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J Skolnick

Publications and source records attributed to J Skolnick.

101 records · Page 6Linked to original sources
PubMed1989

Computer simulations of globular protein folding and tertiary structure.

In summary, although a large number of disparate techniques have been applied to predict the tertiary structure of globular proteins from their amino acid sequence, the solution is not yet at hand. Methodologies for predicting the conformation of constrained, small protein fragments appear to be successful. As the size of the system increases, the level of detail of the treatment decreases; approaches that employ very detailed potentials appear to be limited to about 30-40 residues. Although this is a major advance, methods that reduce the effective number of degrees of freedom are clearly required. Lattice representations coupled to highly efficient Monte Carlo procedures appear to be one such approach. Thus, although a number of theoretical advances in the computer simulation of globular protein structure have been made, much work remains to be done before the globular protein folding problem is solved.

Computer Simulation↗
PubMed1988

Monte Carlo simulations of the folding of beta-barrel globular proteins.

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.

Chemical Phenomena↗
PubMed1987

Possible role of helix-coil transitions in the microscopic mechanism of muscle contraction.

Local helix-coil transitions in the coiled coil portion of myosin have long been implicated as a possible origin of tension generation in muscle. From a statistical mechanical theory of conformational transitions in coiled coils, the free energy required to form a randomly coiled bubble in the hinge region of myosin of the type conjectured by Harrington (Harrington, W. F., 1979, Proc. Natl. Acad. Sci. USA, 76:5066-5070) is estimated to be approximately 25 kcal/mol. Unfortunately this is far more than the free energy available from ATP hydrolysis if the crossbridges operate independently. Thus, in solution such bubbles are predicted to be absent, and the theory requires that the rod portion of myosin be a hingeless, continuously deforming rod. While such bubble formation in vivo cannot be entirely ruled out, it appears to be unlikely. We further conjecture that in solution the swivel located between myosin subfragments 1 and 2 (S-2 and S-1) is due to a locally random conformation of the chains caused by the presence of a proline residue at the point that physically separates the coiled coil from the globular portion of myosin. On attachment of S-1 to actin in the strong binding state, the configurational entropy of the random coil in the swivel region is greatly reduced relative to the case where the ends are free. This produces a spontaneous coil-to-helix transition in the swivel region that causes rotation of S-1 and the translation of actin. Thus, the model predicts that the actin filaments are pushed rather than pulled past the thick filaments by the crossbridges. The specific mechanism of force generation is examined in detail, and a simple statistical mechanical realization of the model is proposed. We find that the model gives a substantial number of qualitative and at times quantitative predictions in accord with experiment, and is particularly appealing in that it provides a simple means of free energy transduction--the well known fact that topological constraints shift the equilibrium between helical and random coil states.

Actins↗
PubMed1986

A theoretical model simulating the anomalous concentration dependence of the equilibrium thermal unfolding curve of noncrosslinked tropomyosin.

Thermal unfolding curves of tropomyosin have so far been fit only semi-quantitatively by the statistical-mechanical theory of the helix-coil transition. The calculated values of helix content are a bit too small for the most dilute solutions and a bit too large for the most concentrated ones. The theory, as hitherto used, assumes a uniform helix-helix interaction, whereas evidence from studies on molecular segments suggests otherwise. A theoretical model incorporating such non-uniformity in helix-helix interaction is used to produce simulated thermal unfolding curves. These simulated curves, when fit to the theory using the assumption of uniformity, reveal precisely the same discrepancies seen with the experimental data. We conclude that non-uniformity in helix-helix interaction along the tropomyosin molecule is responsible for the small discrepancy between experimental data and the uniform-model theory previously employed.

Models, Theoretical↗
PubMed1986

Alpha-helix-to-random-coil transitions of two-chain, coiled coils: a theoretical model for the "pretransition" in cysteine-190-cross-linked tropomyosin.

The thermal unfolding curve for alpha alpha tropomyosin in which the two chains are cross-linked at cysteine-190 shows two striking features that distinguish it from that of its counterpart for non-cross-linked molecules: a "pretransition" at 25-50 degrees C and a shift in the principal transition to higher temperature, but with the same steepness. Previously, the pretransition was explained by postulating that the cross-link produces local strains, yielding a pinched "bubble" of chain-separated random coil about C-190, whereas the rest of the coiled coil remains intact. Results from both enzymatic digestion kinetics and equilibrium calorimetric studies have been interpreted as consistent with the existence of such a bubble. To test this idea further, a theoretical model is devised whereby various physical features can be imposed and the resulting helix content and other properties calculated from the statistical mechanical theory of the helix-coil transition. Short-range interactions employed are the geometric mean values of those in alpha-tropomyosin. The helix-helix interaction free energy is also like that in alpha-tropomyosin, including its nonuniformity; i.e., it is made larger in the amino half of the molecule. Local strain is introduced by setting the helix-helix interaction to zero in a region about the cross-link. The results show that, alone, neither local strain nor nonuniformity serves to mimic the experiments. In concert, however, they reproduce all the main experimental features, if the strain is extensive (approximately 29 residues) and somewhat dissymmetric. Theoretical helix probability profiles, however, show that no bubble of unfolded chains forms about the cross-link. Instead, in the pretransition, residues unfold from the weakly interacting end (residue 284) in to, but not through, the cross-link at C-190. The theory also indicates that the augmented stability for the principal transition occurs largely as a result of loop entropy. The same strain and nonuniformity are then employed to explore the effects of other possible cross-link positions. The thermal curves are shown to depend markedly on cross-link location. The curves are discussed in terms of loop entropy, which has drastic, long-range effects. Under appropriate circumstances it can produce, in the coiled-coil model, a thermal transition that is essentially all or none.

Cysteine↗
PubMed1986

Monte Carlo simulations on an equilibrium globular protein folding model.

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.

Models, Structural↗
PubMed1985

Role of topological constraints in the all-or-none transition of a globular protein model: theory of the helix-coil transition in doubly crosslinked, coiled coils.

Employing a recently developed statistical mechanical theory, the alpha-helix-to-random-coil transition in two-chain, coiled coils is shown to possess many of the essential qualitative features of the equilibrium folding process in globular proteins. The role of short vs. long range interactions in stabilizing the native structure is examined. We demonstrate in doubly crosslinked coiled coils how, due to the role of loop entropy, an intrinsically continuous conformational transition evolves into one well approximated by an all-or-none transition. Thus the present work points out the crucial role played by loop entropy in the conformational transition in coiled coils in particular and perhaps in globular proteins in general.

Models, Chemical↗
PubMedDate not supplied

Enhanced functional annotation of protein sequences via the use of structural descriptors.

In order to circumvent limitations of sequence based methods in the process of making functional predictions for proteins, we have developed a methodology that uses a sequence-to-structure-to-function paradigm. First, an approximate three-dimensional structure is predicted. Then, a three-dimensional descriptor of the functional site, termed a Fuzzy Functional Form, or FFF, is used to screen the structure for the presence of the functional site of interest (Fetrow et al., 1998; Fetrow and Skolnick, 1998). Previously, a disulfide oxidoreductase FFF was developed and applied to predicted structures obtained from a small structural database. Here, using a substantially larger structural database, we expand the analysis of the disulfide oxidoreductase FFF to the B. subtilis genome. To ascertain the performance of the FFF, its results are compared to those obtained using both the sequence alignment method BLAST and three local sequence motif databases: PRINTS, Prosite, and Blocks. The FFF method is then compared in detail to Blocks and it is shown that the FFF is more flexible and sensitive in finding a specific function in a set of unknown proteins. In addition, the estimated false positive rate of function prediction is significantly lower using the FFF structural motif, rather than the standard sequence motif methods. We also present a second FFF and describe a specific example of the results of its whole-genome application to D. melanogaster using a newer threading algorithm. Our results from all of these studies indicate that the addition of three-dimensional structural information adds significant value in the prediction of biochemical function of genomic sequences.

Algorithms↗
PubMedDate not supplied

[When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible].

One still cannot predict the 3D fold of a protein from its amino acid sequence, mainly because of errors in the energy estimates underlying the prediction. However, a recently developed theory [1] shows that having a set of homologs (i.e., the chains with equal, in despite of numerous mutations, 3D folds) one can average the potential of each interaction over the homologs and thus predict the common 3D fold of protein family even when a correct fold prediction for an individual sequence is impossible because the energies are known only approximately. This theoretical conclusion has been verified by simulation of the energy spectra of simplified models of protein chains [2], and the further investigation of these simplified models shows that their true "native" fold can be found by folding of the chain where each interaction potential is averaged over the homologs. In conclusion, the applicability of the "homolog-averaging" approach is tested by recognition of real protein 3D structures. Both the gapless threading of sequences onto the known protein folds [3] and the more practically important gapped threading (which allows to consider not only the known 3D structures, but the more or less similar to them folds as well) shows a significant increase in selectivity of the native chain fold recognition.

Computer Simulation↗