ArticleScientific reports2016
All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- A claudin5-binding peptide enhances the permeability of the blood-brain barrier in vitro.Science advances · 2025Article
- Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization.Chemical science · 2023Article
- Protein Design: From the Aspect of Water Solubility and Stability.Chemical reviews · 2022Review
- Aggregation Behavior of Structurally Similar Therapeutic Peptides Investigated byMolecular pharmaceutics · 2022Article
- Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs.Advances in protein chemistry and structural biology · 2022Review
- Common and unique strategies of myoglobin evolution for deep-sea adaptation of diving mammals.iScience · 2021Article
- Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations.Chemical reviews · 2021Review
- Dissecting the role of glutamine in seeding peptide aggregation.Computational and structural biotechnology journal · 2021Article
- Designing a new bispecific tandem single-chain variable fragment antibody against tumor necrosis factor-α and interleukin-23 using in silico studies for the treatment of rheumatoid arthritis.Journal of molecular modeling · 2020Article
- Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs.Scientific reports · 2019Article
- Self-Association of Antimicrobial Peptides: A Molecular Dynamics Simulation Study on Bombinin.International journal of molecular sciences · 2019Article
- Theoretical analysis on thermodynamic stability of chignolin.Scientific reports · 2019Article
- Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity.Scientific reports · 2019Article
- Energetics of cosolvent effect on peptide aggregation.Biophysics and physicobiology · 2019Review
- Tracing whale myoglobin evolution by resurrecting ancient proteins.Scientific reports · 2018Article
- Towards Controlled Single-Molecule Manipulation Using "Real-Time" Molecular Dynamics Simulation: A GPU Implementation.Micromachines · 2018Article
- Biophysical studies of protein solubility and amorphous aggregation by systematic mutational analysis and a helical polymerization model.Biophysical reviews · 2018Review
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Markov State Models of gene regulatory networks.BMC systems biology · 2017Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
In order to investigate the contribution of individual amino acids to protein and peptide solubility, we carried out 100 ns molecular dynamics (MD) simulations of 10(6) Å(3) cubic boxes containing ~3 × 10(4) water molecules and 27 tetra-peptides regularly positioned at 23 Å from each other and composed of a single amino acid type for all natural amino acids but cysteine and glycine. The calculations were performed using Amber with a standard force field on a special purpose MDGRAPE-3 computer, without introducing any "artificial" hydrophobic interactions. Tetra-peptides composed of I, V, L, M, N, Q, F, W, Y, and H formed large amorphous clusters, and those containing A, P, S, and T formed smaller ones. Tetra-peptides made of D, E, K, and R did not cluster at all. These observations correlated well with experimental solubility tendencies as well as hydrophobicity scales with correlation coefficients of 0.5 to > 0.9. Repulsive Coulomb interactions were dominant in ensuring high solubility, whereas both Coulomb and van der Waals (vdW) energies contributed to the aggregations of low solubility amino acids. Overall, this very first all-atom molecular dynamics simulation of a multi-peptide system appears to reproduce the basic properties of peptide solubility, essentially in line with experimental observations.
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