%0 Journal Article %J Journal of Structural and Functional Genomics %D 2009 %T Distance matrix-based approach to protein structure prediction %A Andrzej Kloczkowski %A Robert L. Jernigan %A Zhijun Wu %A Guang Song %A Lei Yang %A Andrzej Koliński %A Piotr Pokarowski %K Binding Sites %K Computer Simulation %K Databases %K Models %K Molecular %K Principal Component Analysis %K Protein %K Protein Conformation %K Proteins %K Proteins: chemistry %X

Much structural information is encoded in the internal distances; a distance matrix-based approach can be used to predict protein structure and dynamics, and for structural refinement. Our approach is based on the square distance matrix D = [r(ij)(2)] containing all square distances between residues in proteins. This distance matrix contains more information than the contact matrix C, that has elements of either 0 or 1 depending on whether the distance r (ij) is greater or less than a cutoff value r (cutoff). We have performed spectral decomposition of the distance matrices D = sigma lambda(k)V(k)V(kT), in terms of eigenvalues lambda kappa and the corresponding eigenvectors v kappa and found that it contains at most five nonzero terms. A dominant eigenvector is proportional to r (2)–the square distance of points from the center of mass, with the next three being the principal components of the system of points. By predicting r (2) from the sequence we can approximate a distance matrix of a protein with an expected RMSD value of about 7.3 A, and by combining it with the prediction of the first principal component we can improve this approximation to 4.0 A. We can also explain the role of hydrophobic interactions for the protein structure, because r is highly correlated with the hydrophobic profile of the sequence. Moreover, r is highly correlated with several sequence profiles which are useful in protein structure prediction, such as contact number, the residue-wise contact order (RWCO) or mean square fluctuations (i.e. crystallographic temperature factors). We have also shown that the next three components are related to spatial directionality of the secondary structure elements, and they may be also predicted from the sequence, improving overall structure prediction. We have also shown that the large number of available HIV-1 protease structures provides a remarkable sampling of conformations, which can be viewed as direct structural information about the dynamics. After structure matching, we apply principal component analysis (PCA) to obtain the important apparent motions for both bound and unbound structures. There are significant similarities between the first few key motions and the first few low-frequency normal modes calculated from a static representative structure with an elastic network model (ENM) that is based on the contact matrix C (related to D), strongly suggesting that the variations among the observed structures and the corresponding conformational changes are facilitated by the low-frequency, global motions intrinsic to the structure. Similarities are also found when the approach is applied to an NMR ensemble, as well as to atomic molecular dynamics (MD) trajectories. Thus, a sufficiently large number of experimental structures can directly provide important information about protein dynamics, but ENM can also provide a similar sampling of conformations. Finally, we use distance constraints from databases of known protein structures for structure refinement. We use the distributions of distances of various types in known protein structures to obtain the most probable ranges or the mean-force potentials for the distances. We then impose these constraints on structures to be refined or include the mean-force potentials directly in the energy minimization so that more plausible structural models can be built. This approach has been successfully used by us in 2006 in the CASPR structure refinement (http://predictioncenter.org/caspR).

%B Journal of Structural and Functional Genomics %V 10 %P 67–81 %8 mar %G eng %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3018873&tool=pmcentrez&rendertype=abstract %R 10.1007/s10969-009-9062-2 %0 Journal Article %J Biophys J %D 2005 %T Folding of the protein domain hbSBD %A Maksim Kouza %A C. Chang %A S. Hayryan %A T. Yu %A Mai Suan Li %A T. Huang %A C. Hu %X The folding of the alpha-helix domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to evaluate various thermodynamic parameters defining the equilibrium unfolding, which is well described by the two-state model with the folding temperature T(F) = 317.8 +/- 1.95 K and the enthalpy change DeltaH(G) = 19.67 +/- 2.67 kcal/mol. The folding is also studied numerically using the off-lattice coarse-grained Go model and the Langevin dynamics. The obtained results, including the population of the native basin, the free-energy landscape as a function of the number of native contacts, and the folding kinetics, also suggest that the hbSBD domain is a two-state folder. These results are consistent with the biological function of hbSBD in branched-chain alpha-ketoacid dehydrogenase. %B Biophys J %V 89 %P 3353-61 %G eng %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2000 %T Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domain %A Keiko Yamamoto %A Hiroyuki Masuno %A Mihwa Choi %A Kinichi Nakashima %A Tetsuya Taga %A Hiroshi Ooizumi %A Kazuhiko Umesono %A Wanda Sicinska %A Janeen VanHooke %A Hector F. DeLuca %A Sachiko Yamada %X The ligand binding domain of the human vitamin D receptor (VDR) was modeled based on the crystal structure of the retinoic acid receptor. The ligand binding pocket of our VDR model is spacious at the helix 11 site and confined at the β-turn site. The ligand 1α,25-dihydroxyvitamin D3 was assumed to be anchored in the ligand binding pocket with its side chain heading to helix 11 (site 2) and the A-ring toward the β-turn (site 1). Three residues forming hydrogen bonds with the functionally important 1α- and 25-hydroxyl groups of 1α,25-dihydroxyvitamin D3 were identified and confirmed by mutational analysis: the 1α-hydroxyl group is forming pincer-type hydrogen bonds with S237 and R274 and the 25-hydroxyl group is interacting with H397. Docking potential for various ligands to the VDR model was examined, and the results are in good agreement with our previous three-dimensional structure-function theory. %B Proceedings of the National Academy of Sciences %V 97 %P 1467-1472 %G eng %U http://www.pnas.org/content/97/4/1467.abstract %R 10.1073/pnas.020522697 %0 Journal Article %J Polymer Preprints %D 1989 %T Dynamic Monte Carlo Simulation of a melt of ring polymers %A Jeffrey Skolnick %A Andrzej Koliński %A Andrzej Sikorski %A Robert Yaris %B Polymer Preprints %V 30 %P 70–73 %G eng %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 1989 %T Dynamic Monte Carlo study of the folding of a six-stranded Greek key globular protein %A Jeffrey Skolnick %A Andrzej Koliński %A Robert Yaris %K all-or-none transition %K multiple domain protein %K plastocyanin model %X To help elucidate the general rules of equilibrium globular protein folding, dynamic Monte Carlo simulations of a model beta-barrel globular protein having the six-stranded Greek key motif characteristic of real globular proteins were undertaken. The model protein possesses a typical beta-barrel amino acid sequence; however, all residues of a given type (e.g. hydrophobic residues) are identical. Even in the absence of site-specific interactions, starting from a high-temperature denatured state, these models undergo an all-or-none transition to a structurally unique six-stranded beta-barrel. These simulations suggest that the general rules of globular protein folding are rather robust in that the overall tertiary structure is determined by the general pattern of hydrophobic, hydrophilic, and turn-type residues, with site-specific interactions mainly involved in structural fine tuning of a given topology. Finally, these studies suggest that loops may play an important role in producing a unique native state. Depending on the stability of the native conformation of the long loop in the Greek key, the conformational transition can be described by a two-state, three-state, or even larger number of multiple equilibrium states model. %B Proceedings of the National Academy of Sciences of the United States of America %V 86 %P 1229–1233 %G eng %U http://www.pnas.org/content/86/4/1229.long %0 Journal Article %J Biopolymers %D 1989 %T Monte Carlo studies on equilibrium globular protein folding. II. Beta-barrel globular protein models %A Jeffrey Skolnick %A Andrzej Koliński %A Robert Yaris %K Algorithms %K Models %K Monte Carlo Method %K Protein Conformation %K Proteins %K Theoretical %X In the context of dynamic Monte Carlo simulations on a model protein confined to a tetrahedral lattice, the interplay of protein size and tertiary structure, and the requirements for an all-or-none transition to a unique native state, are investigated. Small model proteins having a primary sequence consisting of a central bend neutral region flanked by two tails having an alternating hydrophobic/hydrophilic pattern of residues are seen to undergo a continuous transition to a beta-hairpin collapsed state. On increasing the length of the tails, the beta-hairpin structural motif is found to be in equilibrium with a four-member beta-barrel. Further increase of the tail length results in the shift of the structural equilibrium to the four-member beta-barrel. The random coil to beta-barrel transition is of an all-or-none character, but while the central turn is always the desired native bend, the location of the turns involving the two external strands is variable. That is, beta-barrels having the external stands that are two residues out of register are also observed in the transition region. Introduction into the primary sequence of two additional regions that are at the very least neutral toward turn formation produces an all-or-none transition to the unique, native, four-member beta-barrel. Various factors that can augment the stability of the native conformation are explored. Overall, these folding simulations strongly indicate that the general rules of globular protein folding are rather robust–namely, one requires a general pattern of hydrophobic/hydrophilic residues that allow the protein to have a well-defined interior and exterior and the presence of regions in the amino acid sequence that at the very least are locally indifferent to turn formation. Since no site-specific interactions between hydrophobic and hydrophilic residues are required to produce a unique four-member beta-barrel, these simulations strongly suggest that site specificity is involved in structural fine-tuning. %B Biopolymers %V 28 %P 1059–95 %8 jun %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/2730942 %R 10.1002/bip.360280604 %0 Journal Article %J International Journal of Modern Physics B %D 1989 %T Phenomenological Theory of Polymer Melt Dynamics %A Jeffrey Skolnick %A Robert Yaris %A Andrzej Koliński %X A particularly interesting problem in polymer physics is the mechanism by which an individual polymer chain moves in a polymer melt or concentrated polymer solution. The first rather successful model of polymer dynamics was the reptation model of de Gennes which asserts that due to the effect of entanglements a polymer finds itself confined to a tube. Thus, the dominant long wavelength motion of the chain should be slithering out the ends of the tube. In order to examine the validity of the reptation model, a series of dynamic Monte Carlo simulations were performed. Although the simulations are on chains sufficiently long that agreement with the experimentally observed scaling with degree of polymerization n of the self diffusion constant and terminal relaxation time is observed, reptation does not appear to be the dominant mechanism of long distance motion. Rather the motion is isotropic, with the slowdown from dilute solution behavior arising from the formation of dynamic entanglements — rare long lived contacts where a given chain drags another chain through the melt for times on the order of longest internal relaxation time. Motivated by the simulations results, a phenomenological theory for the diffusive and viscoelastic behavior is developed that is consistent with both simulations and experiment and which does not invoke reptation. The major conclusions arising from the theoretical approach are described, and comparison is made with experiment. %B International Journal of Modern Physics B %V 3 %P 33-64 %G eng %N 01 %R 10.1142/S0217979289000038 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 1988 %T Monte Carlo simulations of the folding of beta-barrel globular proteins %A Jeffrey Skolnick %A Andrzej Koliński %A Robert Yaris %X With the use of dynamic Monte Carlo simulations, the necessary conditions for the collapse from a random-coil denatured state to a structurally unique four-member beta-barrel native state of a model globular protein have been investigated. These systems are free to roam through all of configuration space--both native and nonnative interactions are allowed. The relative importance of hydrophobic and hydrophilic interactions and the presence or absence of statistical bend-forming regions for the formation of a unique native state are examined, and the conditions necessary for a denatured-to-native (and vice versa) conformational transition that is thermodynamically all-or-none and which always results in collapse to the same, four-member beta-barrel are explored. These conditions are found to be a general pattern of hydrophobic/hydrophilic residues that allows the native state to differentiate the interior from the exterior of the protein and the presence of regions that are, at the very least, neutral toward turn formation. The former set of interactions seems to define the mean length of the beta-stretch, and the latter set serves to lock the native state into the lowest free energy state, the native conformation. These folding simulations strongly suggest that the general rules of protein folding are rather robust and that site-specific tertiary interactions are only involved in structural fine tuning. The conditions required for the formation of a structurally unique native state from a manifold of collapsed conformations that are originally quite close in energy is highly suggestive of a mechanism of protein evolution by means of random mutations. The implications of these folding studies for such a mechanism are qualitatively explored. %B Proceedings of the National Academy of Sciences of the United States of America %V 85 %P 5057–5061 %G eng %U http://www.pnas.org/content/85/14/5057.short %0 Journal Article %J The Journal of Chemical Physics %D 1988 %T Phenomenological theory of the dynamics of polymer melts. I. Analytic treatment of self-diffusion %A Jeffrey Skolnick %A Robert Yaris %A Andrzej Koliński %X 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[superscript −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[superscript −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. Finally, comparison is made between the theoretical expressions and MC results for mono- and bidisperse melts %B The Journal of Chemical Physics %V 3 %P 33–64 %G eng %U http://link.aip.org/link/JCPSA6/v88/i2/p1407/s1 %R 10.1063/1.454212 %0 Journal Article %J The Journal of Chemical Physics %D 1987 %T Does reptation describe the dynamics of entangled, finite length polymer systems? A model simulation %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %K Chains %K Computerized Simulation %K dynamics %K Monte Carlo Method %K Polymers %X In order to examine the validity of the reptation model of motion in a dense collection of polymers, dynamic Monte Carlo (MC) simulations of polymer chains composed of n beads confined to a diamond lattice were undertaken as a function of polymer concentration ϕ and degree of polymerization n. We demonstrate that over a wide density range these systems exhibit the experimentally required molecular weight dependence of the center‐of‐mass self‐diffusion coefficient D∼n−2.1 and the terminal relaxation time of the end‐to‐end vector τR∼n3.4. Thus, these systems should represent a highly entangled collection of polymers appropriate to look for the existence of reptation. The time dependence of the average single bead mean‐square displacement, as well as the dependence of the single bead displacement on position in the chain were examined, along with the time dependence of the center‐of‐mass displacement. Furthermore, to determine where in fact a well‐defined tube exists, the mean‐square displacements of a polymer chain down and perpendicular to its primitive path defined at zero time were calculated, and snapshots of the primitive path as a function of time are presented. For an environment where all the chains move, no evidence of a tube, whose existence is central to the validity of the reptation model, was found. However, if a single chain is allowed to move in a partially frozen matrix of chains (where all chains but one are pinned every ne beads, and where between pin points the other chains are free to move), reptation with tube leakage is recovered for the single mobile chain. The dynamics of these chains possesses aspects of Rouse‐like motion; however, unlike a Rouse chain, these chains undergo highly cooperative motion that appears to involve a backflow between chains to conserve constant average density. While these simulations cannot preclude the onset of reptation at higher molecular weight, they strongly argue at a minimum for the existence with increasing n of a crossover regime from simple Rouse dynamics in which reptation plays a minor role at best. %B The Journal of Chemical Physics %V 86 %P 1567–1585 %G eng %U http://link.aip.org/link/JCPSA6/v86/i3/p1567/s1 %R 10.1063/1.452196 %0 Journal Article %J Macromolecules %D 1987 %T Dynamic Monte Carlo study of the conformational properties of long flexible polymers %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %B Macromolecules %V 20 %P 687–689 %G eng %U http://pubs.acs.org/doi/abs/10.1021/ma00168a039 %R 10.1021/ma00168a039 %0 Journal Article %J Accounts of Chemical Research %D 1987 %T Monte Carlo studies of the long-time dynamics of dense polymer systems. The failure of the reptation model %A Jeffrey Skolnick %A Andrzej Koliński %A Robert Yaris %B Accounts of Chemical Research %V 20 %P 350–356 %8 sep %G eng %U http://pubs.acs.org/doi/abs/10.1021/ar00141a006 %R 10.1021/ar00141a006 %0 Journal Article %J Biopolymers %D 1987 %T Monte Carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of beta-barrel proteins %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %K Biological %K Models %K Monte Carlo Method %K Protein Conformation %K Proteins %X Dynamic Monte Carlo studies have been performed on various diamond lattice models of β-proteins. Unlike previous work, no bias toward the native state is introduced; instead, the protein is allowed to freely hunt through all of phase space to find the equilibrium conformation. Thus, these systems may aid in the elucidation of the rules governing protein folding from a given primary sequence; in particular, the interplay of short- vs long-range interaction can be explored. Three distinct models (A[BOND]C) were examined. In model A, in addition to the preference for trans (t) over gauche states (g+ and g−) (thereby perhaps favoring β-sheet formation), attractive interactions are allowed between all nonbonded, nearest neighbor pairs of segments. If the molecules possess a relatively large fraction of t states in the denatured form, on cooling spontaneous collapse to a well-defined β-barrel is observed. Unfortunately, in model A the denatured state exhibits too much secondary structure to correctly model the globular protein collapse transition. Thus in models B and C, the local stiffness is reduced. In model B, in the absence of long-range interactions, t and g states are equally weighted, and cooperativity is introduced by favoring formation of adjacent pairs of nonbonded (but not necessarily parallel) t states. While the denatured state of these systems behaves like a random coil, their native globular structure is poorly defined. Model C retains the cooperativity of model B but allows for a slight preference of t over g states in the short-range interactions. Here, the denatured state is indistinguishable from a random coil, and the globular state is a well-defined β-barrel. Over a range of chain lengths, the collapse is well represented by an all-or-none model. Hence, model C possesses the essential qualitative features observed in real globular proteins. These studies strongly suggest that the uniqueness of the globular conformation requires some residual secondary structure to be present in the denatured state. %B Biopolymers %V 26 %P 937–62 %8 jun %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/3607251 %R 10.1002/bip.360260613 %0 Journal Article %J The Journal of Chemical Physics %D 1987 %T 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 %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %K Chains %K Computerized Simulation %K dynamics %K Liquid Structure %K Matrix Isolation %K Melts %K Monte Carlo Method %K Polymerization %K Polymers %X 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. %B The Journal of Chemical Physics %V 86 %P 7174–7180 %G eng %U http://link.aip.org/link/JCPSA6/v86/i12/p7174/s1 %R 10.1063/1.452367 %0 Journal Article %J The Journal of Chemical Physics %D 1987 %T Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. I. The homopolymeric melt %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %K Chains %K Computerized Simulation %K dynamics %K Liquid Structure %K Melts %K Monte Carlo Method %K Polymers %X Dynamic Monte Carlo simulations of long chains confined to a cubic lattice system at a polymer volume fraction of ϕ=0.5 were employed to investigate the dynamics of polymer melts. It is shown that in the range of chain lengths n, from n=64 to n=800 there is a crossover from a weaker dependence of the diffusion coefficient on chain length to a much stronger one, consistent with D∼n−2. Since the n−2 scaling relation signals the onset of highly constrained dynamics, an analysis of the character of the chain contour motion was performed. We found no evidence for the well‐defined tube required by the reptation model of polymer melt dynamics. The lateral motions of the chain contour are still large even in the case when n=800, and the motion of the chain is essentially isotropic in the local coordinates. Hence, the crossover to the D∼n−2 regime with increasing chain length of this monodisperse model melt is not accompanied by the onset of reptation dynamics. %B The Journal of Chemical Physics %V 86 %P 7164–7174 %G eng %U http://link.aip.org/link/JCPSA6/v86/i12/p7164/s1 %0 Journal Article %J The Journal of Chemical Physics %D 1986 %T The collapse transition of semiflexible polymers. A Monte Carlo simulation of a model system %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %K Chains %K Computerized Simulation %K Conformational Changes %K Diamond Lattices %K Flexibility %K Mathematical Models %K Molecular Structure %K Monte Carlo Method %K Polymers %X 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. %B The Journal of Chemical Physics %V 85 %P 3585–3597 %G eng %U http://link.aip.org/link/JCPSA6/v85/i6/p3585/s1 %R 10.1063/1.450930 %0 Conference Proceedings %B AIP Conference Proceedings %D 1986 %T Monte Carlo dynamics of diamond-lattice multichain systems %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %B AIP Conference Proceedings %V 137 %P 241–245 %G eng %U http://smartech.gatech.edu/handle/1853/27919 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 1986 %T Monte Carlo simulations on an equilibrium globular protein folding model %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %K Models %K Protein Conformation %K Statistics as Topic %K Structural %K Structure-Activity Relationship %K Temperature %K Thermodynamics %X

Monte Carlo simulations were performed on a diamond lattice, globular protein model in which the trans conformational state is energetically favored over the gauche states (thereby perhaps favoring a beta-sheet secondary structure) and in which nonspecific nonbonded nearest-neighbor attractive interactions are allowed. If the attractive interactions are sufficiently weak that the molecule possesses a relatively high fraction of trans states in the denatured state, then on collapse, a beta-barrel tertiary structure, highly reminiscent of the "native" structure seen in beta-proteins, spontaneously forms. If, however, the attractive interactions are dominant, a coil-to-random globule collapse transition is observed. The roles of short-, medium-, and long-range interactions and topological constraints in determining the observed tertiary structure are addressed, and the implications and limitations of the simulations for the equilibrium folding process in renal globular proteins are explored.

%B Proceedings of the National Academy of Sciences of the United States of America %V 83 %P 7267–71 %8 oct %G eng %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=386697&tool=pmcentrez&rendertype=abstract %0 Journal Article %J Macromolecules %D 1986 %T Monte Carlo study of local orientational order in a semiflexible polymer melt model %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %B Macromolecules %V 19 %P 2550–2560 %G eng %U http://pubs.acs.org/doi/abs/10.1021/ma00164a017 %R 10.1021/ma00164a017 %0 Journal Article %J Macromolecules %D 1986 %T Order-Disorder Transitions in Tetrahedral Lattice Polymer Systems %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %B Macromolecules %V 19 %P 2560–2567 %G eng %R 10.1021/ma00164a018 %0 Journal Article %J The Journal of chemical physics %D 1986 %T On the short time dynamics of dense polymeric systems and the origin of the glass transition: A model system %A Andrzej Koliński %A Jeffrey Skolnick %A Robert Yaris %B The Journal of chemical physics %V 84 %P 1922–1931 %G eng %U http://link.aip.org/link/JCPSA6/v84/i3/p1922/s1 %R 10.1021/ma00164a018