Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model

Conference · Mon Dec 01 04:00:00 EST 1997

OSTI ID:548989

Agarwala, R ^[1]; Batzoglou, S ^[2]; Dancik, V ^[3]

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1. National Institutes of Health, Bethesda, MD (United States)
2. MIT Lab. for Computer Science, Cambridge, MA (United States)
3. Univ. of Southern California, Los Angeles, CA (United States); and others

A long standing problem in molecular biology is to determine the three-dimensional structure of a protein, given its amino acid sequence. A variety of simplifying models have been proposed abstracting only the {open_quotes}essential physical properties{close_quotes} of real proteins. In these models, the three dimensional space is often represented by a lattice. Residues which are adjacent in the primary sequence (i.e. covalently linked) must be placed at adjacent points in the lattice. A conformation of a protein is simply a self-avoiding walk along the lattice. The protein folding problem STRING-FOLD is that of finding a conformation of the protein sequence on the lattice such that the overall energy is minimized, for some reasonable definition of energy. This formulation leaves open the choices of a lattice and an energy function. Once these choices are made, one may then address the algorithmic complexity of optimizing the energy function for the lattice. For a variety of such simple models, this minimization problem is in fact NP-hard. In this paper, we consider the Hydrophobic-Polar (HP) Model introduced by Dill. The HP model abstracts the problem by grouping the 20 amino acids into two classes: hydrophobic (or non-polar) residues and hydrophilic (or polar) residues. For concreteness, we will take our input to be a string from (H,P){sup +}, where P represents polar residues, and H represents hydrophobic residues. Dill et.al. survey the literature analyzing this model. 8 refs., 2 figs., 1 tab.

• Research Organization: Association for Computing Machinery, New York, NY (United States); Sloan (Alfred P.) Foundation, New York, NY (United States)
• OSTI ID: 548989
• Report Number(s): CONF-970137--
• Country of Publication: United States
• Language: English

Related Subjects

55 BIOLOGY AND MEDICINE
BASIC STUDIES
99 GENERAL AND MISCELLANEOUS
ALGORITHMS
AMINO ACID SEQUENCE
COMPUTERIZED SIMULATION
COVALENCE
ELECTRONIC STRUCTURE
ENERGY LEVELS
MOLECULAR BIOLOGY
PHYSICAL PROPERTIES
POLAR COMPOUNDS
PROTEIN STRUCTURE
PROTEINS
S CODES
STRUCTURAL MODELS
STRUCTURE-ACTIVITY RELATIONSHIPS
THREE-DIMENSIONAL CALCULATIONS
TWO-DIMENSIONAL CALCULATIONS