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Integration between Computational and Experimental Biophysical Techniques in the Study...
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Integration between Computational and Experimental Biophysical Techniques in the Study of Biologically Relevant Systems

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

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 17005

Special Issue Editors

Dr. Jacopo Sgrignani

E-Mail Website
Guest Editor
Istituto di Ricerca in Biomedicina (IRB), Università della Svizzera Italiana (USI), Via V. Vela 6, CH-6500 Bellinzona, Switzerland
Interests: molecular dynamics; QM/MM; computational drug design; microscale thermophoresis; ligand binding
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Giovanni Grazioso

E-Mail Website
Guest Editor
Department of Pharmaceutical Science, University of Milano, Via L. Mangiagalli 25, Milano, Italy
Interests: drug design; peptides; peptidomimetics; molecular dynamics simulations; MM-GBSA; binding free energy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Today, computational and experimental biophysics methodologies frequently complement each other in the investigation of biological systems.

In particular, the development of new codes and hardware have made it possible to run more extensive simulations and to describe systems with a higher level of resolution. This has simplified the direct comparison between experimental and theoretical observations.

The data obtained from these studies can be used to speed up the development of innovative molecules such as drugs, peptides, recombinant proteins, and antibodies.

For this Special Issue, we invite the submission of original contributions, short communications, or review articles that describe the application of computational techniques to interpret biophysical data, the use of biophysical observations to validate computational methodologies or the integration of computational and experimental approaches in the design of new molecules.

Dr. Jacopo Sgrignani
Prof. Giovanni Grazioso
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

  • computational and experimental biophysics
  • molecular dynamics
  • free energy
  • QM/MM
  • enzymatic kinetics
  • SPR
  • MST
  • molecular binding
  • docking

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Published Papers (3 papers)

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Research

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17 pages, 6942 KiB  
Article
Cryptococcus neoformans Capsular GXM Conformation and Epitope Presentation: A Molecular Modelling Study
by Michelle M. Kuttel, Arturo Casadevall and Stefan Oscarson
Molecules 2020, 25(11), 2651; https://doi.org/10.3390/molecules25112651 - 7 Jun 2020
Cited by 18 | Viewed by 5020
Abstract
The pathogenic encapsulated Cryptococcus neoformans fungus causes serious disease in immunosuppressed hosts. The capsule, a key virulence factor, consists primarily of the glucuronoxylomannan polysaccharide (GXM) that varies in composition according to serotype. While GXM is a potential vaccine target, vaccine development has been [...] Read more.
The pathogenic encapsulated Cryptococcus neoformans fungus causes serious disease in immunosuppressed hosts. The capsule, a key virulence factor, consists primarily of the glucuronoxylomannan polysaccharide (GXM) that varies in composition according to serotype. While GXM is a potential vaccine target, vaccine development has been confounded by the existence of epitopes that elicit non-protective antibodies. Although there is evidence for protective antibodies binding conformational epitopes, the secondary structure of GXM remains an unsolved problem. Here an array of molecular dynamics simulations reveal that the GXM mannan backbone is consistently extended and relatively inflexible in both C. neoformans serotypes A and D. Backbone substitution does not alter the secondary structure, but rather adds structural motifs: β DGlcA and β DXyl side chains decorate the mannan backbone in two hydrophillic fringes, with mannose-6-O-acetylation forming a hydrophobic ridge between them. This work provides mechanistic rationales for clinical observations—the importance of O-acetylation for antibody binding; the lack of binding of protective antibodies to short GXM fragments; the existence of epitopes that elicit non-protective antibodies; and the self-aggregation of GXM chains—indicating that molecular modelling can play a role in the rational design of conjugate vaccines. Full article
(This article belongs to the Special Issue Integration between Computational and Experimental Biophysical Techniques in the Study of Biologically Relevant Systems)
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Review

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18 pages, 2457 KiB  
Review
Combining Experimental Data and Computational Methods for the Non-Computer Specialist
by Reinier Cárdenas, Javier Martínez-Seoane and Carlos Amero
Molecules 2020, 25(20), 4783; https://doi.org/10.3390/molecules25204783 - 18 Oct 2020
Cited by 17 | Viewed by 6427
Abstract
Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus. However, providing a detailed structural interpretation of the results [...] Read more.
Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus. However, providing a detailed structural interpretation of the results is often a very challenging task. While experimental and computational methods are often considered as two different and separate approaches, the power and utility of combining both is undeniable. The integration of the experimental data with computational techniques can assist and enrich the interpretation, providing new detailed molecular understanding of the systems. Here, we briefly describe the basic principles of how experimental data can be combined with computational methods to obtain insights into the molecular mechanism and expand the interpretation through the generation of detailed models. Full article
(This article belongs to the Special Issue Integration between Computational and Experimental Biophysical Techniques in the Study of Biologically Relevant Systems)
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29 pages, 9435 KiB  
Review
Structure and Function of the Human Ryanodine Receptors and Their Association with Myopathies—Present State, Challenges, and Perspectives
by Vladena Bauerová-Hlinková, Dominika Hajdúchová and Jacob A. Bauer
Molecules 2020, 25(18), 4040; https://doi.org/10.3390/molecules25184040 - 4 Sep 2020
Cited by 13 | Viewed by 5039
Abstract
Cardiac arrhythmias are serious, life-threatening diseases associated with the dysregulation of Ca2+ influx into the cytoplasm of cardiomyocytes. This dysregulation often arises from dysfunction of ryanodine receptor 2 (RyR2), the principal Ca2+ release channel. Dysfunction of RyR1, the skeletal [...] Read more.
Cardiac arrhythmias are serious, life-threatening diseases associated with the dysregulation of Ca2+ influx into the cytoplasm of cardiomyocytes. This dysregulation often arises from dysfunction of ryanodine receptor 2 (RyR2), the principal Ca2+ release channel. Dysfunction of RyR1, the skeletal muscle isoform, also results in less severe, but also potentially life-threatening syndromes. The RYR2 and RYR1 genes have been found to harbor three main mutation “hot spots”, where mutations change the channel structure, its interdomain interface properties, its interactions with its binding partners, or its dynamics. In all cases, the result is a defective release of Ca2+ ions from the sarcoplasmic reticulum into the myocyte cytoplasm. Here, we provide an overview of the most frequent diseases resulting from mutations to RyR1 and RyR2, briefly review some of the recent experimental structural work on these two molecules, detail some of the computational work describing their dynamics, and summarize the known changes to the structure and function of these receptors with particular emphasis on their N-terminal, central, and channel domains. Full article
(This article belongs to the Special Issue Integration between Computational and Experimental Biophysical Techniques in the Study of Biologically Relevant Systems)
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