51
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Gutman L, Chakraborty AK. Exotic transitions of random heteropolymers interacting with solid surfaces. J Chem Phys 1996. [DOI: 10.1063/1.472565] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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52
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Timoshenko EG, Kuznetsov YA, Dawson KA. Kinetics of a Gaussian random copolymer as a prototype for protein folding. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1996; 54:4071-4086. [PMID: 9965556 DOI: 10.1103/physreve.54.4071] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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53
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Camacho CJ. Entropic Barriers, Frustration, and Order: Basic Ingredients in Protein Folding. PHYSICAL REVIEW LETTERS 1996; 77:2324-2327. [PMID: 10061915 DOI: 10.1103/physrevlett.77.2324] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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54
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Schiessel H, Blumen A. Instabilities of polyampholytes in external electrical fields. J Chem Phys 1996. [DOI: 10.1063/1.472241] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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55
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Plotkin SS, Wang J, Wolynes PG. Correlated energy landscape model for finite, random heteropolymers. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1996; 53:6271-6296. [PMID: 9964988 DOI: 10.1103/physreve.53.6271] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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56
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Pande VS, Grosberg AY, Joerg C, Tanaka T. Is heteropolymer freezing well described by the random energy model? PHYSICAL REVIEW LETTERS 1996; 76:3987-3990. [PMID: 10061163 DOI: 10.1103/physrevlett.76.3987] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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57
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Schiessel H, Blumen A. Conformations of freely jointed polyampholytes in external fields. J Chem Phys 1996. [DOI: 10.1063/1.471308] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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58
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Wilbur WJ, Major F, Spouge J, Bryant S. The statistics of unique native states for random peptides. Biopolymers 1996; 38:447-59. [PMID: 8867208 DOI: 10.1002/(sici)1097-0282(199604)38:4%3c447::aid-bip2%3e3.0.co;2-t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Given a probability distribution from which the energy spectrum of a random peptide is to be sampled, we derive a general expression for the probability that such a peptide will fold to a unique native state and for the probability distribution of the native energy. This latter result allows us to localize the energy of folding based on model parameters and is one advantage of our formulation. Evidence from both the lattice theory of proteins and protein threading experiments suggest that the energy spectrum for the compact states of a peptide chain is Gaussian in form. For this reason we have derived from the more general framework the specific formulas that apply in the Gaussian case, where one requires only the number of states and the variance of the Gaussian distribution in order to apply the theory. This simplicity allows us to perform calculations that we compare with calculations previously made by others based on statistical thermodynamics. We find qualitative agreement, but a significant correction to prior estimates of folding probability derived from the Gaussian assumption is necessary.
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Affiliation(s)
- W J Wilbur
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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59
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Chakraborty AK, Shakhnovich EI. Phase behavior of random copolymers in quenched random media. J Chem Phys 1995. [DOI: 10.1063/1.469861] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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60
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Gutman L, Chakraborty AK. A field theory of random heteropolymers near solid surfaces: Analysis of interfacial organization and adsorption–desorption phase diagram. J Chem Phys 1995. [DOI: 10.1063/1.469860] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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61
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Schiessel H, Oshanin G, Blumen A. Dynamics and conformational properties of polyampholytes in external electrical fields. J Chem Phys 1995. [DOI: 10.1063/1.470593] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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62
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Betancourt MR, Onuchic JN. Kinetics of proteinlike models: The energy landscape factors that determine folding. J Chem Phys 1995. [DOI: 10.1063/1.470109] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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63
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Barthelemy M, Orland H, Zerah G. Propagation in random media: Calculation of the effective dispersive permittivity by use of the replica method. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 52:1123-1127. [PMID: 9963516 DOI: 10.1103/physreve.52.1123] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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64
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Sfatos CD, Gutin AM, Shakhnovich EI. Critical compositions in the microphase separation transition of random copolymers. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 51:4727-4734. [PMID: 9963185 DOI: 10.1103/physreve.51.4727] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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65
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Cule D, Shapir Y. Glassy roughness of a crystalline surface upon a disordered substrate. PHYSICAL REVIEW LETTERS 1995; 74:114-117. [PMID: 10057712 DOI: 10.1103/physrevlett.74.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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66
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Gutman L, Chakraborty AK. Surface‐induced ordering for confined random block copolymers. J Chem Phys 1994. [DOI: 10.1063/1.467996] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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67
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Sfatos CD, Gutin AM, Shakhnovich EI. Phase transitions in a "many-letter" random heteropolymer. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 50:2898-2905. [PMID: 9962332 DOI: 10.1103/physreve.50.2898] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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68
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Abkevich VI, Gutin AM, Shakhnovich EI. Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations. J Chem Phys 1994. [DOI: 10.1063/1.467320] [Citation(s) in RCA: 173] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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69
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Grosberg A, Izrailev S, Nechaev S. Phase transition in a heteropolymer chain at a selective interface. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 50:1912-1921. [PMID: 9962193 DOI: 10.1103/physreve.50.1912] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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70
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Ramanathan S, Shakhnovich E. Statistical mechanics of proteins with "evolutionary selected" sequences. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 50:1303-1312. [PMID: 9962094 DOI: 10.1103/physreve.50.1303] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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71
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Dinner A, Šali A, Karplus M, Shakhnovich E. Phase diagram of a model protein derived by exhaustive enumeration of the conformations. J Chem Phys 1994. [DOI: 10.1063/1.467769] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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72
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Bryngelson JD. When is a potential accurate enough for structure prediction? Theory and application to a random heteropolymer model of protein folding. J Chem Phys 1994. [DOI: 10.1063/1.467114] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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73
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Gutin AM, Shakhnovich EI. Statistical mechanics of polymers with distance constraints. J Chem Phys 1994. [DOI: 10.1063/1.467193] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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74
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Archontis GZ, Shakhnovich EI. Phase transitions in heteropolymers with "secondary structure". PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 49:3109-3123. [PMID: 9961577 DOI: 10.1103/physreve.49.3109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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75
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76
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Mukherji S, Bhattacharjee SM. Directed polymers with random interaction: An exactly solvable case. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 48:3483-3496. [PMID: 9961007 DOI: 10.1103/physreve.48.3483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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77
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Korshunov SE. Replica symmetry breaking in vortex glasses. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:3969-3975. [PMID: 10008846 DOI: 10.1103/physrevb.48.3969] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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78
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Sfatos CD, Gutin AM, Shakhnovich EI. Phase diagram of random copolymers. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 48:465-475. [PMID: 9960609 DOI: 10.1103/physreve.48.465] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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79
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Goldschmidt YY, Blum T. Manifolds in random media: Multifractal behavior. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 48:161-170. [PMID: 9960578 DOI: 10.1103/physreve.48.161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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80
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Gutin AM, Shakhnovich EI. Ground state of random copolymers and the discrete random energy model. J Chem Phys 1993. [DOI: 10.1063/1.464522] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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81
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Sasai M, Wolynes PG. Unified theory of collapse, folding, and glass transitions in associative-memory Hamiltonian models of proteins. PHYSICAL REVIEW A 1992; 46:7979-7997. [PMID: 9908149 DOI: 10.1103/physreva.46.7979] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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82
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Abstract
We suggest, using dynamical simulations of a simple heteropolymer modelling the alpha-carbon sequence in a protein, that generically the folded states of globular proteins correspond to statistically well-defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well-defined beta-barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the "noisy" molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar. Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well-defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding----folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to the folded state.
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Affiliation(s)
- J D Honeycutt
- Biosym Technologies, Inc., San Diego, California 92121
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83
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Friedrichs MS, Goldstein RA, Wolynes PG. Generalized protein tertiary structure recognition using associative memory Hamiltonians. J Mol Biol 1991; 222:1013-34. [PMID: 1762143 DOI: 10.1016/0022-2836(91)90591-s] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In previous papers, a method of protein tertiary structure recognition was described based on the construction of an associative memory Hamiltonian, which encoded the amino acid sequence and the C alpha co-ordinates of a set of database proteins. Using molecular dynamics with simulated annealing, the ability of the Hamiltonian to successfully recall the structure of a protein in the memory database was successfully demonstrated, as long as the total number of database proteins did not exceed a characteristic value, called the capacity of the Hamiltonian, equal to 0.5N to 0.7N, where N is the number of amino acid residues in the protein to be recalled. In this paper, we describe the development of additional methods to increase the capacity of the Hamiltonian, including use of a more complete representation of the protein backbone and the incorporation of contextual information into the Hamiltonian through the use of secondary structure prediction. In addition, we further extend the ability of associative memory models to predict the tertiary structures of proteins not present in the protein data set, by making the Hamiltonian invariant with respect to biological symmetries that represent site mutations and insertions and deletions. The ability of the Hamiltonian to generalize from homologous proteins to an unknown protein in the presence of other unrelated proteins in the data set is demonstrated.
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84
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Radzihovsky L, Nelson DR. Statistical mechanics of randomly polymerized membranes. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1991; 44:3525-3542. [PMID: 9906370 DOI: 10.1103/physreva.44.3525] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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85
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86
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Abstract
Like macroscopic machines, molecular-sized machines are limited by their material components, their design, and their use of power. One of these limits is the maximum number of states that a machine can choose from. The logarithm to the base 2 of the number of states is defined to be the number of bits of information that the machine could "gain" during its operation. The maximum possible information gain is a function of the energy that a molecular machine dissipates into the surrounding medium (Py), the thermal noise energy which disturbs the machine (Ny) and the number of independently moving parts involved in the operation (dspace): Cy = dspace log2 [( Py + Ny)/Ny] bits per operation. This "machine capacity" is closely related to Shannon's channel capacity for communications systems. An important theorem that Shannon proved for communication channels also applies to molecular machines. With regard to molecular machines, the theorem states that if the amount of information which a machine gains is less than or equal to Cy, then the error rate (frequency of failure) can be made arbitrarily small by using a sufficiently complex coding of the molecular machine's operation. Thus, the capacity of a molecular machine is sharply limited by the dissipation and the thermal noise, but the machine failure rate can be reduced to whatever low level may be required for the organism to survive.
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Affiliation(s)
- T D Schneider
- Frederick Cancer Research and Development Center, Laboratory of Mathematical Biology, MD 21702
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87
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Sasai M, Wolynes PG. Molecular theory of associative memory Hamiltonian models of protein folding. PHYSICAL REVIEW LETTERS 1990; 65:2740-2743. [PMID: 10042680 DOI: 10.1103/physrevlett.65.2740] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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88
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Shakhnovich E, Gutin A. Enumeration of all compact conformations of copolymers with random sequence of links. J Chem Phys 1990. [DOI: 10.1063/1.459480] [Citation(s) in RCA: 213] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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89
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Shakhnovich EI, Gutin AM. Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach. Biophys Chem 1989; 34:187-99. [PMID: 2611345 DOI: 10.1016/0301-4622(89)80058-4] [Citation(s) in RCA: 229] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A replica approach analogous to that used in spin glass systems is implemented to study the configurational space of a heteropolymeric model of protein with a quenched, disordered sequence of links in the limit of a large number of link types. It is shown that there exists a threshold value of chain heterogeneity which separates two qualitatively different types of behavior. For a low degree of heterogeneity the protein globule is like a homopolymer in a collapsed state without definite chain folds: an exponentially large number of folds make a significant contribution to the partition function in this regime. After the threshold heterogeneity has been overcome, the chain freezes drastically but without latent heat; few (approx. 1) frozen states with definite chain folds are thermodynamically dominant in this state. The relation of these results to thermodynamic aspects of protein folding is discussed.
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Affiliation(s)
- E I Shakhnovich
- Institute of Protein Research, Academy of Sciences of the U.S.S.R., Moscow Region
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90
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Friedrichs MS, Wolynes PG. Toward Protein Tertiary Structure Recognition by Means of Associative Memory Hamiltonians. Science 1989; 246:371-3. [PMID: 17747919 DOI: 10.1126/science.246.4928.371] [Citation(s) in RCA: 119] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The statistical mechanics of associative memories and spin glasses suggests ways to design Hamiltonians for protein folding. An associative memory Hamiltonian based on hydrophobicity patterns is shown to have a large capacity for recall and to be capable of recognizing tertiary structure for moderately variant sequences.
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91
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Kholodenko AL. The Thouless–Anderson–Palmer approach to random copolymer glasses. J Chem Phys 1989. [DOI: 10.1063/1.456859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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