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Biomedicines
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Conformational Dynamics of Viral Proteins
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Conformational Dynamics of Viral Proteins

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Cell Biology and Pathology".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 20588

Special Issue Editor

Prof. Dr. Paul Rösch

E-Mail Website
Guest Editor
Forschungszentrum für Bio-Makromoleküle (FZ BIOmac), University of Bayreuth, Bayreuth, Germany
Interests: NMR-spectroscopy; protein structures; viral proteins; bacterial proteins; transcription; translation; allergens; nuclear magnetic resonance; crystallography; electron microscopy; fluorescence spectroscopy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viral proteins are proteins that are encoded in the genome of viruses. Understanding the conformation and dynamics of viral proteins that contribute to receptor-mediated virus cell entry and virus replication is of vital interest to the development of mRNA-based vaccines and antiviral drugs. In recent years, a host of information on these proteins became available through biophysical techniques, such as electron microscopy, X-ray crystallography, and NMR spectroscopy, as well as computational approaches involving molecular dynamics calculations and protein-docking procedures.

This Special Issue of Biomedicines focuses on advanced studies of conformational dynamics of nonstructural viral proteins, in particular those that are involved in molecular interactions, leading to cell entry and the replication of RNA and DNA viruses. The goal is to stimulate basic and applied research in this exciting field with the hope of developing strategies for the prevention of virus-mediated diseases, improve treatment outcomes, and eventually cure infected patients or at least help their recovery.

Prof. Dr. Paul Rösch
Guest Editor

Manuscript Submission Information

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Keywords

  • spike protein
  • polymerase
  • reverse transcriptase
  • integrase
  • corona
  • flu
  • HIV

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Published Papers (5 papers)

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Research

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18 pages, 2813 KiB  
Article
The Importance of Lipid Conjugation on Anti-Fusion Peptides against Nipah Virus
by Marta C. Marques, Diana Lousa, Patrícia M. Silva, André F. Faustino, Cláudio M. Soares and Nuno C. Santos
Biomedicines 2022, 10(3), 703; https://doi.org/10.3390/biomedicines10030703 - 18 Mar 2022
Cited by 2 | Viewed by 2639
Abstract
Nipah virus (NiV) is a recently emerging zoonotic virus that belongs to the Paramyxoviridae family and the Henipavirus genus. It causes a range of conditions, from asymptomatic infection to acute respiratory illness and fatal encephalitis. The high mortality rate of 40 to 90% [...] Read more.
Nipah virus (NiV) is a recently emerging zoonotic virus that belongs to the Paramyxoviridae family and the Henipavirus genus. It causes a range of conditions, from asymptomatic infection to acute respiratory illness and fatal encephalitis. The high mortality rate of 40 to 90% ranks these viruses among the deadliest viruses known to infect humans. Currently, there is no antiviral drug available for Nipah virus disease and treatment is only supportive. Thus, there is an urgent demand for efficient antiviral therapies. NiV F protein, which catalyzes fusion between the viral and host membranes, is a potential target for antiviral drugs, as it is a key protein in the initial stages of infection. Fusion inhibitor peptides derived from the HRC-domain of the F protein are known to bind to their complementary domain in the protein’s transient intermediate state, preventing the formation of a six-helix bundle (6HB) thought to be responsible for driving the fusion of the viral and cell membranes. Here, we evaluated the biophysical and structural properties of four different C-terminal lipid-tagged peptides. Different compositions of the lipid tags were tested to search for properties that might promote efficacy and broad-spectrum activity. Fluorescence spectroscopy was used to study the interaction of the peptides with biomembrane model systems and human blood cells. In order to understand the structural properties of the peptides, circular dichroism measurements and molecular dynamics simulations were performed. Our results indicate a peptide preference for cholesterol-enriched membranes and a lipid conjugation-driven stabilization of the peptide α-helical secondary structure. This work may contribute for the development of highly effective viral fusion against NiV inhibitors. Full article
(This article belongs to the Special Issue Conformational Dynamics of Viral Proteins)
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13 pages, 2751 KiB  
Article
Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide
by Eileen Socher, Marcus Conrad, Lukas Heger, Friedrich Paulsen, Heinrich Sticht, Friederike Zunke and Philipp Arnold
Biomedicines 2021, 9(5), 525; https://doi.org/10.3390/biomedicines9050525 - 8 May 2021
Cited by 27 | Viewed by 5104
Abstract
The B.1.1.7 variant of the SARS-CoV-2 virus shows enhanced infectiousness over the wild type virus, leading to increasing patient numbers in affected areas. Amino acid exchanges within the SARS-CoV-2 spike protein variant of B.1.1.7 affect inter-monomeric contact sites within the trimer (A570D and [...] Read more.
The B.1.1.7 variant of the SARS-CoV-2 virus shows enhanced infectiousness over the wild type virus, leading to increasing patient numbers in affected areas. Amino acid exchanges within the SARS-CoV-2 spike protein variant of B.1.1.7 affect inter-monomeric contact sites within the trimer (A570D and D614G) as well as the ACE2-receptor interface region (N501Y), which comprises the receptor-binding domain (RBD) of the spike protein. However, the molecular consequences of mutations within B.1.1.7 on spike protein dynamics and stability or ACE2 binding are largely unknown. Here, molecular dynamics simulations comparing SARS-CoV-2 wild type with the B.1.1.7 variant revealed inter-trimeric contact rearrangements, altering the structural flexibility within the spike protein trimer. Furthermore, we found increased flexibility in direct spatial proximity of the fusion peptide due to salt bridge rearrangements induced by the D614G mutation in B.1.1.7. This study also implies a reduced binding affinity for B.1.1.7 with ACE2, as the N501Y mutation restructures the RBD–ACE2 interface, significantly decreasing the linear interaction energy between the RBD and ACE2. Our results demonstrate how mutations found within B.1.1.7 enlarge the flexibility around the fusion peptide and change the RBD–ACE2 interface. We anticipate our findings to be starting points for in depth biochemical and cell biological analyses of B.1.1.7. Full article
(This article belongs to the Special Issue Conformational Dynamics of Viral Proteins)
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Review

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21 pages, 3612 KiB  
Review
Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory
by Wai-Yim Ching, Puja Adhikari, Bahaa Jawad and Rudolf Podgornik
Biomedicines 2023, 11(2), 517; https://doi.org/10.3390/biomedicines11020517 - 10 Feb 2023
Cited by 4 | Viewed by 2069
Abstract
The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the [...] Read more.
The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid–amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems. Full article
(This article belongs to the Special Issue Conformational Dynamics of Viral Proteins)
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45 pages, 6964 KiB  
Review
The Hepatitis B Virus Nucleocapsid—Dynamic Compartment for Infectious Virus Production and New Antiviral Target
by Matthias Niklasch, Peter Zimmermann and Michael Nassal
Biomedicines 2021, 9(11), 1577; https://doi.org/10.3390/biomedicines9111577 - 29 Oct 2021
Cited by 27 | Viewed by 5912
Abstract
Hepatitis B virus (HBV) is a small enveloped DNA virus which replicates its tiny 3.2 kb genome by reverse transcription inside an icosahedral nucleocapsid, formed by a single ~180 amino acid capsid, or core, protein (Cp). HBV causes chronic hepatitis B (CHB), a [...] Read more.
Hepatitis B virus (HBV) is a small enveloped DNA virus which replicates its tiny 3.2 kb genome by reverse transcription inside an icosahedral nucleocapsid, formed by a single ~180 amino acid capsid, or core, protein (Cp). HBV causes chronic hepatitis B (CHB), a severe liver disease responsible for nearly a million deaths each year. Most of HBV’s only seven primary gene products are multifunctional. Though less obvious than for the multi-domain polymerase, P protein, this is equally crucial for Cp with its multiple roles in the viral life-cycle. Cp provides a stable genome container during extracellular phases, allows for directed intracellular genome transport and timely release from the capsid, and subsequent assembly of new nucleocapsids around P protein and the pregenomic (pg) RNA, forming a distinct compartment for reverse transcription. These opposing features are enabled by dynamic post-transcriptional modifications of Cp which result in dynamic structural alterations. Their perturbation by capsid assembly modulators (CAMs) is a promising new antiviral concept. CAMs inappropriately accelerate assembly and/or distort the capsid shell. We summarize the functional, biochemical, and structural dynamics of Cp, and discuss the therapeutic potential of CAMs based on clinical data. Presently, CAMs appear as a valuable addition but not a substitute for existing therapies. However, as part of rational combination therapies CAMs may bring the ambitious goal of a cure for CHB closer to reality. Full article
(This article belongs to the Special Issue Conformational Dynamics of Viral Proteins)
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16 pages, 2236 KiB  
Review
Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design
by Qingxin Li and Congbao Kang
Biomedicines 2021, 9(8), 1044; https://doi.org/10.3390/biomedicines9081044 - 19 Aug 2021
Cited by 10 | Viewed by 3687
Abstract
Zika virus (ZIKV)—a member of the Flaviviridae family—is an important human pathogen. Its genome encodes a polyprotein that can be further processed into structural and non-structural proteins. ZIKV protease is an important target for antiviral development due to its role in cleaving the [...] Read more.
Zika virus (ZIKV)—a member of the Flaviviridae family—is an important human pathogen. Its genome encodes a polyprotein that can be further processed into structural and non-structural proteins. ZIKV protease is an important target for antiviral development due to its role in cleaving the polyprotein to release functional viral proteins. The viral protease is a two-component protein complex formed by NS2B and NS3. Structural studies using different approaches demonstrate that conformational changes exist in the protease. The structures and dynamics of this protease in the absence and presence of inhibitors were explored to provide insights into the inhibitor design. The dynamic nature of residues binding to the enzyme cleavage site might be important for the function of the protease. Due to the charges at the protease cleavage site, it is challenging to develop small-molecule compounds acting as substrate competitors. Developing small-molecule compounds to inhibit protease activity through an allosteric mechanism is a feasible strategy because conformational changes are observed in the protease. Herein, structures and dynamics of ZIKV protease are summarized. The conformational changes of ZIKV protease and other proteases in the same family are discussed. The progress in developing allosteric inhibitors is also described. Understanding the structures and dynamics of the proteases are important for designing potent inhibitors. Full article
(This article belongs to the Special Issue Conformational Dynamics of Viral Proteins)
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