Protein structure prediction and potential energy landscape analysis using continuous global minimization

Conference · Mon Dec 01 00:00:00 EST 1997

OSTI ID:549002

Dill, K A ^[1]; Phillips, A T ^[2]; Rosen, J B ^[3]

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1. Univ. of California, San Francisco, CA (United States)
2. United States Naval Academy, Annapolis, MD (United States)
3. Univ. of California, San Diego, CA (United States)

Proteins require specific three-dimensional conformations to function properly. These {open_quotes}native{close_quotes} conformations result primarily from intramolecular interactions between the atoms in the macromolecule, and also intermolecular interactions between the macromolecule and the surrounding solvent. Although the folding process can be quite complex, the instructions guiding this process are specified by the one-dimensional primary sequence of the protein or nucleic acid: external factors, such as helper (chaperone) proteins, present at the time of folding have no effect on the final state of the protein. Many denatured proteins spontaneously refold into functional conformations once denaturing conditions are removed. Indeed, the existence of a unique native conformation, in which residues distant in sequence but close in proximity exhibit a densely packed hydrophobic core, suggests that this three-dimensional structure is largely encoded within the sequential arrangement of these specific amino acids. In any case, the native structure is often the conformation at the global minimum energy. In addition to the unique native (minimum energy) structure, other less stable structures exist as well, each with a corresponding potential energy. These structures, in conjunction with the native structure, make up an energy landscape that can be used to characterize various aspects of the protein structure. 22 refs., 10 figs., 2 tabs.

• Research Organization: Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
• OSTI ID: 549002
• Report Number(s): CONF-970137-; CNN: Grant BIR-9119575; Grant 60NANB4D1615; Grant CCR-9509085; Grant CCR-9527151; TRN: 97:005298-0014
• Resource Relation: Conference: RECOMB `97: 1. annual conference on research in computational molecular biology, Santa Fe, NM (United States), 20-22 Jan 1997; Other Information: PBD: 1997; Related Information: Is Part Of RECOMB 97. Proceedings of the first annual international conference on computational molecular biology; PB: 370 p.
• Country of Publication: United States
• Language: English

Related Subjects

55 BIOLOGY AND MEDICINE
BASIC STUDIES
99 MATHEMATICS
COMPUTERS
INFORMATION SCIENCE
MANAGEMENT
LAW
MISCELLANEOUS
POTENTIAL ENERGY
ENERGY LEVELS
PROTEIN STRUCTURE
CONFORMATIONAL CHANGES
THREE-DIMENSIONAL CALCULATIONS
FUNCTIONAL MODELS
PROTEINS
AMINO ACID SEQUENCE
ELECTRONIC STRUCTURE
STRUCTURE-ACTIVITY RELATIONSHIPS
ATOMS
INTERACTIONS
SOLVENTS
COMPUTER CODES
ALGORITHMS
MOLECULAR BIOLOGY
POLYPEPTIDES