SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 5 million people and is causing a devastating social and economic impact all over the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss vaccine and natural immunity, and increased transmissibility. All circulating VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). In an attempt to understand the effect of RBD mutations in circulating VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis is limited, since it ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some VOCs mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of three circulating VOCs (alpha, beta, and delta). Our results show that in solution, wt RBD presents two distinct conformations: an open conformation where it is free to bind ACE2; and a closed conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants significantly impact the open/closed equilibrium, shifting it towards the open conformation by roughly 20%. This shift likely increases ACE2 binding affinity. Simulations of the currently predominant delta variant RBD were extreme in this regard, in that a closed conformation was never observed. Instead, the system alternated between the before mentioned open conformation and an alternative reversed one, with a significantly changed orientation of the RBM ridge flanking the RBD. This alternate conformation could potentially provide a fitness advantage not only due to increased availability for ACE2 binding, but also by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the delta variant, impact RBD conformational dynamics in a direction that simultaneously promotes efficient binding to ACE2 and antibody escape.

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Dynamic Preference for NADP/H Cofactor Binding/Release in E. coli YqhD Oxidoreductase

Molecules ◽

10.3390/molecules26020270 ◽

2021 ◽

Vol 26 (2) ◽

pp. 270

Author(s):

Rajni Verma ◽

Jonathan M. Ellis ◽

Katie R. Mitchell-Koch

Keyword(s):

Reductase Activity ◽

Conformational Dynamics ◽

Structural Data ◽

Md Simulations ◽

Oxidation States ◽

Data Simulation ◽

E Coli ◽

Cofactor Binding ◽

Open Conformation ◽

Binding Cleft

YqhD, an E. coli alcohol/aldehyde oxidoreductase, is an enzyme able to produce valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. Herein, we report the first computational solution-phase structure-dynamics analysis of YqhD, shedding light on the effect of oxidized and reduced NADP/H cofactor binding on the conformational dynamics of the biocatalyst using molecular dynamics (MD) simulations. The cofactor oxidation states mainly influence the interdomain cleft region conformations of the YqhD monomers, involved in intricate cofactor binding and release. The ensemble of NADPH-bound monomers has a narrower average interdomain space resulting in more hydrogen bonds and rigid cofactor binding. NADP-bound YqhD fluctuates between open and closed conformations, while it was observed that NADPH-bound YqhD had slower opening/closing dynamics of the cofactor-binding cleft. In the light of enzyme kinetics and structural data, simulation findings have led us to postulate that the frequently sampled open conformation of the cofactor binding cleft with NADP leads to the more facile release of NADP while increased closed conformation sampling during NADPH binding enhances cofactor binding affinity and the aldehyde reductase activity of the enzyme.

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Conformational dynamics of active site loops 5, 6 and 7 of enzyme Triosephosphate Isomerase: A molecular dynamics study

10.1101/459198 ◽

2018 ◽

Author(s):

Sarath Chandra Dantu ◽

Gerrit Groenhof

Keyword(s):

Conformational Changes ◽

Active Site ◽

Triosephosphate Isomerase ◽

Conformational Dynamics ◽

Md Simulations ◽

Glycolytic Enzyme ◽

Dihedral Angles ◽

Dihydroxyacetone Phosphate ◽

Closed Conformation ◽

N Terminus

AbstractTriosephosphate Isomerase is a glycolytic enzyme catalyzing the interconversion of Dihydroxyacetone phosphate to Glyceraldehyde-3-phosphate. The active site is comprised of three distinct loops loop-6, loop-7 and loop-8. Based on loop-6 and loop-7 conformation we describe the enzyme as Open TIM and Closed TIM. Various NMR, X-ray crystallography and QM/MM simulation techniques have provided glimpses of individual events of what is essentially a dynamic process. We studied the conformational changes of two distinct loops (loop-6 and loop-7) enveloping the active site, in the presence of natural substrate, reaction intermediates and inhibitor molecules, by means of microsecond atomistic MD simulations in solution and crystal environment. Our studies have revealed that loop-6 samples open and closed conformations in both apo and holo TIM structures. As seen in solution state NMR experiments, we also observe that loop-6 N-terminus and C-terminus move independently. In our simulations we have also observed that backbone dihedrals of loop-7 residues G210 (G210-phi, G210-psi) and G211 (G211-phi) sample open and closed states in both apo and holo TIM structures. Whereas backbone dihedral angles of G211 (G211-psi) and S212 (S212-phi) adopt closed conformation only when the ligand is bound to the active site. As observed in chain-B of 1R2R crystal structures, we also observe that water molecules can also initiate flip of G211-psi and S212-phi dihedral angles into closed conformation. Except, loop-5, which has a dominant effect on the conformational behaviour of loop-6 N-terminus, we do not observe any influence of either loop-6 or loop-7 on the conformational dynamics of the other.

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Effect of Ionic Strength on the Aggregation Propensity of Aβ1-42 Peptide: An In-silico Study

Current Chemical Biology ◽

10.2174/2212796814999200818103157 ◽

2020 ◽

Vol 14 (3) ◽

pp. 216-226

Author(s):

Priyanka Borah ◽

Venkata S.K. Mattaparthi

Keyword(s):

Diffusion Coefficient ◽

Ionic Strength ◽

Marked Effect ◽

Computational Study ◽

Conformational Dynamics ◽

Rapid Change ◽

Md Simulations ◽

Radius Of Gyration ◽

Aggregation Propensity ◽

In Silico Study

Background: Aggregation of misfolded proteins under stress conditions in the cell might lead to several neurodegenerative disorders. Amyloid-beta (Aβ1-42) peptide, the causative agent of Alzheimer’s disease, has the propensity to fold into β-sheets under stress, forming aggregated amyloid plaques. This is influenced by factors such as pH, temperature, metal ions, mutation of residues, and ionic strength of the solution. There are several studies that have highlighted the importance of ionic strength in affecting the folding and aggregation propensity of Aβ1-42 peptide. Objective: To understand the effect of ionic strength of the solution on the aggregation propensity of Aβ1-42 peptide, using computational approaches. Materials and Methods: In this study, Molecular Dynamics (MD) simulations were performed on Aβ1-42 peptide monomer placed in (i) 0 M, (ii) 0.15 M, and (iii) 0.30 M concentration of NaCl solution. To prepare the input files for the MD simulations, we have used the Amberff99SB force field. The conformational dynamics of Aβ1-42 peptide monomer in different ionic strengths of the solutions were illustrated from the analysis of the corresponding MD trajectory using the CPPtraj tool. Results: From the MD trajectory analysis, we observe that with an increase in the ionic strength of the solution, Aβ1-42 peptide monomer shows a lesser tendency to undergo aggregation. From RMSD and SASA analysis, we noticed that Aβ1-42 peptide monomer undergoes a rapid change in conformation with an increase in the ionic strength of the solution. In addition, from the radius of gyration (Rg) analysis, we observed Aβ1-42 peptide monomer to be more compact at moderate ionic strength of the solution. Aβ1-42 peptide was also found to hold its helical secondary structure at moderate and higher ionic strengths of the solution. The diffusion coefficient of Aβ1-42 peptide monomer was also found to vary with the ionic strength of the solution. We observed a relatively higher diffusion coefficient value for Aβ1-42 peptide at moderate ionic strength of the solution. Conclusion: Our findings from this computational study highlight the marked effect of ionic strength of the solution on the conformational dynamics and aggregation propensity of Aβ1-42 peptide monomer.

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Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation

Communications Biology ◽

10.1038/s42003-021-02132-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Komal Soni ◽

Georg Kempf ◽

Karen Manalastas-Cantos ◽

Astrid Hendricks ◽

Dirk Flemming ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Binding Sites ◽

Signal Recognition Particle ◽

Signal Recognition ◽

Closed Conformation ◽

Open Conformation ◽

Structural Database ◽

Alu Rna ◽

Species Specific ◽

Protozoan Species

AbstractThe eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. The canonical Alu domain consists of the SRP9/14 protein heterodimer and a tRNA-like folded Alu RNA that adopts a strictly ‘closed’ conformation involving a loop-loop pseudoknot. Here, we study the structure of the Alu domain from Plasmodium falciparum (PfAlu), a divergent apicomplexan protozoan that causes human malaria. Using NMR, SAXS and cryo-EM analyses, we show that, in contrast to its prokaryotic and eukaryotic counterparts, the PfAlu domain adopts an ‘open’ Y-shaped conformation. We show that cytoplasmic P. falciparum ribosomes are non-discriminative and recognize both the open PfAlu and closed human Alu domains with nanomolar affinity. In contrast, human ribosomes do not provide high affinity binding sites for either of the Alu domains. Our analyses extend the structural database of Alu domains to the protozoan species and reveal species-specific differences in the recognition of SRP Alu domains by ribosomes.

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Correlation of membrane protein conformational and functional dynamics

Nature Communications ◽

10.1038/s41467-021-24660-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Raghavendar Reddy Sanganna Gari ◽

Joel José Montalvo‐Acosta ◽

George R. Heath ◽

Yining Jiang ◽

Xiaolong Gao ◽

...

Keyword(s):

Membrane Protein ◽

Conformational Changes ◽

Single Channel ◽

Conformational Dynamics ◽

Md Simulations ◽

High Temporal Resolution ◽

Dependent Manner ◽

Functional Dynamics ◽

Ph Dependent ◽

Open States

AbstractConformational changes in ion channels lead to gating of an ion-conductive pore. Ion flux has been measured with high temporal resolution by single-channel electrophysiology for decades. However, correlation between functional and conformational dynamics remained difficult, lacking experimental techniques to monitor sub-millisecond conformational changes. Here, we use the outer membrane protein G (OmpG) as a model system where loop-6 opens and closes the β-barrel pore like a lid in a pH-dependent manner. Functionally, single-channel electrophysiology shows that while closed states are favored at acidic pH and open states are favored at physiological pH, both states coexist and rapidly interchange in all conditions. Using HS-AFM height spectroscopy (HS-AFM-HS), we monitor sub-millisecond loop-6 conformational dynamics, and compare them to the functional dynamics from single-channel recordings, while MD simulations provide atomistic details and energy landscapes of the pH-dependent loop-6 fluctuations. HS-AFM-HS offers new opportunities to analyze conformational dynamics at timescales of domain and loop fluctuations.

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Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex

Scientific Reports ◽

10.1038/s41598-021-82669-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yogeeshwar Ajjugal ◽

Kripi Tomar ◽

D. Krishna Rao ◽

Thenmalarchelvi Rathinavelan

Keyword(s):

Mismatch Repair ◽

Conformational Dynamics ◽

Md Simulations ◽

Umbrella Sampling ◽

Base Flipping ◽

Base Pairs ◽

2D Noesy ◽

Junction Formation ◽

Nmr Techniques ◽

Transient Events

AbstractBase pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti & + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery.

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Tethering-induced destabilization and ATP-binding for tandem RRM domains of ALS-causing TDP-43 and hnRNPA1

Scientific Reports ◽

10.1038/s41598-020-80524-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mei Dang ◽

Yifan Li ◽

Jianxing Song

Keyword(s):

Conformational Dynamics ◽

Md Simulations ◽

Atp Binding ◽

Rna Recognition Motif ◽

Rna Recognition ◽

Nucleic Acid Binding ◽

General Role ◽

Nmr Characterization ◽

Lateral Sclerosis

AbstractTDP-43 and hnRNPA1 contain tandemly-tethered RNA-recognition-motif (RRM) domains, which not only functionally bind an array of nucleic acids, but also participate in aggregation/fibrillation, a pathological hallmark of various human diseases including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), alzheimer's disease (AD) and Multisystem proteinopathy (MSP). Here, by DSF, NMR and MD simulations we systematically characterized stability, ATP-binding and conformational dynamics of TDP-43 and hnRNPA1 RRM domains in both tethered and isolated forms. The results reveal three key findings: (1) upon tethering TDP-43 RRM domains become dramatically coupled and destabilized with Tm reduced to only 49 °C. (2) ATP specifically binds TDP-43 and hnRNPA1 RRM domains, in which ATP occupies the similar pockets within the conserved nucleic-acid-binding surfaces, with the affinity slightly higher to the tethered than isolated forms. (3) MD simulations indicate that the tethered RRM domains of TDP-43 and hnRNPA1 have higher conformational dynamics than the isolated forms. Two RRM domains become coupled as shown by NMR characterization and analysis of inter-domain correlation motions. The study explains the long-standing puzzle that the tethered TDP-43 RRM1–RRM2 is particularly prone to aggregation/fibrillation, and underscores the general role of ATP in inhibiting aggregation/fibrillation of RRM-containing proteins. The results also rationalize the observation that the risk of aggregation-causing diseases increases with aging.

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Crystal structures of an E1–E2–ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification

Nature Communications ◽

10.1038/s41467-021-22598-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Lingmin Yuan ◽

Zongyang Lv ◽

Melanie J. Adams ◽

Shaun K. Olsen

Keyword(s):

Complex Formation ◽

Crystal Structures ◽

Molecular Mechanisms ◽

Conformational State ◽

Biochemical Data ◽

Conformational States ◽

Product Release ◽

Closed Conformation ◽

Open Conformation ◽

Conjugating Enzymes

AbstractE1 enzymes function as gatekeepers of ubiquitin (Ub) signaling by catalyzing activation and transfer of Ub to tens of cognate E2 conjugating enzymes in a process called E1–E2 transthioesterification. The molecular mechanisms of transthioesterification and the overall architecture of the E1–E2–Ub complex during catalysis are unknown. Here, we determine the structure of a covalently trapped E1–E2–ubiquitin thioester mimetic. Two distinct architectures of the complex are observed, one in which the Ub thioester (Ub(t)) contacts E1 in an open conformation and another in which Ub(t) instead contacts E2 in a drastically different, closed conformation. Altogether our structural and biochemical data suggest that these two conformational states represent snapshots of the E1–E2–Ub complex pre- and post-thioester transfer, and are consistent with a model in which catalysis is enhanced by a Ub(t)-mediated affinity switch that drives the reaction forward by promoting productive complex formation or product release depending on the conformational state.

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A molecular journey to check the conformational dynamics of tau tubulin kinase 2 mutations associated with Alzheimer's disease

RSC Advances ◽

10.1039/d0ra07659g ◽

2021 ◽

Vol 11 (3) ◽

pp. 1320-1331

Author(s):

Shahzaib Ahamad ◽

Hema Kanipakam ◽

Vijay Kumar ◽

Dinesh Gupta

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Conformational Dynamics ◽

Md Simulations

MD simulations of TTBK2 mutants to study its impact on stability of the protein.

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Making high-dimensional molecular distribution functions tractable through Belief Propagation on Factor Graphs

10.1101/2021.06.28.450193 ◽

2021 ◽

Author(s):

Zachary Smith ◽

Pratyush Tiwary

Keyword(s):

Belief Propagation ◽

Conformational Dynamics ◽

Joint Probability ◽

Md Simulations ◽

Distribution Functions ◽

Factor Graph ◽

High Dimensional ◽

Enhanced Sampling ◽

Small Peptides ◽

Approximate Probability

Molecular dynamics (MD) simulations provide a wealth of high-dimensional data at all-atom and femtosecond resolution but deciphering mechanistic information from this data is an ongoing challenge in physical chemistry and biophysics. Theoretically speaking, joint probabilities of the equilibrium distribution contain all thermodynamic information, but they prove increasingly difficult to compute and interpret as the dimensionality increases. Here, inspired by tools in probabilistic graphical modeling, we develop a factor graph trained through belief propagation that helps factorize the joint probability into an approximate tractable form that can be easily visualized and used. We validate the study through the analysis of the conformational dynamics of two small peptides with 5 and 9 residues. Our validations include testing the conditional dependency predictions through an intervention scheme inspired by Judea Pearl. Secondly we directly use the belief propagation based approximate probability distribution as a high-dimensional static bias for enhanced sampling, where we achieve spontaneous back-and-forth motion between metastable states that is up to 350 times faster than unbiased MD. We believe this work opens up useful ways to thinking about and dealing with high-dimensional molecular simulations.

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