| 1. |
- Irbäck, Anders, et al.
(författare)
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Identification of amino acid sequences with good folding properties in an off-lattice model
- 1997
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Ingår i: Physical Review E. - 1063-651X. ; 55:1 SUPPL. B, s. 860-867
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Tidskriftsartikel (refereegranskat)abstract
- Folding properties of a two-dimensional toy protein model containing only two amino acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences.
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| 2. |
- Irbäck, Anders, et al.
(författare)
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Local interactions and protein folding : A model study on the square and triangular lattices
- 1998
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 108:5, s. 2245-2250
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Tidskriftsartikel (refereegranskat)abstract
- We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength κ of the local interactions; κ=0 corresponds to the well-known HP model [K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989)]. By exhaustive enumerations for short chains, we obtain all structures which act as a unique and pronounced energy minimum for at least one sequence. We find that the number of such designable structures depends strongly on κ. Also, we find that the number of designable structures can differ widely for the two lattices at a given κ. This is the case, for example, at κ=0, which implies that the HP model exhibits different behavior on the two lattices. Our findings clearly show that sequence-independent local properties of the chains can play an important rote in the formation of unique minimum energy structures.
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| 3. |
- Irbäck, Anders, et al.
(författare)
-
Local interactions and protein folding : A three-dimensional off-lattice approach
- 1997
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 107:1, s. 273-282
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Tidskriftsartikel (refereegranskat)abstract
- The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobia and hydrophilic. In absence of local interactions, native structure formation does not occur for the temperatures considered. By including sequence independent local interactions, which qualitatively reproduce local properties of functional proteins, the dominance of a native state for many sequences is observed. As in lattice model approaches, folding takes place by gradual compactification, followed by a sequence dependent folding transition. Our results differ from lattice approaches in that bimodal energy distributions are not observed and that high folding temperatures are accompanied by relatively low temperatures for the peak of the specific heat. Also, in contrast to earlier studies using lattice models, our results convincingly demonstrate that one does not need more than two types of residues to generate sequences with good thermodynamic folding properties in three dimensions.
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| 4. |
- Irbäck, Anders, et al.
(författare)
-
Monte Carlo procedure for protein design
- 1998
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Ingår i: Physical Review E. - 1063-651X. ; 58:5
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Tidskriftsartikel (refereegranskat)abstract
- A method for sequence optimization in protein models is presented. The approach, which has inherited its basic philosophy from recent work by Deutsch and Kurosky [Phys. Rev. Lett. 76, 323 (1996)] by maximizing conditional probabilities rather than minimizing energy functions, is based upon a different and very efficient multisequence Monte Carlo scheme. By construction, the method ensures that the designed sequences represent good folders thermodynamically. A bootstrap procedure for the sequence space search is devised making very large chains feasible. The algorithm is successfully explored on the two-dimensional HP model [K. F. Lau and K. A. Dill, Macromolecules 32, 3986 (1989)] with chain lengths N= 16, 18, and 32.
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| 5. |
- Irbäck, Anders, et al.
(författare)
-
Monte Carlo study of the phase structure of compact polymer chains
- 1999
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 110:24, s. 12256-12262
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Tidskriftsartikel (refereegranskat)abstract
- We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the collapse temperature, signalling a possible low-temperature phase transition. The system size dependence at this maximum is investigated both with and without the local interactions, using chains with up to 50 monomers. The size dependence is found to be weak. The specific heat itself seems not to diverge. The homopolymer results are compared with those for two nonuniform sequences. Our calculations are performed using the methods of simulated and parallel tempering. The performances of these algorithms are discussed, based on careful tests for a small system.
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| 6. |
- Irbäck, Anders, et al.
(författare)
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Sequence dependence of self-interacting random chains
- 1995
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Ingår i: Journal of Physics A: Mathematical and General. - : IOP Publishing. - 0305-4470 .- 1361-6447. ; 28:8, s. 2121-2132
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Tidskriftsartikel (refereegranskat)abstract
- We study the thermodynamic behaviour of the random chain model proposed by Iori, Marinari and Parisi and how this behaviour depends on the actual sequence of interactions along the chain. The properties of randomly chosen sequences are compared to those of designed sequences obtained through a simulated annealing procedure in sequence space. We show that for designed sequences the transition to the folded phase takes place at a smaller strength of the quenched disorder. As a result, folding can be relatively fast for these sequences.
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| 7. |
- Irbäck, Anders, et al.
(författare)
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Studies of an off-lattice model for protein folding : Sequence dependence and improved sampling at finite temperature
- 1995
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Ingår i: Journal of Chemical Physics. - 0021-9606. ; 103:23, s. 10298-10305
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Tidskriftsartikel (refereegranskat)abstract
- We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two dimensional and has two different "amino acids." Using numerical simulations of all chains containing eight or ten monomers, we examine the sequence dependence at a fixed temperature. It is shown that only a few of the chains exist in unique folded state at this temperature, and the energy level spectra of chains with different types of behavior are compared. Furthermore, we use this model as a testbed for two improved Monte Carlo algorithms. Both algorithms are based on letting some parameter of the model become a dynamical variable; one of the algorithms uses a fluctuating temperature and the other a fluctuating monomer sequence. We find that by these algorithms one gains large factors in efficiency in comparison with conventional methods.
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