Excluded-Volume Effect for Two- and Three-Dimensional Lattice Models

Domb, C.

doi:10.1063/1.1733626

Cited by 168 publications

(29 citation statements)

References 12 publications

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“…In a study of excluded volume effects for two- and three-dimensional lattices, Domb demonstrated that < r 2 > ~ n 6/5 for both cubic and tetrahedral lattices 12. Loop formation probabilities for the two lattices vary approximately as P ( n ) ~ n −3.3 (cubic) and P ( n ) ~ n −2.6 (tetrahedral) (see Appendix).…”

Section: Discussionmentioning

confidence: 99%

Synchronous vs Asynchronous Chain Motion in α-Synuclein Contact Dynamics

et al. 2008

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α-Synuclein (α-syn) is an intrinsically unstructured 140-residue neuronal protein of uncertain function that is implicated in the etiology of Parkinson’s disease. Tertiary contact formation rate constants in α-syn, determined from diffusion-limited electron-transfer kinetics measurements, are poorly approximated by simple random polymer theory. One source of the discrepancy between theory and experiment may be that interior-loop formation rates are not well approximated by end-to-end contact dynamics models. We have addressed this issue with Monte Carlo simulations to model asynchronous and synchronous motion of contacting sites in a random polymer. These simulations suggest that a dynamical drag effect may slow interior loop formations rates by about a factor of two in comparison to end-to-end loops of comparable size. The additional deviations from random coil behavior in α-syn likely arise from clustering of hydrophobic residues in the disordered polypeptide.

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Section: Discussionmentioning

confidence: 99%

Synchronous vs Asynchronous Chain Motion in α-Synuclein Contact Dynamics

et al. 2008

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“…x defined by (9) Equations (7)- (9) are considered valid only for macromolecules at the theta temperature. When long-range perturbations associated with the excluded volume are operative, the reduced moments m2p(n) increase with n even for large n and the limiting values as n---'>oo are far short of those given by Eq.…”

Section: Introductionmentioning

confidence: 99%

Rayleigh Scattering by Linear Flexible Macromolecules

Utiyama

Tsunashima

Kurata

1971

The Journal of Chemical Physics

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Precise light-scattering measurements were made on poly-a-methylstyrene samples with sharp molecular weight distribution, the molecular weight ranging from about 400 thousand to 7 million. The specific reduced scattered intensity at infinite dilution was determined for 18 scattering angles in the range of 9°-150°, in trans-decal in at 9.6° (theta temperature), 15.2, 29.4, 91.3°C, and in benzene at 30.0°C. In trans-decalin, the particle scattering factor P obtained is in good agreement with the well-known Debye equation irrespective of the temperature and the molecular weight. Experimental results in good solvent, benzene, are also well represented by the Debye equation for 1~P~O.15, but significant deviation is observed for PN(R)=CNRI exp[-(R/u)tJ, is used for polymer chains of N segments with excluded volume effects. CN is the normalizing constantj u is related to the standard deviation of Rj and 1=2/(1-.), where. is defined by (R2)=AN1+·. A is a numerical constant. The parameter I obtained by fitting the experimental data to the theory was found to increase with. and to be slightly greater than I.

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“…The first-depth algorithm of enumeration of lattice self-avoiding walks was suggested as early as 1947 by Orr (1947) and was used by Domb (1963) to investigate scaling properties of polymers with excluded volume. More recently, this method was further developed and applied to enumeration of compact twodimensional (Lau & Dill, 1989) and three-dimensional conformations of heteropolymers as models of protein globules (Shakhnovich & Cutin, 1990a, 1990b and for enumeration of lattice conformations of proteins within exactly given lattice…”

Section: Exhaustive Enumerationmentioning

confidence: 99%

Exhaustive enumeration of protein conformations using experimental restraints

1995

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We present an efficient new algorithm that enumerates all possible conformations of a protein that satisfy a given set of distance restraints. Rapid growth of all possible self-avoiding conformations on the diamond lattice provides construction of a-carbon representations of a protein fold. We investigated the dependence of the number of conformations on pairwise distance restraints for the proteins crambin, pancreatic trypsin inhibitor, and ubiquitin. Knowledge of between one and two contacts per monomer is shown to be sufficient to restrict the number of candidate structures to approximately 1 , OOO conformations. Pairwise RMS deviations of atomic position comparisons between pairs of these 1,000 structures revealed that these conformations can be grouped into about 25 families of structures. These results suggest a new approach to assessing alternative protein folds given a very limited number of distance restraints. Such restraints are available from several experimental techniques such as NMR, NOESY, energy transfer fluorescence spectroscopy, and crosslinking experiments. This work focuses on exhaustive enumeration of protein structures with emphasis on the possible use of NOESY-determined distance restraints.Keywords: lattice models of proteins; NMR restraints; protein folding; protein structure prediction Determining the solution structure of proteins from highresolution NMR data by restrained molecular dynamical simulated annealing (MDSA) uses distance information determined from NOE data (Briinger et al

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Excluded-Volume Effect for Two- and Three-Dimensional Lattice Models

Cited by 168 publications

References 12 publications

Synchronous vs Asynchronous Chain Motion in α-Synuclein Contact Dynamics

Synchronous vs Asynchronous Chain Motion in α-Synuclein Contact Dynamics

Rayleigh Scattering by Linear Flexible Macromolecules

Exhaustive enumeration of protein conformations using experimental restraints

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