PathMolD-AB: Spatiotemporal pathways of protein folding using parallel molecular dynamics with a coarse-grained model

Hattori, Leandro Takeshi; Pinheiro, Bruna Araujo; Frigori, Rafael B.; Benítez, César Manuel Vargas; Lopes, Heitor Silvério

doi:10.1016/j.compbiolchem.2020.107301

Cited by 2 publications

(3 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To solve this problem, the coarse-grained model is applied to represent proteins, which preserves the biological information of the protein and saves computational resources. In the coarse-grained model, each protein is viewed as a chain of beads, each bead representing an amino acid residue and each amino acid residue is replaced by a corresponding C α atom [13]. One of the widely used simplified lattice models is the HP model.…”

Section: Introductionmentioning

confidence: 99%

Effects of Residual Composition and Distribution on the Structural Characteristics of the Protein

Song

Wu²,

Jin³

et al. 2022

IJMS

View full text Add to dashboard Cite

The effect of ratio and consecutive number of hydrophobic residues in the repeating unit of protein chains was investigated by MD simulation. The modified off-lattice HNP model was applied in this study. The protein chains constituted by different HNP ratios or different numbers of consecutively hydrophobic residues with the same chain length were simulated under a broad temperature range. We concluded that the proteins with higher ratio or larger number of sequentially hydrophobic residues present more orientated and compact structure under a certain low temperature. It is attributed to the lower non-bonded potential energy between H-H residual pairs, especially more hydrophobic residues in a procession among the protein chain. Considering the microscopic structure of the protein, more residue contacts are achieved with the proteins with higher ratios and sequential H residues under the low temperature. Meanwhile, with the ratio and consecutive number of H residues increasing, the distribution of stem length showed a transition from exponential decline to unimodal and even multiple peaks, indicating the specific ordered structure formed. These results provide an insight into 3D structural properties of proteins from their residue sequences, which has a primary structure at molecular level and, ultimately, a practical possibility of applying in biotechnological applications.

show abstract

Section: Introductionmentioning

confidence: 99%

Effects of Residual Composition and Distribution on the Structural Characteristics of the Protein

Song

Wu²,

Jin³

et al. 2022

IJMS

View full text Add to dashboard Cite

show abstract

“…These constraints can be derived from prior knowledge, such as predicted secondary structures, 14,15 residual contacts, 16,17 homologous templates, 18 existing structure prediction programs, 19 or even known experimental structures. 20 To trade off AA accuracy and CG efficiency, multiscale models are developed incrementally. Multiscale models can be categorized as being in serial or in parallel.…”

mentioning

confidence: 99%

“…For coarser models, extra constraints are required to imitate hydrogen bonds and other elaborate interactions in protein folding. These constraints can be derived from prior knowledge, such as predicted secondary structures, , residual contacts, , homologous templates, existing structure prediction programs, or even known experimental structures . It is almost impossible to achieve ab initio folding by complete CG simulations because of the lack of atomistic details.…”

mentioning

confidence: 99%

Adaptively Iterative Multiscale Switching Simulation Strategy and Applications to Protein Folding and Structure Prediction

Zhong

2021

J. Phys. Chem. Lett.

View full text Add to dashboard Cite

Structure prediction is an important means to quickly understand new protein functions. However, the prediction of effects of proteins that have no detectable templates is still to be improved. Molecular dynamics simulation is supposed to be the primary research tool for structure predictions, but it still has limitations of huge computational cost in all-atom (AA) models and rough accuracy in coarse-grained (CG) models. We propose a universal multiscale simulation strategy named AIMS in which simulations can iteratively switch among multiple resolutions in order to adaptively trade off AA accuracy and CG high-efficiency. AIMS follows the idea of CG-guided enhanced sampling so that final results always keep AA accuracy. We successfully achieve four ab initio and four data-assisted protein structure predictions using AIMS. The prediction result is an ensemble rather than a structure and provides special insights on folding metastable states. AIMS is estimated to achieve a computational speed about 40 times faster than that of conventional AA simulations.

show abstract

PathMolD-AB: Spatiotemporal pathways of protein folding using parallel molecular dynamics with a coarse-grained model

Cited by 2 publications

References 57 publications

Effects of Residual Composition and Distribution on the Structural Characteristics of the Protein

Effects of Residual Composition and Distribution on the Structural Characteristics of the Protein

Adaptively Iterative Multiscale Switching Simulation Strategy and Applications to Protein Folding and Structure Prediction

Contact Info

Product

Resources

About