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1.
J Chem Inf Model ; 61(11): 5305-5306, 2021 11 22.
Artigo em Inglês | MEDLINE | ID: mdl-34668709
2.
Cell Rep ; 37(3): 109840, 2021 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-34686332

RESUMO

Nearly one-third of proteins are initially targeted to the endoplasmic reticulum (ER) membrane, where they are correctly folded and then delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated degradation (ERAD) moves these clients from the ER membrane to the cytosol, a process known as retrotranslocation. Our recent work in Saccharomyces cerevisiae reveals a derlin rhomboid pseudoprotease, Dfm1, is involved in the retrotranslocation of ubiquitinated ERAD membrane substrates. In this study, we identify conserved residues of Dfm1 that are critical for retrotranslocation. We find several retrotranslocation-deficient Loop 1 mutants that display impaired binding to membrane substrates. Furthermore, Dfm1 possesses lipid thinning function to facilitate in the removal of ER membrane substrates, and this feature is conserved in its human homolog, Derlin-1, further implicating that derlin-mediated retrotranslocation is a well-conserved process.

3.
Proc Natl Acad Sci U S A ; 118(36)2021 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-34417349

RESUMO

To investigate the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the immune population, we coincupi bated the authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for seven passages, but, after 45 d, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed, at day 80, by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom, South Africa, Brazil, and Japan of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed.


Assuntos
Substituição de Aminoácidos , Enzima de Conversão de Angiotensina 2/imunologia , Anticorpos Neutralizantes/imunologia , Anticorpos Antivirais/imunologia , COVID-19/imunologia , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/imunologia , Enzima de Conversão de Angiotensina 2/química , Enzima de Conversão de Angiotensina 2/genética , Animais , Anticorpos Neutralizantes/química , Anticorpos Neutralizantes/genética , Anticorpos Neutralizantes/farmacologia , Anticorpos Antivirais/química , Anticorpos Antivirais/genética , Anticorpos Antivirais/farmacologia , Sítios de Ligação , COVID-19/genética , COVID-19/virologia , Chlorocebus aethiops , Convalescença , Expressão Gênica , Humanos , Evasão da Resposta Imune , Soros Imunes/química , Modelos Moleculares , Mutação , Testes de Neutralização , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , SARS-CoV-2/efeitos dos fármacos , SARS-CoV-2/imunologia , SARS-CoV-2/patogenicidade , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Células Vero
4.
Nat Chem ; 13(10): 963-968, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34413500

RESUMO

SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded 'down' to an exposed 'up' state to bind the human angiotensin-converting enzyme 2 receptor and infect cells. While snapshots of the 'up' and 'down' states have been obtained by cryo-electron microscopy and cryo-electron tomagraphy, details of the RBD-opening transition evade experimental characterization. Here over 130 µs of weighted ensemble simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD-opening pathways. Together with ManifoldEM analysis of cryo-electron microscopy data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408 and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein represents a landmark study for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.


Assuntos
Polissacarídeos/metabolismo , Glicoproteína da Espícula de Coronavírus/metabolismo , Microscopia Crioeletrônica , Humanos , Simulação de Dinâmica Molecular
5.
Phys Chem Chem Phys ; 23(30): 16401-16416, 2021 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-34318808

RESUMO

Saccharides comprise a significant mass fraction of organic carbon in sea spray aerosol (SSA), but the mechanisms through which saccharides are transferred from seawater to the ocean surface and eventually into SSA are unclear. It is hypothesized that saccharides cooperatively adsorb to other insoluble organic matter at the air/sea interface, known as the sea surface microlayer (SSML). Using a combination of surface-sensitive infrared reflection-absorption spectroscopy and all-atom molecular dynamics simulations, we demonstrate that the marine-relevant, anionic polysaccharide alginate co-adsorbs to an insoluble palmitic acid monolayer via divalent cationic bridging interactions. Ca2+ induces the greatest extent of alginate co-adsorption to the monolayer, evidenced by the ∼30% increase in surface coverage, whereas Mg2+ only facilitates one-third the extent of co-adsorption at seawater-relevant cation concentrations due to its strong hydration propensity. Na+ cations alone do not facilitate alginate co-adsorption, and palmitic acid protonation hinders the formation of divalent cationic bridges between the palmitate and alginate carboxylate moieties. Alginate co-adsorption is largely confined to the interfacial region beneath the monolayer headgroups, so surface pressure, and thus monolayer surface coverage, only changes the amount of alginate co-adsorption by less than 5%. Our results provide physical and molecular characterization of a potentially significant polysaccharide enrichment mechanism within the SSML.

6.
Proc Natl Acad Sci U S A ; 118(31)2021 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-34321356

RESUMO

To advance the mission of in silico cell biology, modeling the interactions of large and complex biological systems becomes increasingly relevant. The combination of molecular dynamics (MD) simulations and Markov state models (MSMs) has enabled the construction of simplified models of molecular kinetics on long timescales. Despite its success, this approach is inherently limited by the size of the molecular system. With increasing size of macromolecular complexes, the number of independent or weakly coupled subsystems increases, and the number of global system states increases exponentially, making the sampling of all distinct global states unfeasible. In this work, we present a technique called independent Markov decomposition (IMD) that leverages weak coupling between subsystems to compute a global kinetic model without requiring the sampling of all combinatorial states of subsystems. We give a theoretical basis for IMD and propose an approach for finding and validating such a decomposition. Using empirical few-state MSMs of ion channel models that are well established in electrophysiology, we demonstrate that IMD models can reproduce experimental conductance measurements with a major reduction in sampling compared with a standard MSM approach. We further show how to find the optimal partition of all-atom protein simulations into weakly coupled subunits.

7.
J Phys Chem Lett ; 12(20): 5023-5029, 2021 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-34024101

RESUMO

Lipopolysaccharides (LPS) in sea spray aerosol (SSA) particles have recently been shown to undergo heterogeneous reactions with HNO3 in the atmosphere. Here, we integrate theory and experiment to further investigate how the most abundant sea salt cations, Na+, Mg2+, and Ca2+, impact HNO3 reactions with LPS-containing SSA particles. Aerosol reaction flow tube studies show that heterogeneous reactions of SSA particles with divalent cation (Mg2+ and Ca2+) and LPS signatures were less reactive with HNO3 than those dominated by monovalent cations (Na+). All-atom molecular dynamics simulations of model LPS aggregates suggest that divalent cations cross-link the oligosaccharide chains to increase molecular aggregation and rigidity, which changes the particle phase and morphology, decreases water diffusion, and consequently decreases the reactive uptake of HNO3. This study provides new insight into how complex chemical interactions between ocean-derived salts and biogenic organic species can impact the heterogeneous reactivity of SSA particles.


Assuntos
Cálcio/química , Lipopolissacarídeos/química , Magnésio/química , Ácido Nítrico/química , Água do Mar/química , Sódio/química , Aerossóis/química , Cátions/química , Tamanho da Partícula , Sais/química , Propriedades de Superfície
8.
Viruses ; 13(4)2021 04 12.
Artigo em Inglês | MEDLINE | ID: mdl-33921405

RESUMO

APOBEC3B (A3B) is one of seven human APOBEC3 DNA cytosine deaminases that restrict viral infections as part of the overall innate immune response, but it also plays a major role in tumor evolution by mutating genomic DNA. Given the importance of A3B as a restriction factor of viral infections and as a driver of multiple human cancers, selective antibodies against A3B are highly desirable for its specific detection in various research and possibly diagnostic applications. Here, we describe a high-affinity minimal antibody, designated 5G7, obtained via a phage display screening against the C-terminal catalytic domain (ctd) of A3B. 5G7 also binds APOBEC3A that is highly homologous to A3Bctd but does not bind the catalytic domain of APOBEC3G, another Z1-type deaminase domain. The crystal structure of 5G7 shows a canonical arrangement of the heavy and light chain variable domains, with their complementarity-determining region (CDR) loops lining an antigen-binding cleft that accommodates a pair of α-helices. To understand the mechanism of A3Bctd recognition by 5G7, we used the crystal structures of A3Bctd and 5G7 as templates and computationally predicted the A3B-5G7 complex structure. Stable binding poses obtained by the simulation were further tested by site-directed mutagenesis and in vitro binding analyses. These studies mapped the epitope for 5G7 to a portion of C-terminal α6 helix of A3Bctd, with Arg374 playing an essential role. The same region of A3Bctd was used previously as a peptide antigen for generating a rabbit monoclonal antibody (mAb 5210-87-13), suggesting that this region is particularly immunogenic and that these antibodies from very different origins may share similar binding modes. Our studies provide a platform for the development of selective antibodies against A3B and other APOBEC3 family enzymes.


Assuntos
Anticorpos Monoclonais/química , Anticorpos Monoclonais/metabolismo , Citidina Desaminase/imunologia , Citidina Desaminase/metabolismo , Antígenos de Histocompatibilidade Menor/imunologia , Antígenos de Histocompatibilidade Menor/metabolismo , Anticorpos de Cadeia Única/química , Anticorpos de Cadeia Única/isolamento & purificação , Anticorpos Monoclonais/imunologia , Sítios de Ligação de Anticorpos , Cristalização , Células HEK293 , Humanos , Imunidade Inata , Simulação de Dinâmica Molecular , Ligação Proteica , Anticorpos de Cadeia Única/metabolismo
9.
J Med Chem ; 64(9): 5787-5801, 2021 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-33872011

RESUMO

The use of epigenetic bromodomain inhibitors as anticancer therapeutics has transitioned from targeting bromodomain extraterminal domain (BET) proteins into targeting non-BET bromodomains. The two most relevant non-BET bromodomain oncology targets are cyclic AMP response element-binding protein (CBP) and E1A binding protein P300 (EP300). To explore the growing CBP/EP300 interest, we developed a highly efficient two-step synthetic route for dimethylisoxazole-attached imidazo[1,2-a]pyridine scaffold-containing inhibitors. Our efficient two-step reactions enabled high-throughput synthesis of compounds designed by molecular modeling, which together with structure-activity relationship (SAR) studies facilitated an overarching understanding of selective targeting of CBP/EP300 over non-BET bromodomains. This led to the identification of a new potent and selective CBP/EP300 bromodomain inhibitor, UMB298 (compound 23, CBP IC50 72 nM and bromodomain 4, BRD4 IC50 5193 nM). The SAR we established is in good agreement with literature-reported CBP inhibitors, such as CBP30, and demonstrates the advantage of utilizing our two-step approach for inhibitor development of other bromodomains.


Assuntos
Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico/antagonistas & inibidores , Proteína p300 Associada a E1A/antagonistas & inibidores , Isoxazóis/química , Piridinas/química , Sítios de Ligação , Proteínas de Ciclo Celular/antagonistas & inibidores , Proteínas de Ciclo Celular/metabolismo , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Cristalografia por Raios X , Proteína de Ligação ao Elemento de Resposta ao AMP Cíclico/metabolismo , Proteína p300 Associada a E1A/metabolismo , Humanos , Simulação de Acoplamento Molecular , Piridinas/metabolismo , Piridinas/farmacologia , Relação Estrutura-Atividade , Fatores de Transcrição/antagonistas & inibidores , Fatores de Transcrição/metabolismo
10.
bioRxiv ; 2021 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-33821277

RESUMO

High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3'-to-5' exoribonuclease (ExoN) in non-structural protein 14 (nsp14), which excises nucleotides including antiviral drugs mis-incorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here we determined a 1.6-Å resolution crystal structure of SARS-CoV-2 ExoN in complex with its essential co-factor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3' end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. Molecular dynamics simulations further show remarkable flexibility of multi-domain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA-binding to support its exoribonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN-nsp10 complex serves as a platform for future development of anti-coronaviral drugs or strategies to attenuate the viral virulence.

11.
Elife ; 102021 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-33661099

RESUMO

Class I Phosphoinositide 3-kinases (PI3Ks) are master regulators of cellular functions, with the class IB PI3K catalytic subunit (p110γ) playing key roles in immune signalling. p110γ is a key factor in inflammatory diseases and has been identified as a therapeutic target for cancers due to its immunomodulatory role. Using a combined biochemical/biophysical approach, we have revealed insight into regulation of kinase activity, specifically defining how immunodeficiency and oncogenic mutations of R1021 in the C-terminus can inactivate or activate enzyme activity. Screening of inhibitors using HDX-MS revealed that activation loop-binding inhibitors induce allosteric conformational changes that mimic those in the R1021C mutant. Structural analysis of advanced PI3K inhibitors in clinical development revealed novel binding pockets that can be exploited for further therapeutic development. Overall, this work provides unique insights into regulatory mechanisms that control PI3Kγ kinase activity and shows a framework for the design of PI3K isoform and mutant selective inhibitors.

12.
Biophys J ; 120(6): 983-993, 2021 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-33609494

RESUMO

Changeux et al. (Changeux et al. C. R. Biol. 343:33-39.) recently suggested that the SARS-CoV-2 spike protein may interact with nicotinic acetylcholine receptors (nAChRs) and that such interactions may be involved in pathology and infectivity. This hypothesis is based on the fact that the SARS-CoV-2 spike protein contains a sequence motif similar to known nAChR antagonists. Here, we use molecular simulations of validated atomically detailed structures of nAChRs and of the spike to investigate the possible binding of the Y674-R685 region of the spike to nAChRs. We examine the binding of the Y674-R685 loop to three nAChRs, namely the human α4ß2 and α7 subtypes and the muscle-like αßγδ receptor from Tetronarce californica. Our results predict that Y674-R685 has affinity for nAChRs. The region of the spike responsible for binding contains a PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. The conformational behavior of the bound Y674-R685 is highly dependent on the receptor subtype; it adopts extended conformations in the α4ß2 and α7 complexes but is more compact when bound to the muscle-like receptor. In the α4ß2 and αßγδ complexes, the interaction of Y674-R685 with the receptors forces the loop C region to adopt an open conformation, similar to other known nAChR antagonists. In contrast, in the α7 complex, Y674-R685 penetrates deeply into the binding pocket in which it forms interactions with the residues lining the aromatic box, namely with TrpB, TyrC1, and TyrC2. Estimates of binding energy suggest that Y674-R685 forms stable complexes with all three nAChR subtypes. Analyses of simulations of the glycosylated spike show that the Y674-R685 region is accessible for binding. We suggest a potential binding orientation of the spike protein with nAChRs, in which they are in a nonparallel arrangement to one another.


Assuntos
Receptores Nicotínicos/metabolismo , Glicoproteína da Espícula de Coronavírus/metabolismo , Glicosilação , Humanos , Simulação de Dinâmica Molecular , Peptídeos/química , Peptídeos/metabolismo , Ligação Proteica , Receptores Nicotínicos/química , Glicoproteína da Espícula de Coronavírus/química , Termodinâmica
13.
bioRxiv ; 2021 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-33619492

RESUMO

SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded "down" to an exposed "up" state in order to bind the human ACE2 receptor and infect cells. While snapshots of the "up" and "down" states have been obtained by cryoEM and cryoET, details of the RBD opening transition evade experimental characterization. Here, over 130 µs of weighted ensemble (WE) simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD opening pathways. Together with ManifoldEM analysis of cryo-EM data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408, and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein achieves a new high-water mark for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.

14.
Nat Commun ; 12(1): 856, 2021 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-33558528

RESUMO

Through the efforts of many groups, a wide range of fluorescent protein reporters and sensors based on green fluorescent protein and its relatives have been engineered in recent years. Here we explore the incorporation of sensing modalities into de novo designed fluorescence-activating proteins, called mini-fluorescence-activating proteins (mFAPs), that bind and stabilize the fluorescent cis-planar state of the fluorogenic compound DFHBI. We show through further design that the fluorescence intensity and specificity of mFAPs for different chromophores can be tuned, and the fluorescence made sensitive to pH and Ca2+ for real-time fluorescence reporting. Bipartite split mFAPs enable real-time monitoring of protein-protein association and (unlike widely used split GFP reporter systems) are fully reversible, allowing direct readout of association and dissociation events. The relative ease with which sensing modalities can be incorporated and advantages in smaller size and photostability make de novo designed fluorescence-activating proteins attractive candidates for optical sensor engineering.


Assuntos
Proteínas Luminescentes/metabolismo , Acetilcolina/metabolismo , Animais , Células COS , Cálcio/metabolismo , Chlorocebus aethiops , Fluorescência , Corantes Fluorescentes/metabolismo , Proteínas de Fluorescência Verde/metabolismo , Células HEK293 , Humanos , Concentração de Íons de Hidrogênio , Proteínas Luminescentes/química , Modelos Moleculares
15.
Biomolecules ; 11(1)2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33430019

RESUMO

RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucleoproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. SMUG1 may be required for post-transcriptional regulation and quality control of rRNAs, partly by regulating rRNA and stability.


Assuntos
Processamento Pós-Transcricional do RNA , RNA Ribossômico/metabolismo , Uracila-DNA Glicosidase/metabolismo , Animais , Humanos , Modelos Moleculares , Estabilidade de RNA , RNA Ribossômico/química
16.
Curr Opin Struct Biol ; 67: 187-194, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33401096

RESUMO

The tumor suppressor p53 plays a vital role in responding to cell stressors such as DNA damage, hypoxia, and tumor formation by inducing cell-cycle arrest, senescence, or apoptosis. Expression level alterations and mutational frequency implicates p53 in most human cancers. In this review, we show how both computational and experimental methods have been used to provide an integrated view of p53 dynamics, function, and reactivation potential. We argue that p53 serves as an exceptional case study for developing methods in modeling intrinsically disordered proteins. We describe how these methods can be leveraged to improve p53 reactivation molecule design and other novel therapeutic modalities, such as PROteolysis TARgeting Chimeras (PROTACs).


Assuntos
Neoplasias , Proteína Supressora de Tumor p53 , Apoptose , Biologia Computacional , Dano ao DNA , Humanos , Neoplasias/genética , Proteólise , Proteína Supressora de Tumor p53/genética , Proteína Supressora de Tumor p53/metabolismo
17.
Chembiochem ; 22(3): 565-570, 2021 02 02.
Artigo em Inglês | MEDLINE | ID: mdl-32975902

RESUMO

The 55-residue OCRE domains of the splicing factors RBM5 and RBM10 contain 15 tyrosines in compact, globular folds. At 25 °C, all 15 tyrosines show symmetric 1 H NMR spectra, with averaged signals for the pairs of δ- and ϵ-ring hydrogens. At 4 °C, two tyrosines were identified as showing 1 H NMR line-broadening due to lowered frequency of the ring-flipping. For the other 13 tyrosine rings, it was not evident, from the 1 H NMR data alone, whether they were either all flipping at high frequencies, or whether slowed flipping went undetected due to small chemical-shift differences between pairs of exchanging ring hydrogen atoms. Here, we integrate 1 H NMR spectroscopy and molecular dynamics (MD) simulations to determine the tyrosine ring-flip frequencies. In the RBM10-OCRE domain, we found that, for 11 of the 15 tyrosines, these frequencies are in the range 2.0×106 to 1.3×108  s-1 , and we established an upper limit of <1.0×106  s-1 for the remaining four residues. The experimental data and the MD simulation are mutually supportive, and their combined use extends the analysis of aromatic ring-flip events beyond the limitations of routine 1 H NMR line-shape analysis into the nanosecond frequency range.


Assuntos
Proteínas de Ciclo Celular/química , Proteínas de Ligação a DNA/química , Simulação de Dinâmica Molecular , Fatores de Processamento de RNA/química , Proteínas de Ligação a RNA/química , Proteínas Supressoras de Tumor/química , Tirosina/química , Motivos de Aminoácidos , Humanos , Espectroscopia de Prótons por Ressonância Magnética
18.
Biophys J ; 120(6): 1097-1104, 2021 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-33253634

RESUMO

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and ongoing development of a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion. Data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data become publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.


Assuntos
Simulação de Dinâmica Molecular , SARS-CoV-2/química , Vírion/química , COVID-19 , Análise de Componente Principal , Proteínas Virais/química
19.
Biophys J ; 120(6): 1072-1084, 2021 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-33189680

RESUMO

The coronavirus disease 2019 (COVID-19) pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine development efforts are underway, there are many outstanding questions on the mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and host cell entry. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular spike glycoprotein and at the receptor-binding domain (RBD)-receptor interface, suggesting a role in infection. Here, we perform explicitly solvated, all-atom, molecular dynamics simulations of the glycosylated, full-length, membrane-bound ACE2 receptor in both an apo and spike RBD-bound state to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full-length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer and suggests a mechanical contribution of the host receptor toward the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can potentially be exploited for the rational design of effective SARS-CoV-2 therapeutics.


Assuntos
Enzima de Conversão de Angiotensina 2/metabolismo , COVID-19/enzimologia , COVID-19/virologia , SARS-CoV-2/fisiologia , Enzima de Conversão de Angiotensina 2/química , Humanos , Simulação de Dinâmica Molecular , Multimerização Proteica
20.
J Chem Inf Model ; 60(12): 5724-5726, 2020 12 28.
Artigo em Inglês | MEDLINE | ID: mdl-33378852

Assuntos
COVID-19 , Humanos , SARS-CoV-2
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