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Molecules
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Molecular Simulation of Protein Structure, Dynamics and Interactions
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Molecular Simulation of Protein Structure, Dynamics and Interactions

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (31 March 2019) | Viewed by 13611

Special Issue Editors

Prof. Dr. Ricardo L. Mancera

E-Mail Website
Guest Editor
Curtin Medical School, Curtin University, Perth, WA 6845, Australia
Interests: molecular dynamics simulation; biological membranes; protein structure and dynamics; protein-protein and protein-ligand interactions; structure-based drug design
Special Issues, Collections and Topics in MDPI journals
Dr. Evelyne Deplazes

E-Mail Website
Guest Editor
School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, WA 6845, Australia
Interests: peptides and toxins; peptide–membrane and peptide–protein interactions; membrane structure; structure-based drug design; membrane proteins

Special Issue Information

Dear Colleagues,

The combined development of sophisticated and enhanced sampling methods and better parameterized force fields with ever-increasing computational resources, is allowing the investigation of complex phenomena involving proteins. These advances have often come in hand with extensive use of structural and biophysical experimental data for parameterization and validation. The characterization of protein folding pathways, the aggregation of intrinsically-disordered proteins, the mechanism of activation of membrane bound receptors and the formation of large macromolecular complexes are some examples where molecular simulation approaches have been playing a key role. This Special Issue aims to provide a resource for researchers about the latest developments, applications and expert opinion on the use of molecular simulation methods to describe the structure, dynamics and interactions of proteins.

Prof. Dr. Ricardo L. Mancera
Dr. Evelyne Deplazes
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Protein force fields
  • Enhanced sampling methods
  • Protein folding
  • Protein aggregation
  • Protein structure and stability
  • Membrane-bound protein receptors
  • Protein-protein and protein-small molecule interactions
  • Interactions of proteins/peptides with membranes

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Published Papers (2 papers)

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21 pages, 4680 KiB  
Article
Tripleurin XIIc: Peptide Folding Dynamics in Aqueous and Hydrophobic Environment Mimic Using Accelerated Molecular Dynamics
by Chetna Tyagi, Tamás Marik, András Szekeres, Csaba Vágvölgyi, László Kredics and Ferenc Ötvös
Molecules 2019, 24(2), 358; https://doi.org/10.3390/molecules24020358 - 19 Jan 2019
Cited by 10 | Viewed by 4703
Abstract
Peptaibols are a special class of fungal peptides with an acetylated N-terminus and a C-terminal 1,2-amino alcohol along with non-standard amino acid residues. New peptaibols named tripleurins were recently identified from a strain of the filamentous fungal species Trichoderma pleuroti, which [...] Read more.
Peptaibols are a special class of fungal peptides with an acetylated N-terminus and a C-terminal 1,2-amino alcohol along with non-standard amino acid residues. New peptaibols named tripleurins were recently identified from a strain of the filamentous fungal species Trichoderma pleuroti, which is known to cause green mould disease on cultivated oyster mushrooms. To understand the mode of action of these peptaibols, the three-dimensional structure of tripleurin (TPN) XIIc, an 18-mer peptide, was elucidated using an enhanced sampling method, accelerated MD, in water and chloroform solvents. Non-standard residues were parameterized by the Restrained Electrostatic Potential (RESP) charge fitting method. The dihedral distribution indicated towards a right-handed helical formation for TPN XIIc in both solvents. Dihedral angle based principal component analysis revealed a propensity for a slightly bent, helical folded conformation in water solvent, while two distinct conformations were revealed in chloroform: One that folds into highly bent helical structure that resembles a beta-hairpin and another with an almost straight peptide backbone appearing as a rare energy barrier crossing event. The hinge-like movement of the terminals was also observed and is speculated to be functionally relevant. The convergence and efficient sampling is addressed using Cartesian PCA and Kullback-Leibler divergence methods. Full article
(This article belongs to the Special Issue Molecular Simulation of Protein Structure, Dynamics and Interactions)
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Review

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37 pages, 9199 KiB  
Review
Characterisation of the Structure and Oligomerisation of Islet Amyloid Polypeptides (IAPP): A Review of Molecular Dynamics Simulation Studies
by Sandra J. Moore, Krushna Sonar, Prashant Bharadwaj, Evelyne Deplazes and Ricardo L. Mancera
Molecules 2018, 23(9), 2142; https://doi.org/10.3390/molecules23092142 - 25 Aug 2018
Cited by 30 | Viewed by 8170
Abstract
Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein whose abnormal aggregation into amyloid fibrils is a pathological feature in type 2 diabetes, and its cross-aggregation with amyloid beta has been linked to an increased risk of Alzheimer’s disease. The [...] Read more.
Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein whose abnormal aggregation into amyloid fibrils is a pathological feature in type 2 diabetes, and its cross-aggregation with amyloid beta has been linked to an increased risk of Alzheimer’s disease. The soluble, oligomeric forms of hIAPP are the most toxic to β-cells in the pancreas. However, the structure of these oligomeric forms is difficult to characterise because of their intrinsic disorder and their tendency to rapidly aggregate into insoluble fibrils. Experimental studies of hIAPP have generally used non-physiological conditions to prevent aggregation, and they have been unable to describe its soluble monomeric and oligomeric structure at physiological conditions. Molecular dynamics (MD) simulations offer an alternative for the detailed characterisation of the monomeric structure of hIAPP and its aggregation in aqueous solution. This paper reviews the knowledge that has been gained by the use of MD simulations, and its relationship to experimental data for both hIAPP and rat IAPP. In particular, the influence of the choice of force field and water models, the choice of initial structure, and the configurational sampling method used, are discussed in detail. Characterisation of the solution structure of hIAPP and its mechanism of oligomerisation is important to understanding its cellular toxicity and its role in disease states, and may ultimately offer new opportunities for therapeutic interventions. Full article
(This article belongs to the Special Issue Molecular Simulation of Protein Structure, Dynamics and Interactions)
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