J. Shimada, E.L. Kussell, and E.I. Shakhnovich. The folding thermodynamics and kinetics of crambin using an all-atom monte carlo simulation. Journal of Molecular Biology, 308(1):79--95, 2001.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....are distributed according to the Boltzmann distribution: 5 # ( where . # ( is the normalization constant. So any subset is sampled with ) MC simulation is also an important tool to study molecular motion [SKS01, KS96] However, it is computationally intensive. Each simulation run yields a series of sampled conformations defining a single pathway. Due to the high potential variance between independent runs, the simulation must be run many times over extended durations in order to produce accurate ....

J. Shimada, E.L. Kussell, and E.I. Shakhnovich. The folding thermodynamics and kinetics of crambin using an all-atom monte carlo simulation. J. Mol. Biol., 308(1):79--95, 2001.

....by proteins is an important topic in structural biology. MCS [6] is one common methodology for this study. In this context, it has been used for two purposes: 1) estimating thermodynamic quantities over a protein s conformation space [29, 39, 63] and, in some cases, even kinetic properties [50, 51]; and (2) searching for low energy conformations of a protein, including its native structure [2, 3, 64] The approach was originally proposed in [43] but many variants and improvements have later been suggested [28] MCS is a series of randomly generated trial steps in the conformation space of ....

....approach was originally proposed in [43] but many variants and improvements have later been suggested [28] MCS is a series of randomly generated trial steps in the conformation space of the studied molecule. Each such step consists of perturbing some degrees of freedom (DOFs) of the molecule [40, 50, 51, 63, 64], in general torsion (dihedral) angles around bonds (see Section 1.2) Classically, a trial step is accepted i.e. the simulation actually moves to the new conformation with probability min 1, e #E k b T (the so called Metropolis criterion [43] where E is an energy function defined ....

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J. Shimada, E. Kussell, and E. Shakhnovich. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J. of Molecular Biology, 308(1):79--95, April 2001.

....the sampled conformations are distributed according to the Boltzmann distribution: #(q) exp( E(q) k B T ) exp( E(q) k B T ) dq is the normalization constant. So any subset S is sampled with probability #(q) dq. MC simulation is also an important tool to study molecular motion [SKS01, KS96] However, it is computationally intensive. Each simulation run yields a series of sampled conformations defining a single pathway. Due to the high potential variance between independent runs, the simulation must be run many times over extended durations in order to produce accurate ....

J. Shimada, E.L. Kussell, and E.I. Shakhnovich. The folding thermodynamics and kinetics of crambin using an all-atom monte carlo simulation. J. Mol. Biol., 308(1):79--95, 2001.

.... but also physical on the lattice, it is known what potential to use in order for stable and fast folding sequences to exist (a simple contact potential is sucient) How to satisfy these criteria for o lattice chains is, by contrast, largely unknown, and therefore many current o lattice models [5,8 14] use G o type potentials [7] where non native interactions are ignored. The use of the G o approximation has some support from the nding that the native structure is a determinant for folding kinetics [15,16] However, it is an uncontrolled approximation, and it is, of course, useless when it ....

....were strong. Under these conditions, the helix formation was found to be fast, whereas the collapse was the rate limiting step. However, a G o like model ignores a large fraction of the interactions that drive the collapse, which can make the collapse arti cially slow. In a recent G o model study [14], this problem was addressed by eliminating backbone terms from the potential until a reasonable helix stability was achieved. No such calibration was carried out in Ref. 10] This may explain why these authors nd a behavior that our model cannot reproduce. Let us nally mention that we also ....

Shimada J, Kussell EL, Shakhnovich EI. The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J. Mol. Biol. 2001 ; 308 : 79-95.

.... paper we also discuss how this behavior depends on (ffl hb ; ffl AA ) Our main finding, however, is that the model does show the listed properties for the choice (ffl hb ; ffl AA ) ffl hb ; ffl AA ) Qualitatively similar results have been obtained before for C ff [6, 17, 18] and all atom [19] off lattice chains, but, as far as we know, only in Go type models. The paper is organized as follows. In Section 2 we give a brief description of the model. Results are presented in Section 3. Here, we first summarize the results obtained in [11] for (ffl hb ; ffl AA ) ffl hb ; ffl AA ) ....

Shimada, J., Kussell, E.L. and Shakhnovich, E.I.: The Folding Thermodynamics and Kinetics of Crambin Using a Monte Carlo Simulation at Atomic Resolution, submitted to Proc. Natl. Acad. Sci. USA.

....only. Let us finally stress the fact that we find a first order like folding transition without using the Go approximation. Evidence for first order like folding transitions has been found for proteins with similar lengths in some C ff models [5, 14,17,33] and also in a model at atomic resolution [37], but these studies use this approximation. Acknowledgements This work was in part supported by the Swedish Foundation for Strategic Research. 12 ....

Shimada, J., Kussell, E.L. & Shakhnovich, E.I. (2000) "The Folding Thermodynamics and Kinetics of Crambin Using a Monte Carlo Simulation at Atomic Resolution", submitted to Proc. Natl. Acad. Sci. USA. 15

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J. Shimada, E.L. Kussell, and E.I. Shakhnovich. The folding thermodynamics and kinetics of crambin using an all-atom monte carlo simulation. Journal of Molecular Biology, 308(1):79--95, 2001.

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