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  • 1
    Electronic Resource
    Electronic Resource
    Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 2608-2617 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Employing a high coordination lattice model and conformational sampling based on dynamic and entropy sampling Monte Carlo protocols, computer experiments were performed on three small globular proteins, each representing one of the three secondary structure classes. The goal was to explore the thermodynamic character of the conformational transition and possible mechanisms of topology assembly. Depending on the stability of isolated elements of secondary structure, topology assembly can proceed by various mechanisms. For the three-helix bundle, protein A, which exhibits substantial helix content in the denatured state, a diffusion–collision mechanism of topology assembly dominates, and here, the conformational transition is predicted to be continuous. In contrast, a model β protein, which possesses little intrinsic denatured state secondary structure, exhibits a sequential "on-site" assembly mechanism and a conformational transition that is well described by a two-state model. Augmenting the cooperativity of tertiary interactions led to a slight shift toward the diffusion–collision model of assembly. Finally, simulations of the folding of the α/β protein G, while only partially successful, suggest that the C-terminal β hairpin should be an early folding conformation and that the N-terminal β hairpin is considerably less stable in isolation. Implications of these results for our general understanding of the process of protein folding and their utility for de novo structure prediction are briefly discussed. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.475646
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  • 2
    Electronic Resource
    Electronic Resource
    Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactions (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 107 (1997), S. 953-964 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The effect of tertiary interactions on the observed secondary structure found in the native conformation of globular proteins was examined in the context of a reduced protein model. Short-range interactions are controlled by knowledge based statistical potentials that reflect local conformational regularities seen in a database of three-dimensional protein structures. Long-range interactions are approximated by mean field, single residue based, centrosymmetric hydrophobic burial potentials. Even when pairwise specific long-range interactions are ignored, the inclusion of such burial preferences noticeably modifies the equilibrium chain conformations, and the observed secondary structure is closer to that seen in the folded state. For a test set of 10 proteins (belonging to various structural classes), the accuracy of secondary structure prediction is about 66% and increases by 9% with respect to a related model based on short-range interactions alone [Kolinski et al., J. Chem. Phys. 103, 4312 (1995)]. The increased accuracy is due to the interplay between the short-range conformational propensities and the burial and compactness requirements built into the present model. While the absolute level of accuracy assessed on a per residue basis is comparable to more standard techniques, in contrast to these approaches, the conformation of the chain now has a better defined geometric context. For example, the assumed spherical domain protein model that simulates the segregation of residues between the hydrophobic core and the hydrophilic surface allows for the prediction of surface loops/turns where the polypeptide chain changes its direction. The implications of having such self-consistent secondary structure predictions for the prediction of protein tertiary structure are briefly discussed. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.474448
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  • 3
    Electronic Resource
    Electronic Resource
    Computer design of idealized β-motifs (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 10286-10297 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A lattice model of protein conformation and dynamics is used to explore the requirements for the de novo folding from an arbitrary random coil state of idealized models of four and six-member β-barrels. A number of possible conjectures for the factors giving rise to the structural uniqueness of globular proteins are examined. These include the relative role of generic hydrophilic/ hydrophobic amino acid patterns, the relative importance of the specific identity of the hydrophobic amino acids that form the core of the protein and the possible role played by polar groups in destabilizing alternative, misfolded conformations. These studies may also provide some insights into the relative importance of short range interactions, cooperative hydrogen bonding and tertiary interactions in determining the uniqueness of the native state, as well as the cooperativity of the folding process. Thus, these simulations may provide guidelines for the early stages of the protein design process. Possible applications to the general protein folding problem are also briefly discussed. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469930
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  • 4
    Electronic Resource
    Electronic Resource
    Dynamic Monte Carlo study of the conformational properties of long flexible polymers (1987)
    s.l. : American Chemical Society
    Macromolecules 20 (1987), S. 438-440 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma00168a039
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  • 5
    Electronic Resource
    Electronic Resource
    Monte Carlo study of local orientational order in a semiflexible polymer melt model (1986)
    s.l. : American Chemical Society
    Macromolecules 19 (1986), S. 2550-2560 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma00164a017
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  • 6
    Electronic Resource
    Electronic Resource
    Order-disorder transitions in tetrahedral lattice polymer systems (1986)
    s.l. : American Chemical Society
    Macromolecules 19 (1986), S. 2560-2567 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma00164a018
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  • 7
    Electronic Resource
    Electronic Resource
    Phenomenological theory of the dynamics of polymer melts. I. Analytic treatment of self-diffusion (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 88 (1988), S. 1407-1417 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In the context of dynamic Monte Carlo (MC) simulations on dense collections of polymer chains confined to a cubic lattice, the nature of the dynamic entanglements giving rise to the degree of polymerization n, dependence of the self-diffusion constant D∼n−2 is examined. Consistent with our previous simulation results, which failed to find evidence for reptation as the dominant mechanism of polymer melt motion [J. Chem. Phys. 86, 1567, 7164, 7174 (1987)], long-lived dynamic entanglement contacts between pairs of segments belonging to different chains are extremely rare and are mobile with respect to the laboratory fixed frame. It is suggested that dynamic entanglements involve the dragging of one chain by another through the melt for times on the order of the terminal relaxation time of the end-to-end vector. Employing the physical description provided by the MC simulation, the general expression of Hess [Macromolecules 19, 1395 (1986)] for the friction constant increment experienced by a polymer due to the other polymers forms the basis of a phenomenological derivation of D∼n−2 for monodisperse melts that does not require the existence of reptation. Rather, such behavior is dependent on the relatively benign assumptions that the long distance global motions of the chains are uncorrelated, that the dynamic contacts can be truncated at the pair level, and that the propagator describing the evolution between dynamic contacts contains a free Rouse chain component. The mean distance between dynamic entanglements is predicted to depend inversely on concentration, in agreement with experiment. Moreover, as the free Rouse component is frozen out, for chains greater than an entanglement length ne, a molecular weight independent glass transition is predicted. Extension to bidisperse melts predicts that the probe diffusion coefficient Dp depends on the matrix degree of polymerization, nm, as n−1m. Finally, comparison is made between the theoretical expressions and MC results for mono- and bidisperse melts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.454212
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  • 8
    Electronic Resource
    Electronic Resource
    The collapse transition of semiflexible polymers. A Monte Carlo simulation of a model system (1986)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 85 (1986), S. 3585-3597 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Monte Carlo simulations have been performed on a diamond lattice model of semiflexible polymers for a range of flexibilities and a range of chain lengths from 50 to 800 segments. The model includes both repulsive (excluded volume) and attractive segment–segment interactions. It is shown that the polymers group into two classes, "flexible'' and "stiff.'' The flexible polymers exhibit decreasing chain dimensions as the temperature decreases with a gradual collapse from a loose random coil, high temperature state to a dense random coil, low temperature state. The stiffer polymers, on the other hand, exhibit increasing chain dimensions with decreasing temperature until at a critical temperature there is a sudden collapse to an ordered high density, low temperature state. This difference is due to the relative strength of the segment–segment attractive interactions compared to the energetic preference for a trans conformational state over a gauche state. When the attractive interaction is relatively strong (flexible case) the polymer starts to collapse before rotational degrees of freedom freeze out, leading to a disordered dense state. When the attractive interaction is relatively weak (stiff case) the polymer starts to freeze out rotational degrees of freedom before it finally collapses to a highly ordered dense state.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.450930
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  • 9
    Electronic Resource
    Electronic Resource
    On the short time dynamics of dense polymeric systems and the origin of the glass transition: A model system (1986)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 84 (1986), S. 1922-1931 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In order to model the short time (and distance) scale motions for dense polymeric systems, we have performed dynamic Monte Carlo simulations of chains on a diamond lattice at considerably greater densities than those done previously. Chain dynamics were simulated by a random sequence of three- and four-bond kink motions and end moves. For times shorter than the chain diffusion time, the single bead autocorrelation function g(t) exhibits three distinct regimes: a short time Rouse-like regime where g(t)∼t1/2; a mid-region where g(t)∼t β, followed by a longer time, Rouse-like regime where g(t)∼t1/2. There is a smooth crossover from Rouse-like dynamics, β=1/2, at low density to smaller values of β at higher density, and β=0 at the glass transition density (φG =0.92±0.01). It is shown that the major motion of the chains is transverse to the chain contour rather than along the chain. The observed motion is successfully analyzed in terms of the motion of defects (holes) through the sample. It is shown that the glass transition at φG =0.92 is caused by the shutting down of the orientation changing four-bond motions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.450442
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  • 10
    Electronic Resource
    Electronic Resource
    Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. II. Probe polymer in a matrix of different degrees of polymerization (1987)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 86 (1987), S. 7174-7180 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dynamics of a probe chain consisting of nP =100 segments in a matrix of chains of length of nM=50 up to nM=800 at a total volume fraction of polymer φ=0.5 have been simulated by means of cubic lattice Monte Carlo dynamics. The diffusion coefficient of the probe chain over the range of nM under consideration decreases by about 30%, a behavior rather similar to that seen in real melts of very long chains. Furthermore, the analysis of the probe chain motion shows that the mechanism of motion is not reptation-like and that the cage effect of the matrix is negligible. That is, the local fluctuations of the topological constraints imposed by the long matrix chains (even for nM=800) are sufficiently large to provide for essentially isotropic, but somewhat slowed down, motion of the probe, nP =100, chains relative to the homopolymer melt. The results of these MC experiments are discussed in the context of theoretical predictions and experimental findings for related systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.452367
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