Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133--7155.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....to reveal an understanding of the function and behavior of proteins, the building blocks of life. Such an understanding would greatly in uence many areas in biology and medicine such as drug design. One of the most popular models of protein folding is the hydrophilic hydrophobic (H P) model [2, 4, 6], which de nes both a geometry and a quality metric of foldings. This combinatorial model is attractive in its simplicity, and already seems to capture several essential features of protein folding such as the tendency for the hydrophobic components to fold to the center of a globular protein [2] ....

K. A. Dill. Dominant forces in protein folding. Biochemistry, 29(31):7133-7155, August 1990.

.... energy function allows us to separate the kinematics of folding (the Monte Carlo moves wriggling or thrashing) from the dynamics of folding (the mechanisms in the energy function conformational entropy, charge charge interactions, hydrogen bonds, van der Waals interactions, hydrophobicity [11, 12]) Because there is no simple relationship between the carbon rmsd and an energy, and because wriggling changes the e ective temperature, we conducted our simulations at absolute zero rather than at physiological temperatures or at that of liquid nitrogen. Each of our tests consisted of 8 or 10 ....

K. A. Dill, Dominant forces in protein folding, Biochemistry 29 (1990) 7133-7155.

....from the true native state. One possible approximation method, which can be applied to molecules that form a linear chain, represents the molecular structure as a string of beads where the position of each bead is defined by its location relative to the previous three beads in the sequence (see [4]) In this model, the chain monomers come in two forms, H (hydrophobic) and P (polar) where the H type monomers exhibit a strong pairwise attraction, and hence the lowest free energy is obtained by those conformations with the greatest number of HH contacts (see [4] 10] One significant ....

.... beads in the sequence (see [4] In this model, the chain monomers come in two forms, H (hydrophobic) and P (polar) where the H type monomers exhibit a strong pairwise attraction, and hence the lowest free energy is obtained by those conformations with the greatest number of HH contacts (see [4], 10] One significant advantage of this formulation of the folding problem is that it allows the model to take advantage of known scientific knowledge about the chemical structure of sequences of molecules. The use of knowledge such as the Ramachandran plot (see [7] which specifies the ....

K.A. Dill, Dominant Forces in Protein Folding, Biochemistry 29 (1990), 7133-7155.

.... energy function allows us to separate the kinematics of folding (the Monte Carlo moves wriggling or thrashing) from the dynamics of folding (the mechanisms in the energy function conformational entropy, charge charge interactions, hydrogen bonds, van der Waals interactions, hydrophobicity [11, 12]) Because there is no simple relationship between the # carbon rmsd and an energy, and because wriggling changes the e#ective temperature, we conducted our simulations at absolute zero rather than at physiological temperatures or at that of liquid nitrogen. Each of our tests consisted of 8 or 10 ....

K. A. Dill, Dominant forces in protein folding, Biochemistry 29 (1990) 7133--7155.

....conformational searches will never be tractable. Practical search strategies for the protein folding problem currently require a simplified, yet sufficiently realistic, molecular model with an associated potential energy function representing the dominant forces involved in protein folding [4]. In a one such simplified model, each residue in the primary sequence of a protein is characterized by its backbone components NH C ff H C 0 O and one of 20 possible amino acid sidechains attached to the central C ff atom. The threedimensional structure of the chain is determined by internal ....

.... backbone dihedral angle pairs (OE; Since the residues in this model come in only two forms, hydrophobic and polar, where the hydrophobic monomers exhibit a strong pairwise attraction, the lowest free energy state involves those conformations with the greatest number of hydrophobic contacts [4] and intrastrand hydrogen bonds. Simplified potential functions have been successful in studies by Sun, Thomas, and Dill [11] by Srinivasan and Rose [10] and by Yue and Dill [12] A simple modification of the Sun Thomas Dill energy function is used here. The convex global underestimator. One ....

Dill, K.A.: `Dominant forces in protein folding', Biochemistry 29 (1990), 7133--7155.

....and of the fact that our results are very preliminary. But we believe that the method can have some validity because a better understanding of the folding process itself, even in the limited case of very short sequences, can have useful results. For the present time we, as many others (e.g. Lau Dill, 1990; Unger Moult, 1993; Sali et al. 1994) have modelled the primary structure of proteins in an extremely simplified way. Amino acid side chains are represented as spheres connected to the corresponding C a of backbone with a link of fixed length (see Fig. 1) the backbone is represented as a ....

.... (i.e. the aversion for water of nonpolar residues) while Van der Waals interactions (i.e. interactions between dipoles) hydrogen bond interactions (i.e. sharing of an hydrogen atom between two electronegative atoms) and electrostatics interactions in general appear to play a secondary role (Dill, 1990). However, as Dill states very clearly, driving forces are only half of the story. Another fundamental component that determines the folding process appears to be a opposing forces, e.g. the impossibility that two chain segments simultaneously occupy the same volume of space. Because the folding ....

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Dill, K. A. (1990). Dominant Forces in Protein Folding. Biochemistry, 29, 7133-7155.

....On the other hand, it also makes interactions such as hydrogen bonds easier to define. The formation of native structure is, in this model, driven by hydrogen bond formation and effective hydrophobicity forces; hydrophobicity is widely held as the most important stability factor in proteins [9, 10], and hydrogen bonds are essential to properly model the formation of secondary structure. In this model, we study in particular a three helix bundle protein with 54 amino acids, which represents a truncated and simplified version of the four helix bundle protein de novo designed by Regan and ....

Dill, K.A. (1990) "Dominant Forces in Protein Folding", Biochemistry 29, 7133-- 7155.

....models. On the other hand, it also makes interactions such as hydrogen bonds easier to define. The formation of native structure is in this model driven by hydrogen bond formation and effective hydrophobicity forces; hydrophobicity is widely held as the most important stability factor in proteins [9, 10], and hydrogen bonds are essential in order to properly model the formation of secondary structure. In this model we in particular study a three helix bundle protein with 54 amino acids, which represents a truncated and simplified version of the four helix bundle protein de novo designed by Regan ....

Dill, K.A. (1990) "Dominant Forces in Protein Folding", Biochemistry 29, 7133-- 7155.

....interresidue interactions can serve as a tool for studying the thermodynamics and kinetics of protein models. Introduction The vast dimensionality of the protein conformational space [1] makes the folding time too long to be reachable by direct computational approaches [2 4] Simplified models [5 14] became popular due to their ability to reach reasonable time scales and to reproduce the basic thermodynamic and kinetic properties of real proteins [3,15,16] firstly, a unique native state, that is, there should exist a single conformation with the lowest potential energy; secondly, a ....

Dill, K.A. (1990). Dominant forces in protein folding. Biochemistry 29, 7133-7155.

....This problem has been investigated under a wide variety of models, each of which attempts to emphasize different aspects of the problem. Perhaps the simplest, and combinatorially most appealing of the widely studied models is the socalled hydrophobic hydrophilic model, or HP model of Dill [5, 6]. Here a protein is represented as a string over the two letter alphabet fH; Pg, with the symbol H representing hydrophobic monomers and P hydrophilic (or polar) monomers. Conformations of the protein correspond to embeddings of the string in Z 3 (a discretization of 3 dimensional space) The ....

K.A. Dill. Dominant forces in protein folding. Biochemistry 29 (1990), pp. 7133--7155.

....This problem has been investigated under a wide variety of models, each of which attempts to emphasize different aspects of the problem. Perhaps the simplest, and combinatorially most appealing of the widely studied models is the so called hydrophobic hydrophilic model, or HP model of Dill [6, 7]. Here a protein is represented as a string over the two letter alphabet fH; Pg, with the symbol H representing hydrophobic monomers and P hydrophilic (or polar) monomers. Conformations of the protein correspond to embeddings of the string in Z 3 (a discretization of 3 dimensional space) The ....

K.A. Dill. Dominant forces in protein folding. Biochemistry 29 (1990), pp. 7133--7155.

....string in a grid so as to maximize the number of pairs of matching symbols at adjacent grid points. This version of the folding problem involves a mixture of combinatorial, geometric and topological considerations. Our model is based on the hydrophobic hydrophilic (HP) model proposed by Dill [2,3], in which a binary alphabet is used, with H representing nonpolar (hydrophobic) monomers and P representing polar (hydrophilic) monomers. The aim is to maximize the number of adjacencies between H s, since the hydrophobic reactions make an important contribution to the free energy of the ....

....by at least one of its literals. 2 5 Open Problems and Conclusion To obtain our results, we needed to allow an alphabet of unbounded size. The principal open problem that remains is to resolve the complexity of STRING FOLD in Z 2 and Z 3 for the hydrophobic hydrophilic model considered by [2,3,6]. This corresponds to a binary alphabet in which only one symbol forms bonds. An intermediate problem, which still seems challenging, is to extend our NP hardness results to some fixed finite alphabet. The grids Z 2 and Z 3 that we have used are bipartite, and parity arguments were helpful in ....

K.A. Dill. Dominant forces in protein folding. Biochemistry 29, (1990), 7133-- 7155.

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Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133--7155.

No context found.

K.A. Dill, Dominant Forces in Protein Folding, Biochemistry 29 (1990), 7133-7155.

.... dihedral angle pairs (j,y) Since the residues in this model come in only two forms, H (hydrophobic) and P (polar) where the H type monomers exhibit a strong pairwise attraction, the lowest free energy state is obtained by those conformations with the greatest number of H H contacts (see [1], 7] Despite its simplicity, the use of this type of potential function has already proven successful in studies conducted independently by Sun, Thomas, and Dill [8] and by Srinivasan and Rose [6] Both groups have demonstrated that this type of potential function is sufficient to accurately ....

K.A. Dill, Dominant Forces in Protein Folding, Biochemistry 29 (1990), 7133-7155.

....conformations which do not exist. Since the residues in this model come in only two forms, H (hydrophobic) and P (polar) where the H type monomers exhibit a strong pairwise attraction, the lowest free energy state is obtained by those conformations with the greatest number of H H contacts (see [1], 12] One significant advantage of this detailed formulation of the folding problem is that it allows the model to take advantage of known scientific knowledge about the chemical structure of real sequences of molecules. The use of knowledge such as the Ramachandran plot (see [4] which ....

K.A. Dill, Dominant Forces in Protein Folding, Biochemistry 29 (1990), 7133-7155.

....N H O C j Figure 1 Simple Polypeptide Model C a C s N H O C j y C a C a C s N H O C j y 4 K.A. DILL, A.T. PHILLIPS, AND J.B. ROSEN exhibit a strong pairwise attraction, the lowest free energy state involves those conformations with the greatest number of hydrophobic contacts [1] and intrastrand hydrogen bonds. Simplified potential function have been successful in studies by Sun, Thomas, and Dill [10] by Srinivasan and Rose [7] and by Yue and Dill [11] We used here a simple modification of the Sun Thomas Dill energy function. One practical means for finding the global ....

K.A. Dill, Dominant Forces in Protein Folding, Biochemistry 29 (1990), 7133-7155.

....Our model natives (in the Sun model) always have lower energies than the true natives (PDB) In the context of this work, this is good news because it shows that the flaws are in the energy function, not the search strategy. The model native structures are not correct, but they are protein like [7]: they are compact, with hydrophobic cores and hydrogen bonded secondary structure (Figure 1.5) Hence, if we can push the search speeds still higher, we could then refine energy functions, or include more degrees of freedom, to improve the model. 3. The computer time required to find the native ....

Dill, K.A. (1990), Dominant forces in protein folding, Biochemistry 29(31):7133-7155.

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K. A. Dill. Dominant Forces in Protein Folding. Biochemistry, 29:7133-7155, 1990.

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K.A. Dill. Dominant forces in protein folding. Biochemistry, 29:7133--7155, 1990.

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K.A. Dill. Dominant forces in protein folding. Biochemistry 29 (1990), pp. 7133--7155.

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Dill, K. A. Dominant forces in protein folding. Biochemistry 1990, 29, 7133-7155.

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Dill KA. Dominant forces in protein folding. Biochemistry 1990;29: 7133--7155.

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Dill, K. (1990). Dominant forces in protein folding. Biochemistry 31, 7133--7155.

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K. A. Dill, Dominant forces in protein folding, Biochemistry 29, 7133-7155 (1990)

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