Folding free‐energy landscape of a 10‐residue mini‐protein, chignolin

Satoh, Daisuke; Shimizu, Kentaro; Nakamura, Shugo; Terada, Tohru

doi:10.1016/j.febslet.2006.05.015

Cited by 100 publications

(141 citation statements)

References 19 publications

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“…26 It should be noted that the present method only calculate free energy along reactive trajectories whereas MSFEL have done extensive search on broader conformational space. Despite this difference, the misfolded structure 46 was detected from the present FEL calculation. Free energy difference around native, misfolded and intermediate states and the transition pathways between them is relatively small (<2k B T).…”

Section: Free Energy Landscape Calculations Along Reactive Trajectmentioning

confidence: 84%

“…These hydrogen bond distances were employed as the indicator of the folding and misfolding. 46 The formation of HB3 has been identified as a trigger of the folding. The formation of additional HB1 is essential for folding into the native structure and that of HB2 induces misfolding.…”

Section: A Folding Of Chignolinmentioning

confidence: 99%

“…4(a), upon folding of chignolin, one structure of ten candidates survived preferentially up to the 9th cycle, indicating that strong structural selection is needed for fast folding into the native structure. To examine the detail folding process of chignolin, reactive trajectories were projected onto a sub-space spanned by two reaction coordinates defined in the past studies; 26,46,47 Donor-acceptor distances, Asp3:N-Thr8:O, Asp3:N-Gly7:O, and Asp3:O-Gly7:N, are defined as HB1, HB2, and HB3, respectively. These hydrogen bond distances were employed as the indicator of the folding and misfolding.…”

Section: A Folding Of Chignolinmentioning

confidence: 99%

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Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway

Harada

Kitao

2013

The Journal of Chemical Physics

125

189

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Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular simulation method to generate conformational transition pathway under the condition that a set of "reactant" and "product" structures is known a priori. In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the product structure for the next cycle are repeated until the simulated structures move sufficiently close to the product. Folding of 10-residue mini-protein chignolin from the extended to native structures and open-close conformational transition of T4 lysozyme were investigated by PaCS-MD. In both cases, tens of cycles of 100-ps MD were sufficient to reach the product structures, indicating the efficient generation of conformational transition pathway in PaCS-MD with a series of conventional MD without additional external biases. Using the snapshots along the pathway as the initial coordinates, free energy landscapes were calculated by the combination with multiple independent umbrella samplings to statistically elucidate the conformational transition pathways. © 2013 AIP Publishing LLC.

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Section: Free Energy Landscape Calculations Along Reactive Trajectmentioning

confidence: 84%

Section: A Folding Of Chignolinmentioning

confidence: 99%

Section: A Folding Of Chignolinmentioning

confidence: 99%

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Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway

Harada

Kitao

2013

The Journal of Chemical Physics

125

189

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“…The structure is stabilized in water by van der Waals interactions of the side chain of Tyr2 with those of Pro4 and Trp9 and several hydrogen bonds, among which the hydrogen bond of Gly7(NH)ÁÁÁAsp3(O) exhibits strong resistance against the amide H-D exchange experiment. 34 This miniprotein has recently attracted increasing attention as a model peptide to test and evaluate simulation methodologies [64][65][66] and solvent models. 67 To demonstrate the efficiency of the SAAP force field, the Monte Carlo simulation was carried out for chignolin in water at 300 and 500 K.…”

Section: Simulation For Chignolinmentioning

confidence: 99%

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

et al. 2009

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Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side-chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met-enkephalin (CHO-Tyr-Gly-Gly-Phe-Met-NH2) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard-Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H-Gly-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Gly-OH) reasonably reproduced a native-like beta-hairpin structure in water although the C-terminal and side-chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units.

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“…The folding properties of the peptide have recently been studied by computer simulation methods. 51,52 In our study, the TIGER2 algorithm was further tested by comparing simulation results with the corresponding REMD results and the experimental observations for this peptide model.…”

Section: Chignolinmentioning

confidence: 99%

TIGER2: An improved algorithm for temperature intervals with global exchange of replicas

Latour

Stuart

2009

The Journal of Chemical Physics

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An empirical sampling method for molecular simulation based on "temperature intervals with global exchange of replicas" ͑TIGER2͒ has been developed to reduce the high demand for computational resources and the low computational efficiency of the conventional replica-exchange molecular dynamics ͑REMD͒ method. This new method overcomes the limitation of its previous version, called TIGER, which requires the assumption of constant heat capacity during quenching of replicas from elevated temperatures to the baseline temperature. The robustness of the TIGER2 method is examined by comparing it against a Metropolis Monte Carlo simulation for sampling the conformational distribution of a single butane molecule in vacuum, a REMD simulation for sampling the behavior of alanine dipeptide in explicit solvent, and REMD simulations for sampling the folding behavior of two peptides, ͑AAQAA͒ 3 and chignolin, in implicit solvent. The agreement between the results from these conventional sampling methods and the TIGER2 simulations indicates that the TIGER2 algorithm is able to closely approximate a Boltzmann-weighted ensemble of states for these systems but without the limiting assumptions that were required for the original TIGER algorithm. TIGER2 is an efficient replica-exchange sampling method that enables the number of replicas that are used for a replica-exchange simulation to be substantially reduced compared to the conventional REMD method.

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Folding free‐energy landscape of a 10‐residue mini‐protein, chignolin

Cited by 100 publications

References 19 publications

Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway

Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway

The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides

TIGER2: An improved algorithm for temperature intervals with global exchange of replicas

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