Free energy and stability of macromolecules studied by the double scanning simulation procedure

Journal Article · Mon Jan 15 04:00:00 EST 1990 · Journal of Chemical Physics; (USA)

DOI:https://doi.org/10.1063/1.458134· OSTI ID:7023776

Meirovitch, H ^[1]; Vasquez, M; Scheraga, H A ^[2]

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1. Supercomputer Computations Research Institute, Florida State University, Tallahassee, Florida 32306-4052 (USA)
2. Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301 (USA)

The double scanning method (DSM) is a computer simulation technique suggested recently by Meirovitch (J. Chem. Phys. {bold 89}, 2514 (1988)). This method is a variant of the usual or single'' scanning method (SSM) of the same author, which was extended by us to polypeptides (Biopolymers {bold 27}, 1189 (1988); this paper is designated here as paper II). The two methods are step-by-step construction procedures from which the entropy and the free energy can be estimated. The transition probabilities are obtained by scanning the so-called future'' chains, which are continuations of the chain in future steps up to a maximum of {ital b} steps. With the SSM, the process is carried out by exact enumeration of the future chains; this is time consuming, and therefore {ital b} is limited to small values. With the DSM, on the other hand, only a relatively small sample of the future chains is generated by applying an additional scanning procedure. This enables one to increase {ital b} at the expense of approximating the transition probabilities. Increasing of {ital b}, however, is important in order to treat medium- and long-range interactions more properly. In this paper (as in our paper II), we apply the DSM to a model of decaglycine without solvent, described by the potential energy function ECEPP at 100 and 300 K. Using the SSM with the maximal value, {ital b}=4, we found in paper II that, at 100 K, the {alpha} helix rather than the statistical coil is the most stable state. The present DSM simulation at {ital T}=100 K (based on {ital b}=5) is more efficient than the SSM, and a structure with significantly lower energy than that of the {alpha} helix is found. It is argued that {ital b} can be increased further to 7 at this temperature. At 300 K the DSM, like the SSM, shows that the statistical coil is the most stable state of decaglycine. However, the DSM is found to be less efficient than the SSM.

• DOE Contract Number: FC05-85ER25000
• OSTI ID: 7023776
• Journal Information: Journal of Chemical Physics; (USA), Journal Name: Journal of Chemical Physics; (USA) Vol. 92:2; ISSN JCPSA; ISSN 0021-9606
• Country of Publication: United States
• Language: English

Related Subjects

640302* -- Atomic
Molecular & Chemical Physics-- Atomic & Molecular Properties & Theory
74 ATOMIC AND MOLECULAR PHYSICS
COMPUTERIZED SIMULATION
ENERGY
FREE ENERGY
MATHEMATICAL MODELS
MOLECULAR MODELS
MOLECULAR STRUCTURE
NUCLEIC ACIDS
ORGANIC COMPOUNDS
PEPTIDES
PHYSICAL PROPERTIES
POLYMERS
POLYPEPTIDES
PROTEINS
SIMULATION
STABILITY
THERMODYNAMIC PROPERTIES