Ensemble-based analysis of the pH-dependence of stability of...

Data processing: structural design – modeling – simulation – and em – Simulating nonelectrical device or system – Biological or biochemical

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C702S019000, C365S094000, C700S001000

Reexamination Certificate

active

07027969

ABSTRACT:
The present invention relates to a computer-based algorithm that is used to determine the pKa, pH stability and electrostatic interactions of a protein.

REFERENCES:
patent: 6403312 (2002-06-01), Dahiyat et al.
Lehninger Biochemistry Second Edition Worth Publishers, Inc. New York pp. 161-165 (1975).
Murzin et al, “SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures,” J. Mol. Biol. (1995) 247, 536-540.
Delagrave et al, “Searching Sequence Space to Engineer Proteins: Exponential Ensemble Mutagenesis,” BioTechnology vol. 11, Dec. 1993, 1548-1552.
Antosiewicz, Jan, et al.; Prediction of pH-dependent Properties of Proteins; J. Mol. Biol. (1994) 238, 415-436.
Bai, Yawen, et al.; Protein Foldling Intermediates: Native-State Hydrogen Exchange; Protein Folding Intermediates: Native-State Hydrogen Exchange; Science, vol. 269(5221), pp 192-197, Jul. 14, 1995.
Baldwin, Robert L.; Temperature dependence of the hydrophobic interaction in protein folding; Proc. Natl. Acad. Sci. USA (Biochemistry), vol. 83, pp 8069-8072, Nov. 1986.
D'Aquino, J. Alejandro, et al.; The Magnitude of the Backbone Conformational Entropy Change in Protein Folding; PROTEINS: Structure, Function, and Genetics 25:143-156 (1996).
Englander, S. Walter; Protein Folding Intermediates and Pathways Studied by Hydrogen Exchange; Annu. Rev. Biophys. Biomol. Struct. 200, 29:213-238.
Freire, Ernesto, et al.; Thermodynamics of Transfer Ribonucleic Acids: The Effect of Sodium on the Thermal Unfolding of Yeast tRNAPhe; Biopolymers, vol. 17, pp 1257-1272 (1978).
Freire, Ernesto; Statistical Thermodynamic Linkage Between Conformational and Binding Equilibria; Advances in Protein Chemistry, vol. 51, pp 255-279, 1998.
Freire, Ernesto; The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to lysozyme; Proc. natl. Acad. Sci. USA (Biophysics), vol. 96, pp 10118-10122, Aug. 1999.
Gomez, Javier, et al.; Thermodynamic Mapping of the Inhibitor Site of the Aspartic Protease Endothiapepsin; J. Mol. Biol. (1995) 252, 337-350.
Gomez, Javier, et al.; The Heat Capacity of Proteins; PROTEINS: Structure, Function, and Genetics 22:404-412, 1995.
Habermann, Susan M., et al.; Energetics of hydrogen bonding in proteins: A model compound study; Protein Science (1996), 5:1229-1239.
Hilser, Vincent J., et al.; Structure-based Calculation of the Equilibrium Folding Pathway of Proteins. Correlation with Hydrogen Exchange Protection Factors; J. Mol. Biol. (1996) 262, 756-772.
Elcock, Adrian H.; Realistic Modeling of the Denatured States of Proteins Alloys Accurate Calculations of the pH Dependence of Protein Stability; J. Mol. Biol. (1999) 294, 1051-1062.
Hilser, Vincent J., et al.; Structure-based statistical thermodynamic analysis of T4 lysozyme mutants: structural mapping of cooperative interactions; Biophysical Chemistry 64 (1997) 69-79.
Hilser, Vincent J., et al.; The structural distribution of cooperative interactions in proteins: Analysis of the native state ensemble; Proc. Natl. Acad. Sci. USA (Biophysics), vol. 95, pp 9903-9908, Aug. 1998.
Jayaram, B., et al.; The Electrostatic Potential of B-DNA; Biopolymers, vol. 28, 975-993 (1989).
Kim, Peter S., et al.; Intermediates in the Folding Reactions of Small Proteins; Annu. Rev. Biochem. 1990, 59:631-660.
Johnson, Mark S., et al.; Alignment and Searching for Common Protein Folds Using a Data Bank of Structural Templates; J. Mol. Biol. (1993) 231, 735-752.
Johannesson, Petra, et al.; Bicyclic Tripeptide Mimetics with Reverse Turn Inducing Properties; J. Med. Chem. 1999, 42, 601-608.
Klapper, Isaac, et al.; Focusing of Electric Fields in the Active Site of Cu-Zn Superoxide Dismutase: Effects of Ionic Strength and Amino-Acid Modification; PROTEINS: Structure, Function, and Genetics 1:47-59 (1986).
Kuwajima, Kunihiro; Review Article: The Molten Globule State as a Clue for Understanding the Folding and Cooperativity of Globular-Protein Structure; PROTEINS: Structure, Function, and Genetics 6:87-103 (1989).
Lee, B., et al.; The Interpretation of Protein Structures: Estimation of Static Accessibility; J. Mol. Biol. (1971) 55, 379-400.
Lee, Kon Ho, et al.; Estimation of Changes in Side Chain Configurational Entropy in Binding and Folding: General Methods and Application to Helix Formation; PROTEINS: Structure, Function, and Genetics 20:68-84 (1994).
Matthew, James B., et al.; Calculation of Electrostatic Interactions in Proteins; Methods in Enzymology, vol. 130, pp 413-436, 1986.
Matthew, James B., et al.; pH-Dependent Processes in Proteins; CRC Critical Reviews in Biochemistry, vol. 18 (2), pp 91-197, 1985.
Mayne, Leland, et al.; Two-state vs. multistate protein unfolding studied by optical melting and hydrogen exchange; Protein Science (2000), 9:1873-1877.
Milne, John S., et al.; Experimental Study of the Protein Folding Landscape: Unfolding Reactions in Cytochrome c; J. Mol. Biol. (1999) 290, 811-822.
Murphy, Kenneth P., et al.; Molecular Basis of Co-operativity in Protein Folding. III. Structural Identification of Cooperative Folding Units and Foldilng Intermediates; J. Mol. Biol. (1992) 227, 293-306.
Nozaki, Yasuhiko, et al.; Acid-Base Titrations in Concentrated Guanidine Hydrochloride. Dissociation Constants of the Guanidinium Ion and of Some Amino Acids; Journal of the American Chemical Society, 89(4):736-742, Feb. 15, 1967.
Roxby, Robert, et al.; Hydrogen Ion Titration Curve of Lysozyme in 6MGuanidine Hydrochloride; Biochemistry, vol. 10 (18), pp 3348-3352, 1971.
Pan, Hong, et al.; Binding sites inEscherichia colidihydrofolate reductase communicate by modulating the conformational ensemble; PNAS 97 (22), pp 12020-12025, Oct. 24, 2000.
Schaefer, Michael, et al.; Electrostatic Contributions to Molecular Free Energies in Solution; Advances in Protein Chemistry, vol. 51, pp 1-57, 1998.
Shortle, David, et al.; Residual Structure in Large Fragments of Staphylococcal Nuclease: Effects of Amino Acid Substitutions; Biochemistry, 1989, 28, 936-944.
Tanford, Charles; The Interpretation of Hydrogen Ion Titration Curves of Proteins; Adv. Protein Chem. 27:69-165, 1962.
Tanford, Charles, et al.; Theory of Protein Titration Curves. I. General Equations for Impenetrable Spheres; J. Am Chem. Soc., 79 (20):5333-5339, Oct. 22, 1957.
Vita, Claudio, et al.; Novel Miniproteins Engineered by the Transfer of Active Sites to Small Natural Scaffolds; Biopolymers (Peptide Science) 47:93-100, 1998.
Warwicker, J.; Continuum Dielectric Modelling of the Protein-Solvent System, and Calculation of the Long-range Electrostatic Field of the Enzyme Phosphoglycerate Mutase; J. Theor. Biol. (1986) 121, 199-210.
Whitten, Steven T., et al.; pH Dependence of Stability of Staphylococcal Nuclease: Evidence of Substantial Electrostatic Interactions in the Denatured State; Biochemistry 2000, 39:14292-14304.
Wooll, John O., et al.; Communication: Ensemble Modulation as an Origin of Denaturant-independent Hydrogen Exchange in Proteins; J, Mol. Biol. (2000) 301:247-256.
Xie, Dong, et al.; Structure Based Prediction of Protein Folding Intermediates; J. Mol. Biol. (1994) 242, 62-80.
Xie, Dong, et al.; Molecular Basis of Cooperativity in Protein Folding. V. Thermodynamic and Structural Conditions for the Stabilization of Compact Denatured States; PROTEINS: Structure, Function, and Genetics 19:291-301 (1994).
WeiBhoff, Hardy, et al.; Minicry of βII'-turns of proteins in cyclic pentapeptides with one and without D-amino acids; Eur. J. Biochem. 259, 776-788 (1999).
Tanford, Charles; Protein Denaturation; Adv. Protein Chem. 23: 121-282, 1968.

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Ensemble-based analysis of the pH-dependence of stability of... does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Ensemble-based analysis of the pH-dependence of stability of..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Ensemble-based analysis of the pH-dependence of stability of... will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-3610948

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.