scholarly journals Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion

2017 ◽  
Vol 114 (42) ◽  
pp. 11157-11162 ◽  
Author(s):  
Alexandra C. Walls ◽  
M. Alejandra Tortorici ◽  
Joost Snijder ◽  
Xiaoli Xiong ◽  
Berend-Jan Bosch ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Energy Landscape ◽  
Limited Proteolysis ◽  
Subunit Vaccines ◽  
Virus Family ◽  
The Past ◽  
Structural Framework ◽  
Molecular Events ◽  
Evolutionary Relatedness

The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. The coronavirus spike (S) glycoprotein initiates infection by promoting fusion of the viral and cellular membranes through conformational changes that remain largely uncharacterized. Here we report the cryoEM structure of a coronavirus S glycoprotein in the postfusion state, showing large-scale secondary, tertiary, and quaternary rearrangements compared with the prefusion trimer and rationalizing the free-energy landscape of this conformational machine. We also biochemically characterized the molecular events associated with refolding of the metastable prefusion S glycoprotein to the postfusion conformation using limited proteolysis, mass spectrometry, and single-particle EM. The observed similarity between postfusion coronavirus S and paramyxovirus F structures demonstrates that a conserved refolding trajectory mediates entry of these viruses and supports the evolutionary relatedness of their fusion subunits. Finally, our data provide a structural framework for understanding the mode of neutralization of antibodies targeting the fusion machinery and for engineering next-generation subunit vaccines or inhibitors against this medically important virus family.

scholarly journals Metastable Intermediates as Stepping Stones on the Maturation Pathways of Viral Capsids

mBio ◽  
2014 ◽  
Vol 5 (6) ◽  
Author(s):  
Giovanni Cardone ◽  
Robert L. Duda ◽  
Naiqian Cheng ◽  
Lili You ◽  
James F. Conway ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Structural Changes ◽  
Energy Landscape ◽  
Potential Hazard ◽  
Stepping Stones ◽  
Scanning Calorimetry ◽  
Conformational Effects ◽  
Capsid Maturation ◽  
Capsid Integrity

ABSTRACT As they mature, many capsids undergo massive conformational changes that transform their stability, reactivity, and capacity for DNA. In some cases, maturation proceeds via one or more intermediate states. These structures represent local minima in a rich energy landscape that combines contributions from subunit folding, association of subunits into capsomers, and intercapsomer interactions. We have used scanning calorimetry and cryo-electron microscopy to explore the range of capsid conformations accessible to bacteriophage HK97. To separate conformational effects from those associated with covalent cross-linking (a stabilization mechanism of HK97), a cross-link-incompetent mutant was used. The mature capsid Head I undergoes an endothermic phase transition at 60°C in which it shrinks by 7%, primarily through changes in its hexamer conformation. The transition is reversible, with a half-life of ~3 min; however, >50% of reverted capsids are severely distorted or ruptured. This observation implies that such damage is a potential hazard of large-scale structural changes such as those involved in maturation. Assuming that the risk is lower for smaller changes, this suggests a rationalization for the existence of metastable intermediates: that they serve as stepping stones that preserve capsid integrity as it switches between the radically different conformations of its precursor and mature states. IMPORTANCE Large-scale conformational changes are widespread in virus maturation and infection processes. These changes are accompanied by the release of conformational free energy as the virion (or fusogenic glycoprotein) switches from a precursor state to its mature state. Each state corresponds to a local minimum in an energy landscape. The conformational changes in capsid maturation are so radical that the question arises of how maturing capsids avoid being torn apart. Offering proof of principle, severe damage is inflicted when a bacteriophage HK97 capsid reverts from the (nonphysiological) state that it enters when heated past 60°C. We suggest that capsid proteins have been selected in part by the criterion of being able to avoid sustaining collateral damage as they mature. One way of achieving this—as with the HK97 capsid—involves breaking the overall transition down into several smaller steps in which the risk of damage is reduced.

scholarly journals Molecular Mechanisms of Merkel Cell Polyomavirus Transformation and Replication

2020 ◽  
Vol 7 (1) ◽  
pp. 289-307 ◽  
Author(s):  
Wei Liu ◽  
Jianxin You
Keyword(s):  
Molecular Mechanisms ◽  
Human Tumor ◽  
Merkel Cell Polyomavirus ◽  
Merkel Cell ◽  
Virus Family ◽  
The Past ◽  
Molecular Events ◽  
Cellular Tropism ◽  
Novel Virus

Viral infection underlies a significant share of the global cancer burden. Merkel cell polyomavirus (MCPyV) is the newest member of the human oncogenic virus family. Its discovery over a decade ago marked the beginning of an exciting era in human tumor virology. Since then, significant evidence has emerged to support the etiologic role of MCPyV in Merkel cell carcinoma (MCC), an extremely lethal form of skin cancer. MCPyV infection is widespread in the general population. MCC diagnoses have tripled over the past 20 years, but effective treatments are currently lacking. In this review, we highlight recent discoveries that have shaped our understanding of MCPyV oncogenic mechanism and host cellular tropism, as well as the molecular events occurring in the viral infectious life cycle. These insights will guide future efforts in developing novel virus-targeted therapeutic strategies for treating the devastating human cancers associated with this new tumorigenic virus.

scholarly journals Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling

2020 ◽  
Author(s):  
Samuel Lotz ◽  
Alex Dickson
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Modular Design ◽  
Software Tool ◽  
Software Framework ◽  
Simulation Framework ◽  
Domain Experts ◽  
Full Support ◽  
Molecular Events ◽  
Python Package

This paper describes the software tool "wepy", an implementation of the weighted ensemble algorithm in python. Wepy was designed to be a flexible simulation framework for rare or long-timescale molecular events, such as protein (un)folding, ligand (un)binding, and large-scale conformational changes or rearrangements. It is implemented as a pure python package, which works well with the OpenMM python library and can easily leverage other python tools for that are useful for molecular simulation and analysis such as mdtraj, scikit-learn, numpy and scipy. It has full support for high-dimensional adaptive resampling algorithms (WExplore and REVO) and provides a framework to easily facilitate the development of new resampling algorithms. Its modular design allows domain experts to write their own analysis functions and progress variables, while taking advantage of a vetted framework for parallel simulation and weighted ensemble resampling.

scholarly journals Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility

2021 ◽  
Vol 118 (30) ◽  
pp. e2100370118
Author(s):  
Lena M. Grass ◽  
Jan Wollenhaupt ◽  
Tatjana Barthel ◽  
Iwan Parfentev ◽  
Henning Urlaub ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Bound States ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Limited Proteolysis ◽  
Rna Helicase ◽  
Crystal Structure Analysis ◽  
Helicase Activity ◽  
Bacterial Survival ◽  
Antibiotics Susceptibility

Many bacteria harbor RNA-dependent nucleoside-triphosphatases of the DEAH/RHA family, whose molecular mechanisms and cellular functions are poorly understood. Here, we show that the Escherichia coli DEAH/RHA protein, HrpA, is an ATP-dependent 3 to 5′ RNA helicase and that the RNA helicase activity of HrpA influences bacterial survival under antibiotics treatment. Limited proteolysis, crystal structure analysis, and functional assays showed that HrpA contains an N-terminal DEAH/RHA helicase cassette preceded by a unique N-terminal domain and followed by a large C-terminal region that modulates the helicase activity. Structures of an expanded HrpA helicase cassette in the apo and RNA-bound states in combination with cross-linking/mass spectrometry revealed ratchet-like domain movements upon RNA engagement, much more pronounced than hitherto observed in related eukaryotic DEAH/RHA enzymes. Structure-based functional analyses delineated transient interdomain contact sites that support substrate loading and unwinding, suggesting that similar conformational changes support RNA translocation. Consistently, modeling studies showed that analogous dynamic intramolecular contacts are not possible in the related but helicase-inactive RNA-dependent nucleoside-triphosphatase, HrpB. Our results indicate that HrpA may be an interesting target to interfere with bacterial tolerance toward certain antibiotics and suggest possible interfering strategies.

scholarly journals Cryo-EM structures reveal a multistep mechanism of Hsp90 activation by co-chaperone Aha1

2020 ◽  
Author(s):  
Yanxin Liu ◽  
Ming Sun ◽  
Alexander G. Myasnikov ◽  
Daniel Elnatan ◽  
Nicolas Delaeter ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Atp Hydrolysis ◽  
Activation Mechanism ◽  
Client Protein ◽  
Protein Maturation ◽  
Structural Framework ◽  
Cryo Electron Microscopy ◽  
Client Proteins ◽  
Rate Limiting

AbstractHsp90 is a ubiquitous molecular chaperone that facilitates the folding and maturation of hundreds of cellular “client” proteins. The ATP-driven client maturation process is regulated by a large number of co-chaperones. Among them, Aha1 is the most potent activator of Hsp90 ATPase activity and thus dramatically affects Hsp90’s client proteins. To understand the Aha1 activation mechanism, we determined full-length Hsp90:Aha1 structures in six different states by cryo-electron microscopy, including nucleotide-free semi-closed, nucleotide-bound pre-hydrolysis, and semi-hydrolyzed states. Our structures demonstrate that the two Aha1 domains can each interact with Hsp90 in two different modes, uncovering a complex multistep activation mechanism. The results show that Aha1 accelerates the chemical step of ATP hydrolysis like a conventional enzyme, but most unusually, catalyzes the rate-limiting large-scale conformational changes of Hsp90 fundamentally required for ATP hydrolysis. Our work provides a structural framework to guide small molecule development targeting this critical modulator of client protein maturation.

Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions

2016 ◽  
Vol 18 (42) ◽  
pp. 29170-29182 ◽  
Author(s):  
Qiang Shao
Keyword(s):  
Configuration Space ◽  
Conformational Changes ◽  
In Silico ◽  
Quantitative Data ◽  
Large Scale ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Conformational Transitions ◽  
Conformational Sampling

A novel in silico approach (NMA–ITS) is introduced to rapidly and effectively sample the configuration space and give quantitative data for exploring the conformational changes of proteins.

Physics of Biomolecular Recognition and Conformational Dynamics

2021 ◽  
Author(s):  
Wen-Ting Chu ◽  
Zhiqiang Yan ◽  
Xiakun Chu ◽  
Xiliang Zheng ◽  
Zuojia Liu ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Conformational Changes ◽  
Large Scale ◽  
Energy Landscape ◽  
Conformational Dynamics ◽  
Experimental Investigations ◽  
Biomolecular Recognition ◽  
Energy Landscape Theory ◽  
Landscape Theory ◽  
Underlying Mechanisms

Abstract Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to affinity, specificity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic specificity based on the underlying energy landscape theory provides a practical way to quantify the specificity. Optimization of affinity and specificity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying flexible binding or binding-folding mechanisms. In this review, we first introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) specificity quantification of molecular recognition; (2) evolution and design in molecular recognition; (3) flexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.

scholarly journals Using DelPhi Capabilities to Mimic Protein’s Conformational Reorganization with Amino Acid Specific Dielectric Constants

2013 ◽  
Vol 13 (1) ◽  
pp. 13-30 ◽  
Author(s):  
Lin Wang ◽  
Zhe Zhang ◽  
Walter Rocchia ◽  
Emil Alexov
Keyword(s):  
Dielectric Constant ◽  
Amino Acid ◽  
Conformational Changes ◽  
Large Scale ◽  
Computing Time ◽  
Point Of View ◽  
Dielectric Constants ◽  
Folding Energy ◽  
Molecular Events ◽  
Internal Dielectric Constant

AbstractMany molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to be considered mostly electrostatics in origin and to be calculated with DelPhi assigning residue-specific value of the internal dielectric constant of protein. The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations. The best fit between experimental values and predicted changes is used to find out the effective value of the internal dielectric constant for each type of amino acid. The predicted folding free energy changes with the optimal, amino acid specific, dielectric constants are within RMSD=0.86 kcal/mol from experimentally measured changes.

scholarly journals Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling

2020 ◽  
Author(s):  
Samuel Lotz ◽  
Alex Dickson
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Modular Design ◽  
Software Tool ◽  
Software Framework ◽  
Simulation Framework ◽  
Domain Experts ◽  
Full Support ◽  
Molecular Events ◽  
Python Package

This paper describes the software tool "wepy", an implementation of the weighted ensemble algorithm in python. Wepy was designed to be a flexible simulation framework for rare or long-timescale molecular events, such as protein (un)folding, ligand (un)binding, and large-scale conformational changes or rearrangements. It is implemented as a pure python package, which works well with the OpenMM python library and can easily leverage other python tools for that are useful for molecular simulation and analysis such as mdtraj, scikit-learn, numpy and scipy. It has full support for high-dimensional adaptive resampling algorithms (WExplore and REVO) and provides a framework to easily facilitate the development of new resampling algorithms. Its modular design allows domain experts to write their own analysis functions and progress variables, while taking advantage of a vetted framework for parallel simulation and weighted ensemble resampling.

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