A Designed Conformational Shift To Control Protein Binding Specificity

Michielssens, Servaas; Peters, Jan Henning; Ban, David; Pratihar, Supriya; Seeliger, Daniel; Sharma, Monika; Giller, Karin; Sabo, T. Michael; Becker, Stefan; Lee, Dong Hoon; Griesinger, Christian; Groot, Bert L. de

doi:10.1002/anie.201403102

Cited by 46 publications

(47 citation statements)

References 21 publications

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“…We propose that the conformational landscape of the B domains in the context of the SARS-CoV S trimer, sampling open and closed conformations, decreases the apparent binding affinity for ACE2 and S230 due to masking of their binding sites in the closed state. A similar effect has previously been described for ubiquitin (Michielssens et al, 2014). The higher binding affinity of S230 for SARS-CoV S, compared to ACE2 ( Figure S7 Refolding to the postfusion conformation was detected by the appearance of a proteinase-Kresistant band migrating at approximately 55 kDa (Matsuyama and Taguchi, 2009).…”

Section: Activation Mechanism Of Coronavirus Membrane Fusionsupporting

confidence: 80%

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

Walls

Xiong

Park

et al. 2019

Cell

630

800

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Graphical Abstract Highlights d MERS-CoV/SARS-CoV S composite glycan shields analyzed by cryo-EM and mass spectrometry d Structures of MERS-CoV/SARS-CoV S with neutralizing antibodies from survivors d LCA60 inhibits receptor binding by interacting with MERS-CoV S protein/glycans d S230 blocks receptor binding and triggers fusogenic rearrangements via functional mimicry In Brief Structural analysis of the SARS-CoV S and MERS-CoV S glycoproteins in complex with neutralizing antibodies from human survivors sheds light into the mechanisms of membrane fusion and neutralization Walls et al., SUMMARYRecent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies. To understand the humoral immune response elicited upon natural infections with coronaviruses, we structurally characterized the SARS-CoV and MERS-CoV S glycoproteins in complex with neutralizing antibodies isolated from human survivors. Although the two antibodies studied blocked attachment to the host cell receptor, only the anti-SARS-CoV S antibody triggered fusogenic conformational changes via receptor functional mimicry. These results provide a structural framework for understanding coronavirus neutralization by human antibodies and shed light on activation of coronavirus membrane fusion, which takes place through a receptor-driven ratcheting mechanism.

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Section: Activation Mechanism Of Coronavirus Membrane Fusionsupporting

confidence: 80%

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

Walls

Xiong

Park

et al. 2019

Cell

630

800

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“…In recent years, the binding of ubiquitin to its various protein binding partners has become a key model system for investigations of conformational selection versus induced fit in protein/protein interactions (Bezsonova et al, 2008; Fenwick et al, 2011; Korzhnev et al, 2009; Lange et al, 2008; Michielssens et al, 2014; Phillips et al, 2013). While both mechanisms have been reported, some of the studies have been controversial and uncertainty persists in the field (Lange et al, 2008; Michielssens et al, 2014; Phillips et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…While both mechanisms have been reported, some of the studies have been controversial and uncertainty persists in the field (Lange et al, 2008; Michielssens et al, 2014; Phillips et al, 2013). We briefly discuss below results with ubiquitin to highlight similarities and differences with the experimental approach presented here for recoverin.…”

Section: Discussionmentioning

confidence: 99%

“…Follow-up papers have shown that the conformational ensemble calculated from NMR RDCs overestimated the amplitude of motions (Fenwick et al, 2011; Grishaev et al, 2010; Maltsev et al, 2014), calling the interpretation of the results into question. Subsequent studies employed computationally designed mutant proteins, changing the population of the binding-competent state of ubiquitin for its partner dsk2 and measuring differences in overall K D values (Michielssens et al, 2014). This is an interesting approach, and experimental measurements of population and flux showing actual differences between wild-type and mutant proteins could indeed address directly the question of CS versus IF for ubiquitin in the future.…”

Section: Discussionmentioning

confidence: 99%

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Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis

et al. 2016

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SUMMARY Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsin kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Protein dynamics in free recoverin limits the overall rate of binding.

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“…Later, de Groot and coworkers used a similar approach to shift the conformational equilibrium of ubiquitin 148 . Ubiquitin populates both an open and closed state and dynamically fluctuates between the two via a pincer-like motion.…”

Section: Engineering Functional Regions Into Proteinsmentioning

confidence: 99%

Insights from molecular dynamics simulations for computational protein design

Childers

Daggett

2017

Mol. Syst. Des. Eng.

167

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A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

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A Designed Conformational Shift To Control Protein Binding Specificity

Cited by 46 publications

References 21 publications

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis

Insights from molecular dynamics simulations for computational protein design

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