All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery

The hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130, represent an important antiviral paradigm based on disrupting the timing of genome packaging. Here, all-atom molecular dynamics simulations of an intact AT130-bound HBV capsid reveal that the compound increases spike flexibility and improves recovery of helical secondary structure in the spike tips. Regions of the capsid-incorporated dimer that undergo correlated motion correspond to established sub-domains that pivot around the central chassis. AT130 alters patterns of correlated motion and other essential dynamics. A new conformational state of the dimer is identified, which can lead to dramatic opening of the intradimer interface and disruption of communication within the spike tip. A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these sub-domains. Altogether, results describe a dynamical connection between the intra- and interdimer interfaces and enable mapping of allostery traversing the entire core protein dimer.

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All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery

10.1101/2021.02.08.430329 ◽

2021 ◽

Author(s):

Carolina Pérez Segura ◽

Boon Chong Goh ◽

Jodi A. Hadden-Perilla

Keyword(s):

Small Molecules ◽

Drug Target ◽

Structural Changes ◽

Salt Bridge ◽

Md Simulations ◽

Health Concern ◽

Protein Dimer ◽

B Virus ◽

Flexible Protein ◽

Dynamics Simulations

AbstractThe hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130, represent an important anti-viral paradigm based on disrupting the timing of genome encapsulation. Crystallographic studies of AT130-bound complexes have been essential in explaining the effects of the small molecule on HBV capsid structure; however, computational examination reveals that key changes attributed to AT130 were erroneous, likely a consequence of interpreting poor resolution arising from a highly flexible protein. Here, all-atom molecular dynamics simulations of an intact AT130-bound HBV capsid reveal that, rather than damaging spike helicity, AT130 enhances the capsid’s ability to recover it. A new conformational state is identified, which can lead to dramatic opening of the intradimer interface and disruption of communication within the spike tip. A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these domains. Combined with dynamical network analysis, results describe a connection between the intra- and interdimer interfaces and enable mapping of allostery traversing the entire capsid protein dimer.

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Dynamics of the ACE2 - SARS-CoV/SARS-CoV-2 spike protein interface reveal unique mechanisms

10.1101/2020.06.10.143990 ◽

2020 ◽

Author(s):

Amanat Ali ◽

Ranjit Vijayan

Keyword(s):

Salt Bridge ◽

Spike Protein ◽

Health Concern ◽

Treatment Modalities ◽

Receptor Binding Domain ◽

Public Health Concern ◽

Angiotensin Converting Enzyme 2 ◽

Dynamics Simulations ◽

And Function ◽

Host Target

AbstractThe coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major public health concern. A handful of static structures now provide molecular insights into how SARS-CoV-2 and SARS-CoV interact with its host target, which is the angiotensin converting enzyme 2 (ACE2). Molecular recognition, binding and function are dynamic processes. To evaluate this, multiple all atom molecular dynamics simulations of at least 500 ns each were performed to better understand the structural stability and interfacial interactions between the receptor binding domain of the spike protein of SARS-CoV-2 and SARS-CoV bound to ACE2. Several contacts were observed to form, break and reform in the interface during the simulations. Our results indicate that SARS-CoV and SARS-CoV-2 utilizes unique strategies to achieve stable binding to ACE2. Several differences were observed between the residues of SARS-CoV-2 and SARS-CoV that consistently interacted with ACE2. Notably, a stable salt bridge between Lys417 of SARS-CoV-2 spike protein and Asp30 of ACE2 as well as three stable hydrogen bonds between Tyr449, Gln493, and Gln498 of SARS-CoV-2 and Asp38, Glu35, and Lys353 of ACE2 were observed, which were absent in the SARS-CoV-ACE2 interface. Some previously reported residues, which were suggested to enhance the binding affinity of SARS-CoV-2, were not observed to form stable interactions in these simulations. Stable binding to the host receptor is crucial for virus entry. Therefore, special consideration should be given to these stable interactions while designing potential drugs and treatment modalities to target or disrupt this interface.

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Hepatitis B virus capsid particles are assembled from core-protein dimer precursors.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.89.21.10046 ◽

1992 ◽

Vol 89 (21) ◽

pp. 10046-10050 ◽

Cited By ~ 83

Author(s):

S. Zhou ◽

D. N. Standring

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Core Protein ◽

Virus Capsid ◽

Protein Dimer ◽

B Virus

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Hepatitis B virus core protein dimer‑dimer interface is critical for viral replication

Molecular Medicine Reports ◽

10.3892/mmr.2018.9620 ◽

2018 ◽

Cited By ~ 3

Author(s):

Chang‑Long Zheng ◽

Yong‑Mei Fu ◽

Zhan‑Xue Xu ◽

Yong Zou ◽

Kai Deng

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Viral Replication ◽

Core Protein ◽

Dimer Interface ◽

Virus Core ◽

Protein Dimer ◽

B Virus

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Full-Length Hepatitis B Virus Core Protein Packages Viral and Heterologous RNA with Similarly High Levels of Cooperativity

Journal of Virology ◽

10.1128/jvi.00586-10 ◽

2010 ◽

Vol 84 (14) ◽

pp. 7174-7184 ◽

Cited By ~ 94

Author(s):

J. Zachary Porterfield ◽

Mary Savari Dhason ◽

Daniel D. Loeb ◽

Michael Nassal ◽

Stephen J. Stray ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Rna Binding ◽

Core Protein ◽

Viral Polymerase ◽

Critical Feature ◽

Protein Dimer ◽

B Virus

ABSTRACT A critical feature of a viral life cycle is the ability to selectively package the viral genome. In vivo, phosphorylated hepatitis B virus (HBV) core protein specifically encapsidates a complex of pregenomic RNA (pgRNA) and viral polymerase; it has been suggested that packaging is specific for the complex. Here, we test the hypothesis that core protein has intrinsic specificity for pgRNA, independent of the polymerase. For these studies, we also evaluated the effect of core protein phosphorylation on assembly and RNA binding, using phosphorylated core protein and a phosphorylation mimic in which S155, S162, and S170 were mutated to glutamic acid. We have developed an in vitro system where capsids are disassembled and assembly-active core protein dimer is purified. With this protein, we have reassembled empty capsids and RNA-filled capsids. We found that core protein dimer bound and encapsidated both the HBV pregenomic RNA and heterologous RNA with high levels of cooperativity, irrespective of phosphorylation. In direct competition assays, no specificity for pregenomic RNA was observed. This suggests that another factor, such as the viral polymerase, is required for specific packaging. These results also beg the question of what prevents HBV core protein from assembling on nonviral RNA, preserving the protein for virus production.

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Variance of Atomic Coordinates as a Dynamical Metric to Distinguish Proteins and Protein-Protein Interactions in Molecular Dynamics Simulations

10.26434/chemrxiv.11684367 ◽

2020 ◽

Author(s):

Sanjoy Paul ◽

Sri Rama Koti Ainavarapu ◽

Ravindra Venkatramani

Keyword(s):

Protein Interactions ◽

Structural Changes ◽

Md Simulations ◽

Comparative Assessment ◽

Protein Protein Interactions ◽

Multiple Protein ◽

Functional Consequences ◽

Global Equilibrium ◽

Dynamics Simulations ◽

Atomic Coordinates

In this manuscript, we introduce the Cumulative Variance of Coordinate Fluctuations (CVCF) along atomistic MD trajectories, as a dynamical metric to examine protein dynamics and sampling convergence in MD simulations. Using model 1D and 2D PES, we first show that CVCF, which traces over the fluctuations of protein atoms as a function of sampling coordinate (time in MD simulations), captures both local and global equilibria to distinguish the underlying PES of proteins. For both model PES and protein trajectories, we compare the information content present in CVCF traces with that obtained using other measures proposed in literature to reveal conditions under which a consistent interpretation of data can be obtained. Importantly, we show that independent of convergence to either local or global equilibrium, the values and features of protein CVCF can provide a comparative assessment of the ruggedness and curvature of the underlying PES sampled by proteins along MD trajectories. Trends in CVCF therefore enable us to compare features of the PES across multiple protein systems using MD simulations. We demonstrate some of the attractive features of a CVCF based analysis on multi-microsecond (ms) MD trajectories of structurally homologous ubiquitin family proteins which present a particularly striking example in nature wherein sequence changes and complexation which do not lead to prominent structural changes bring about dramatic functional consequences.

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Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.807577 ◽

2022 ◽

Vol 8 ◽

Author(s):

Alexander A. Malär ◽

Morgane Callon ◽

Albert A. Smith ◽

Shishan Wang ◽

Lauriane Lecoq ◽

...

Keyword(s):

Hepatitis B Virus ◽

Solid State ◽

Hepatitis B ◽

Solid State Nmr ◽

Md Simulation ◽

Core Protein ◽

Relaxation Times ◽

Md Simulations ◽

Blind Spot ◽

B Virus

Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from 240 copies of the Cp149 core protein. We measure both T1 and T1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.

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Molecular Dynamics Simulations of Dislocations in TlBr Crystals under an Electrical Field

MRS Advances ◽

10.1557/adv.2016.506 ◽

2016 ◽

Vol 1 (35) ◽

pp. 2459-2464 ◽

Cited By ~ 3

Author(s):

X. W. Zhou ◽

M. E. Foster ◽

P. Yang ◽

F. P. Doty

Keyword(s):

Molecular Dynamics ◽

Structural Changes ◽

Vacancy Concentration ◽

Radiation Detection ◽

Md Simulations ◽

Electrical Field ◽

Electrical Fields ◽

Charge Model ◽

Aging Mechanisms ◽

Dynamics Simulations

ABSTRACTTlBr crystals have superior radiation detection properties; however, their properties degrade in the range of hours to weeks when an operating electrical field is applied. To account for this rapid degradation using the widely-accepted vacancy migration mechanism, the vacancy concentration must be orders of magnitude higher than any conventional estimates. The present work has incorporated a new analytical variable charge model in molecular dynamics (MD) simulations to examine the structural changes of materials under electrical fields. Our simulations indicate that dislocations in TlBr move under electrical fields. This discovery can lead to new understanding of TlBr aging mechanisms under external fields.

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Understanding SARS-CoV-2 budding through molecular dynamics simulations of M and E protein complexes

10.1101/2021.07.26.453874 ◽

2021 ◽

Author(s):

Logan Thrasher Collins ◽

Tamer Elkholy ◽

Shafat Mubin ◽

Ricky Williams ◽

Kayode Ezike ◽

...

Keyword(s):

Molecular Dynamics ◽

Protein Complexes ◽

Md Simulations ◽

Membrane Curvature ◽

M Protein ◽

E Proteins ◽

E Protein ◽

Protein Dimers ◽

Protein Dimer ◽

Dynamics Simulations

SARS-CoV-2 and other coronaviruses pose a major threat to global health, yet treatment efforts have largely ignored the process of envelope assembly, a key part of the coronaviral life cycle. When expressed together, the M and E proteins are sufficient to facilitate coronavirus envelope assembly. Envelope assembly leads to budding of coronavirus particles into the ER-Golgi intermediate compartment (ERGIC) and subsequent maturation of the virus, yet the mechanisms behind the budding process remain poorly understood. Better understanding of budding may enable new types of antiviral therapies. To this end, we ran atomistic molecular dynamics (MD) simulations of SARS-CoV-2 envelope assembly using the Feig laboratory's refined structural models of the M protein dimer and E protein pentamer. Our MD simulations consisted of M protein dimers and E protein pentamers in patches of virtual ERGIC membrane. By examining how these proteins induce membrane curvature in silico, we have obtained insights around how the budding process may occur. In our simulations, M protein dimers acted cooperatively to induce membrane curvature. By contrast, E protein pentamers kept the membrane planar. These results could help guide the development of novel antiviral therapeutics which inhibit coronavirus budding.

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