp KA. Atomic charge parameters for the finite difference Poisson-Boltzmann method using electronegativity neutralization.
J Chem Theory Comp 2006;2:1152 - 1167
Song, X.-J., P. F. Flynn, K. A. Sharp, and A. J. Wand. 2007. Temperature dependence of fast dynamics in proteins. Biophys. J. 92:L43-45. PMID: 17218465
Sharp KA, Skinner J. Pump-Probe Molecular Dynamics as a tool for studying protein motion and long range coupling.
Proteins: Structure, Function, and Genetics 2006; 65: 347-61.
Rahi SJ, Sharp KA. Mapping complication surfaces to a sphere. International
Journal of Computational Geometry and Applications 2006; V17
Prabhu N, Sharp K. Protein-Solvent Interactions.
Chemical Reviews 2006;106:1616-1623 .
Dashnau JL, Nucci N, Sharp KA, Vanderkooi JM. Hydrogen bonding and the cryoprotective properties of glycerol/water mixtures.
J Phys Chem B 2006; 110: 13670-7.
Coleman RG, Sharp KA. Travel depth, a new shape descriptor for macromolecules: Application to ligand binding.
J Mol Biol 2006; 362:441-458 .

2000-2005
Yang C, Sharp K. Hydrophobic tendency of polar group hydration as a major force in type I antifreeze protein recognition.
Proteins 2005;59:266-274 .
Prabhu N, Sharp K. Heat Capacity in Proteins.
Annual Review of Physical Chemistry 2005;56:521-548 .
Sharp, K. (2005). Potential functions for virtual screening and ligand binding calculations: Some theoretical considerations. Virtual Screening in Drug Discovery. J. Alvarez and B. Shoichet, Eds. Crc Press: Chapter 9
Dashnau JL, Sharp KA, Vanderkooi JM. Carbohydrate intramolecular hydrogen bonding cooperativity and its effect on water structure.
J Phys Chem B 2005;109:24152-24159 .
Zelent B, Kaposi A, Nucci N, Sharp KA, Dalosto S, Wright W, Vanderkooi J. Water channel of horseradish peroxidase studied by the charge-transfer absorption band of ferric heme.
J Phys Chem B 2004;108:10317-10324 .
Yang C, Sharp KA. Mechanism of Type III Antifreeze protein Action: A Computational Study.
Biophysical Chemistry 2004;109:137-148 .
Prabhu NV, Zhu P-J, Sharp KA. Implementation and Testing of Stable, Fast Implicit Solvation in Molecular Dynamics using the Smooth-Permittivity Finite Difference Poisson-Boltzmann Method.
J Comp Chem 2004;25:2049-2064 .
Dalosto S, Vanderkooi JM, Prabhu NV, Sharp KA. Vibrational Stark effects on carbonyl, nitrile and nitrosyl compounds including heme ligands, CO, CN, and NO, studied with density functional theory.
J Phys Chem (B) 2004;108:6450-6457 .
Prabhu N, Lee A, Wand JW, Sharp KA. Dynamics and Entropy of a Calmodulin-Peptide Complex studied by NMR and Molecular dynamics.
Biochemistry 2003;42:562-570 .
Khajehpour M, Rietveld I, Vinogradov S, Prabhu NV, Sharp KA, Vanderkooi JM. Accessibility of oxygen with respect to the heme pocket in horseradish peroxidase.
Proteins 2003;53(3):656-666
Kaposi AD, Prabhu NV, Dalosto SD, Sharp KA, Wright WW, Stavrov SS, Vanderkooi JM. Solvent dependent and independent motions of CO-Horseradish peroxidase examined by infrared spectroscopy and molecular dynamics calculations.
Biophysical Chemistry 2003;106:1-14 .
Gallagher K, Sharp KA. A new angle on heat capacity changes in hydrophobic solvation.
JACS 2003;125:9863-9860 .
Gallagher K, Sharp KA. Analysis of water structure around type 3 thermal hysteresis protein using the random network model.
Biophysical Chemistry 2003;105:195-209 .
Dalosto SD, Prabhu NV, Vanderkooi JM, Sharp KA. A Density Functional Theory Study of Conformers with Distinct Fe-C-O Configuration in the Ferrous CO Complex of Horseradish Peroxidase.
J Phys Chem B 2003;107:1884-1892 .
Sale K, Sár C, Sharp KA, Hideg K, Fajer PG. Structural determination of spin label immobilization and orientation: A Monte Carlo minimization approach.
J Mag Res 2002;156(1):104-112 .
Prabhu NV, Dalosto SD, Sharp KA, Wright WW, Vanderkooi JM. Optical spectra of Fe(II) cytochrome c interpreted using molecular dynamics simulations and quantum mechanical calculations.
J Phys Chem 2002;106:5561-5571 .
Luo H, Sharp KA. On the calculation of absolute binding free energies.
PNAS 2002;99(16):10399-10404 .
Lee AL, Sharp KA, Kranz JK, Song X, Wand AJ. Temperature Dependence of the Internal Dynamics of a Calmodulin-Peptide Complex. Biochemistry 2002;41:13814-13825.
Brooijmans N, Sharp KA, Kuntz ID. The stability of macromolecular complexes. Proteins 2002;48(4):645-653.
Sharp KA. Electrostatic interactions in proteins. In: Rossman GR, Arnold, E., editor. Crystallography Tables. Volume F; 2001. p Ch. 22.21.21.
Sharp KA. Water: Structure and Properties. Encyclopedia of Life Sciences. New York: MacMillan; 2001.
Sharp K. Entropy-enthalpy compensation: fact or artifact? Protein Science 2001;10:661-667.
Sharp KA, Madan B. Hydration Heat Capacity of Nucleic Acid Constituents Determined from the Random Network Model. Biophysical Journal 2001;81:1881-1887.
Sharp K, Madan B, Manas E, Vanderkooi J. Water Structure Changes Induced by Hydrophobic and Polar Solutes Revealed by Simulations and IR Spectroscopy. J Chem Phys 2001;114:1791-1796.
Rasnik I, Sharp KA, Fee JA, Vanderkooi JM. Spectral analysis of cytochrome c: Effect of heme conformation, axial ligand, peripheral substituents, and local electric fields. J Phys Chem B 2001;105:282-286.
Manas E, Wright W, Sharp K, Friedrich J, Vanderkooi J. The influence of protein environment on the low temperature electronic spectroscopy of Zn substituted cytochrome c. J Phys Chem 2000;104:6932-6941.
Madan B, Sharp KA. Heat capacity changes accompanying hydrophobic and ionic solvation: a Monte-Carlo and random network model study. J Phys Chem 2000;104:12047-12047.

1996-1999
Manas E, Sharp K, Vanderkooi J. The Effects of Protein Environment on the Low Temperature Electronic Spectroscopy of Cytochrome c and Microperoxidase-11. J Phys Chem 1999;103:6334-6348.
Madan B, Sharp K. Changes in water structure induced by a hydrophobic solute probed by simulation of the water hydrogen bond angle and radial distribution functions. Biophys Chem 1999;78:33-41.
Kuntz ID, Chen K, Sharp K, Kollman P. The maximal affinity of ligands. PNAS 1999;96:9997-10002.
Dieckmann G, Lear J, Zhong Q, Klein M, Sharp K, DeGrado W. Exploration of the structural features defining the conduction properties of a synthetic ion channel. Biophysical Journal 1999;76:618-630.
Chin K, Sharp KA, Honig B, Pyle A. Calculating electrostatic potentials of RNA: Providing new insights into molecular interactions and function. Nature Structural Biology 1999;6:1055-1061.
Vanzi F, Madan B, Sharp K. Effect of the protein denaturants urea and guanidinium on water structure: a structural and thermodynamic study. JACS 1998;120:10748-10753.
Sharp K. Continuum Solvent Models. In: Schleyer P, editor. Encyclopedia of Computational Chemistry. Chichester, England: John Wiley and Sons; 1998.
Sharp KA. Calculation of Electron Transfer Reorganization Energies using the Finite Difference Poisson-Boltzmann Model. Biophys J 1998;73:1241-1250.
Sharp KA. Calculation of HyHel10-Lysozyme Binding Free Energies Changes: Effect of Ten Point Mutations. Proteins 1998;33:39-48.
Laberge M, Sharp KA, Vanderkooi J. Effect of charge interactions on the carboxylate vibrational stretch frequency in c-type cytochromes investigated by continuum electrostatic calculations and FTIR spectroscopy. Biophysical Chemistry 1998;71:9-20.
Gallagher K, Sharp KA. Electrostatic Contributions to Heat Capacity Changes of DNA-Ligand Binding. Biophys J 1998;75:769-776.
Dieckmann G, McRorie D, Lear J, Sharp K, DeGrado W, Pecoraro V. The role of protonation and metal chelation preferences in defining the properties of mercury-binding coiled coils. J Mol Biol 1998;280:897-912.
Sharp KA, Madan B. The hydrophobic effect, water structure and heat capacity changes. J Phys Chem 1997;101:4343-4348.
Sharp KA. Electrostatic interactions in proteins. In: Naray-Szabo G, Warshel A, editors. Computational Approaches to Enzymatic Reactivity. Amsterdam: Kluwer Academic; 1997. p 199-235.
Novotny J, Bruccoleri RE, Davis M, Sharp KA. Empirical free energy calculations: A blind test and further improvements to the method. J Mol Biol 1997;268:401-411.
Madan B, Sharp KA. Molecular origin of hydration heat capacity changes of hydrophobic solutes: Perturbation of water structure around alkanes. J Phys Chem 1997;101:11237-11242.
Laberge M, Sharp KA, Vanderkooi J. Protein electric field effects on the CO stretch frequency of carbonmonoxycytochromes c. J Phys Chem 1997;101:7364-7367.
Brady GP, Sharp KA. Entropy changes in protein folding and protein-protein interactions. Curr Op Struct Biol 1997;7:215-221.
Brady GP, Sharp KA. Energetics of cyclic dipeptide crystal packing and solvation. Biophysical Journal 1997;72:913-927.
Sharp KA. Electrostatic Interactions in Hirudin-Thrombin Binding. Biophysical Chemistry 1996;61:37-49.
Sharp KA, Kumar S, Rossky PJ, Friedman R, Honig B. Size dependence of transfer free energies. II Hard sphere models. J Phys Chem 1996;100:14166-14177.
Madan B, Sharp KA. Heat capacity changes accompanying hydrophobic and ionic solvation: a Monte-Carlo and random network model study. J Phys Chem 1996;100:7713-7721.
Laberge M, Vanderkooi JM, Sharp KA. The effect of a protein electric field on the CO-stretch frequency. Finite Difference Poisson-Boltzmann calculations on carbonmonoxy cytochrome c. J Phys Chem 1996;100:10793-10801.
Bruccoleri RE, Novotny J, Sharp KA, Davis ME. Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge anti-aliasing. J Comp Chem 1996;18:268-276.
Brady GP, Szabo A, Sharp KA. On the Decomposition of Free Energies. J Mol Biol 1996;263:123-125.

1990-1995
Sridharan S, Nicholls A, Sharp KA. A rapid method for calculating derivatives of solvent accessible surface areas of molecules. J Comp Chem 1995;16:1038-1044.
Sharp KA, Honig B. Salt effects in nucleic acids. Curr Op Struct Biol 1995;5:323-328.
Sharp KA, Friedman R, Misra V, Hecht J, Honig B. Salt effects on polyelectrolyte-ligand binding: Comparison of Poisson-Boltzmann and limiting law counterion binding models. Biopolymers 1995;36:245-262.
Sharp KA. Polyelectrolyte electrostatics: Salt dependence, entropic and enthalpic contributions to free energy in the nonlinear Poisson-Boltzmann model. Biopolymers 1995;36:227-243.
Peitzsch RM, Eisenberg M, Sharp KA, McLaughlin S. Calculations of the electrostatic potential adjacent to model phospholipid bilayers. Biophys J 1995;68:729-738.
Kumar SK, Szleifer I, Sharp KA, Rossky P, Friedman R, Honig B. Size dependence of transfer free energies. I A Flory-Huggins approach. J Phys Chem 1995;99:8382-8391.
Brady GP, Sharp KA. Decomposition of interaction free energies in proteins and other complex systems. J Mol Biol 1995;254:77-85.
Sitkoff D, Lockhart DJ, Sharp KA, Honig B. Calculation of electrostatic effects at the amino terminus of an alpha helix. Biophysical Journal 1994;64:1-10.
Sitkoff D, Sharp K, Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 1994;98:1978-1988.
Sitkoff D, Sharp KA, Honig H. Correlating solvation free energies and surface tensions of hydrocarbons. Biophys Chem 1994;51:397-409.
Sharp KA, Englander SW. How much is a stabilizing bond worth? TIBS 1994;19:526-529.
Sharp KA. Electrostatic Interactions in Macromolecules. Current Opinion in Structural Biology 1994;4:234-239.
Misra V, Sharp K, Friedman R, Honig B. Salt effects on ligand-DNA binding: Minor groove antibiotics. J Mol Biol 1994;238:245-263.
Misra V, Hecht J, Sharp K, Friedman R, Honig B. Salt effects on Protein-DNA interactions: The Lambda cI repressor and Eco R1 endonuclease. J Mol Biol 1994;238:264-280.
Anni E, Vanderkooi JM, Sharp KA, Yonetani T, Hopkins S, Herenyi L, Fidy J. Electric field and conformational effects of cytochrome C and solvent on cytochrome C peroxidase studied by high resolution fluorescence spectroscopy. Biochemistry 1994;33:3475-3486.
Yang A, Gunner M, Sampogna R, Sharp K, Honig B. On the Calculation of Pka's in Proteins. Proteins-Structure Function and Genetics 1993;15:252-265.
Sharp KA. Inclusion of solvent effects in molecular mechanics force-fields. In: van Gunsteren WF, Weiner PK, Wilkinson AJ, editors. Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications. Leiden: Escom; 1993.
Honig B, Sharp K, Yang A. Macroscopic models of aqueous solvation: Biological and Chemical Applications. J Phys Chem 1993;97:1101-1109.
Yang A, Sharp K, Honig B. Analysis of the heat capacity dependence of protein folding. J Mol Biol 1992;227:889-900.
Sharp KA, Jean-Charles A, Honig B. A local dielectric constant model for solvation free energies which accounts for solute polarizability. J Phys Chem 1992;96:3822-3828.
Novotny J, Sharp K. Electrostatic fields in antibodies and antibody/antigen complexes. Prog Biophys Molec Biol 1992;58:203-224.
Brooks DE, Van Alstine JM, Sharp KA, Stocks SJ. PEG derivatized ligands with hydrophobic and immunological specificity: Applications in cell separation and contact angle control. Polyethylene-glycol Chemistry. New York: Plenum Press; 1992. p 57-71.
Sharp KA. The hydrophobic effect. Curr Opin Struct Biol 1991;1:171-174.
Sharp KA, Nicholls A, Friedman R, Honig B. Extracting Hydrophobic Free Energies From Experimental Data: Relationship to Protein Folding and Theoretical Models. Biochemistry 1991;30:9686-9697.
Sharp KA, Nicholls A, Fine RM, Honig B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 1991;252:106-109.
Sharp KA. Incorporating Solvent and Ion Screening into Molecular Dynamics Using the Finite-Difference Poisson-Boltzmann Method. J Comp Chem 1991;12:454-468.
Nicholls A, Sharp KA, Honig H. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 1991;11:281-296.
Langsetmo K, Fuchs JA, Woodward C, Sharp KA. Linkage of Thioredoxin stability to titration of ionizable groups with perturbed pKa. Biochemistry 1991;30:7609-7614.
Jean-Charles A, Nicholls A, Sharp K, Honig B, Tempczyk A, Hendrickson T, Still C. Electrostatic contributions to solvation energies: Comparison of free energy perturbation and continuum calculations. J Am Chem Soc 1991;113:1454-1455.
Sharp KA, Honig B. Applications of the Finite Difference Poisson Boltzmann Method to Proteins and Nucleic Acids. In: Sarma RH, Sarma MH, editors. DNA Protein Complexes and Proteins. Volume 2, Structure and Methods: Adenine Press; 1990. p 211.
Sharp K, Honig B, Harvey S. Electrical Potential of Transfer RNAs: Codon-Anticodon Recognition. Biochemistry 1990;29:340-346.
Sharp KA, Nicholls A, Honig B. DelPhi: A macromolecular electrostatics software package. Copyright Dept. of Biochemistry and Molecular Biophysics, Columbia University, New York; 1990.
Sharp K, Honig B. Calculating total electrostatic energies with the non-linear Poisson-Boltzmann Equation. J Phys Chem 1990;94:7684-7692.
Sharp K, Honig B. Electrostatic Interactions in Macromolecules: Theory and Applications. Ann Rev Biophys Biophys Chem 1990;19:301-332.
Jayaram B, Swaminathan S, Beveridge DL, Sharp K, Honig B. Monte Carlo Simulation Studies on the Structure of the Counterion Atmosphere of B-DNA. Variations on the Primitive Dielectric Model. Macromolecules 1990;23:3156-3165.

1983-1989
Sharp K, Honig B. Lattice models of Electrostatic Interaction: The Finite Difference Poisson-Boltzmann Method. Chemica Scripta 1989;29A:71.
Jayaram B, Fine R, Sharp KA, Honig B. Free Energy Calculations of Ion Hydration: An Analysis of the Born Model in Terms of Microscopic Simulations. J Phys Chem 1989;93:4320-4327.
Jayaram B, Sharp KA, Honig B. The Electrostatic Potential of B-DNA. Biopolymers 1989;28:975-993.
Honig B, Sharp K, Gilson M. Electrostatic Interactions in Proteins. In: Rein R, Golombek A, editors. Computer Assisted Modeling of Receptor Ligand Interactions. New York: Alan R. Liss; 1989. p 65.
Gilson M, Sharp KA, Honig B. Calculating the Electrostatic Potential of Molecules in Solution: Method and Error Assessment. J Comp Chem 1988;9:327-335.
Brooks DE, Sharp KA, Stocks J. Immuno-affinity separation of cells in two polymer aqueous phase system. Macromolecular Chemistry 1988;17:387-399.
Sharp K, Gilson M, Fine R, Honig B. Electrostatic Interactions in Proteins. In: Oxender DL, editor. Protein Structure, Folding and Design. Volume 69, UCLA Symposium on Molecular and Cell Biology; 1987. p 235.
Sharp K, Fine R, Honig B. Computer Simulations of the Diffusion of a Substrate to an Enzyme Active Site. Science 1987;236:1460.
Sharp K, Fine R, Schulten K, Honig B. Brownian Dynamics Simulations of Diffusion to Irregular Bodies. J Phys Chem 1987;91:3624.
Van Alstine J, Sharp K, Brooks DE. Critical Micelle Concentration Dependence on Head Group Size in Polyoxyethylene Nonionic Surfactants. Colloids and Surfaces 1986;17:115.
Sharp K, Yalpani M, Howard S, Brooks DE. Synthesis and Application of a Poly(ethylene glycol)-Antibody Affinity Ligand for Cell Separations in Aqueous Polymer Two-Phase Systems. Anal Biochem 1986;154:110.
McDaniel R, Sharp KA, Brooks DE, McLaughlin AC, Winiski AP, Cafiso D, McLaughlin S. Electrokinetic and Electrostatic Properties of Bilayers Containing Gangliosides Gm1, Gd1a, of Gt1. Biophys J 1986;49:741-752.
Klapper I, Hagstrom R, Fine R, Sharp K, Honig B. Focusing of Electrical Fields in the Active Site of Cu-Zn Superoxide Dismutase: Effects of Ionic Strength and Amino-Acid Modifications. Proteins 1986;1:47-59.
Brooks DE, Sharp K, Fisher D. Theoretical aspects of partitioning. In: Walter H, Brooks DE, Fisher D, editors. Partitioning in Aqueous Two Phase Systems: Academic Press; 1986 Ch.3.
Bamberger S, Brooks DE, Sharp K, Van-Alstine J, Webber T. Preparation of phase systems and measurement of their physicochemical properties. In: Walter H, Brooks DE, Fisher D, editors. Partitioning in Aqueous Two Phase Systems: Academic Press; 1986. p Ch.2.
Sharp KA, Brooks DE. Calculation of the Electrophoretic Mobility of a Particle Bearing Bound Polyelectrolyte using the Non-linear Poisson-Boltzmann Equation. Biophys J 1985;47:563.
Brooks DE, Sharp K, Bamberger S, Tamblyn CH, Seaman GV, Walter H. Electrostatic and electrokinetic potentials in two polymer aqueous phase systems. J Coll and Int Sci 1984;102:1.
Bamberger S, Seaman GV, Sharp K, Brooks DE. The effects of salts on the interfacial tension of aqueous dextran poly(ethylene glycol) phase systems. J Coll and Int Sci 1984;99:194.
Levine S, Levine M, Sharp K, Brooks DE. Theory of the Electrokinetic Behavior of Human Erythrocytes. Biophysical J 1983;42:127.

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