Structural models of full-length JAK2 kinase

AbstractThe protein JAK2 is a prototypical member of the Janus kinase family, and mediates signals from numerous cytokine receptors. The constitutively active V617F mutant of JAK2 is prevalent in many bone marrow disorders, blood cancers, and autoimmune diseases, and is an important drug target. Structures have been determined for each of the four individual domains making up JAK2, and for certain pairs of these domains, but no structure of full-length JAK2 is available, and thus the mechanisms underlying JAK2 regulation and the aberrant activity of the V617F mutant have been incompletely understood. Here we propose structural models of full-length JAK2 in both its active and inactive forms. Construction of these models was informed by long-timescale molecular dynamics simulations. Subsequent mutagenesis experiments showed that mutations at the putative interdomain interfaces modulated JAK2 activity. The models provide a structural basis for understanding JAK2 autoinhibition and activation, and suggest that the constitutive activity of the V617F mutant may arise from a dual effect of destabilizing the inactive conformation and stabilizing the active conformation.

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Mechanisms of activation and desensitization of full-length glycine receptor in membranes

10.1101/788695 ◽

2019 ◽

Cited By ~ 3

Author(s):

Arvind Kumar ◽

Sandip Basak ◽

Shanlin Rao ◽

Yvonne Gicheru ◽

Megan L. Mayer ◽

...

Keyword(s):

Conformational Changes ◽

Single Channel ◽

Glycine Receptor ◽

Full Length ◽

Structural Basis ◽

Molecular Architecture ◽

Channel Conductance ◽

Single Channel Conductance ◽

The Central Nervous System ◽

Dynamics Simulations

AbstractGlycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyR) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structural studies have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unknown. Here, we present Cryo-EM structures of the full-length GlyR protein reconstituted into lipid nanodiscs that are captured in the unliganded (closed) and glycine-bound (open and desensitized) conformations. A comparison of the three states reveals global conformational changes underlying GlyR channel gating. The functional state assignments were validated by molecular dynamics simulations of the structures incorporated in a lipid bilayer. Observed permeation events are in agreement with the anion selectivity of the channel and the reported single-channel conductance of GlyR. These studies establish the structural basis for gating, selectivity, and single-channel conductance of GlyR in a physiological environment.

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Plumbagin and oridonin reveal new CRM1 binding sites and NES-binding groove features

10.1101/2020.08.05.237479 ◽

2020 ◽

Author(s):

Yuqin Lei ◽

Yuling Li ◽

Yuping Tan ◽

Da Jia ◽

Qingxiang Sun

Keyword(s):

Binding Sites ◽

Nuclear Export ◽

Drug Target ◽

Structural Basis ◽

Inhibitor Binding ◽

Anti Cancer ◽

Binding Groove ◽

First Time ◽

Further Development ◽

Important Drug

AbstractCRM1 is an important drug target in diseases such as cancer and viral infection. Plumbagin and oridonin, the herbal ingredients with known anti-cancer activities, were reported to inhibit CRM1-mediated nuclear export. However, their modes of CRM1 inhibition are unclear. Here, a multi-mutant of yeast CRM1 was engineered to enable the crystallization of these two small molecules in CRM1’s NES-binding groove. Each structure showed three inhibitor-binding sites, among which two are conserved in humans. Besides the known binding site, another site also participated in oridonin and plumbagin’s CRM1 inhibition. While the plumbagin-bound NES groove resembled the NES-bound groove state, the oridonin-bound groove revealed for the first time a more open NES groove, which may potentially improve cargo-loading through a capture-and-tighten mechanism. Our work thus provides a tool for CRM1 inhibitor crystallization, new insights of CRM1-cargo interaction, and a structural basis for further development of these or other CRM1 inhibitors.

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Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family

eLife ◽

10.7554/elife.00708 ◽

2013 ◽

Vol 2 ◽

Cited By ~ 28

Author(s):

Anton Arkhipov ◽

Yibing Shan ◽

Eric T Kim ◽

Ron O Dror ◽

David E Shaw

Keyword(s):

Molecular Dynamics ◽

Tyrosine Kinase ◽

Molecular Dynamics Simulations ◽

Receptor Tyrosine Kinase ◽

Drug Target ◽

Activation Mechanism ◽

Structural Basis ◽

Egfr Family ◽

Dynamics Simulations ◽

Necessary And Sufficient

The receptor tyrosine kinase Her2, an intensely pursued drug target, differs from other members of the EGFR family in that it does not bind EGF-like ligands, relying instead on heterodimerization with other (ligand-bound) EGFR-family receptors for activation. The structural basis for Her2 heterodimerization, however, remains poorly understood. The unexpected recent finding of asymmetric ectodomain dimer structures of Drosophila EGFR (dEGFR) suggests a possible structural basis for Her2 heterodimerization, but all available structures for dimers of human EGFR family ectodomains are symmetric. Here, we report results from long-timescale molecular dynamics simulations indicating that a single ligand is necessary and sufficient to stabilize the ectodomain interface of Her2 heterodimers, which assume an asymmetric conformation similar to that of dEGFR dimers. This structural parallelism suggests a dimerization mechanism that has been conserved in the evolution of the EGFR family from Drosophila to human.

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Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

Current Pharmaceutical Design ◽

10.2174/1381612825666190903153043 ◽

2019 ◽

Vol 25 (31) ◽

pp. 3339-3349 ◽

Cited By ~ 6

Author(s):

Indrani Bera ◽

Pavan V. Payghan

Keyword(s):

Molecular Dynamics ◽

Drug Discovery ◽

Molecular Dynamics Simulations ◽

Drug Target ◽

Structural Information ◽

Drug Binding ◽

Structure Based Drug Design ◽

Drug Designing ◽

Target Binding ◽

Dynamics Simulations

Background: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. Objective: The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. Method: This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. Results: This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. Conclusion: The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

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Small Molecule Inhibitors of Influenza Virus Entry

Pharmaceuticals ◽

10.3390/ph14060587 ◽

2021 ◽

Vol 14 (6) ◽

pp. 587

Author(s):

Zhaoyu Chen ◽

Qinghua Cui ◽

Michael Caffrey ◽

Lijun Rong ◽

Ruikun Du

Keyword(s):

Influenza Virus ◽

Membrane Fusion ◽

Small Molecule ◽

Drug Target ◽

Small Molecule Inhibitors ◽

Virus Entry ◽

Critical Role ◽

Structural Basis ◽

Future Directions ◽

The Past

Hemagglutinin (HA) plays a critical role during influenza virus receptor binding and subsequent membrane fusion process, thus HA has become a promising drug target. For the past several decades, we and other researchers have discovered a series of HA inhibitors mainly targeting its fusion machinery. In this review, we summarize the advances in HA-targeted development of small molecule inhibitors. Moreover, we discuss the structural basis and mode of action of these inhibitors, and speculate upon future directions toward more potent inhibitors of membrane fusion and potential anti-influenza drugs.

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Structural basis for activation and allosteric modulation of full-length calcium-sensing receptor

Science Advances ◽

10.1126/sciadv.abg1483 ◽

2021 ◽

Vol 7 (23) ◽

pp. eabg1483

Author(s):

Tianlei Wen ◽

Ziyu Wang ◽

Xiaozhe Chen ◽

Yue Ren ◽

Xuhang Lu ◽

...

Keyword(s):

Conformational Changes ◽

Bound States ◽

Hormone Secretion ◽

Allosteric Modulation ◽

Full Length ◽

Structural Basis ◽

Endocrine Disorders ◽

Calcium Sensing Receptor ◽

Calcium Sensing ◽

Class C

Calcium-sensing receptor (CaSR) is a class C G protein–coupled receptor (GPCR) that plays an important role in calcium homeostasis and parathyroid hormone secretion. Here, we present multiple cryo–electron microscopy structures of full-length CaSR in distinct ligand-bound states. Ligands (Ca2+ and l-tryptophan) bind to the extracellular domain of CaSR and induce large-scale conformational changes, leading to the closure of two heptahelical transmembrane domains (7TMDs) for activation. The positive modulator (evocalcet) and the negative allosteric modulator (NPS-2143) occupy the similar binding pocket in 7TMD. The binding of NPS-2143 causes a considerable rearrangement of two 7TMDs, forming an inactivated TM6/TM6 interface. Moreover, a total of 305 disease-causing missense mutations of CaSR have been mapped to the structure in the active state, creating hotspot maps of five clinical endocrine disorders. Our results provide a structural framework for understanding the activation, allosteric modulation mechanism, and disease therapy for class C GPCRs.

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Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics

Nature Communications ◽

10.1038/s41467-021-24674-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Bertrand Beckert ◽

Elodie C. Leroy ◽

Shanmugapriya Sothiselvam ◽

Lars V. Bock ◽

Maxim S. Svetlov ◽

...

Keyword(s):

Antibiotic Resistance Genes ◽

Structural Basis ◽

Sequence Motifs ◽

Specific Sequence ◽

Bacterial Ribosome ◽

Translational Arrest ◽

Exit Tunnel ◽

Mechanistic Basis ◽

Dynamics Simulations ◽

Context Specific

AbstractMacrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics.

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Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly

Nanoscale ◽

10.1039/c9nr09135a ◽

2020 ◽

Vol 12 (9) ◽

pp. 5422-5434 ◽

Cited By ~ 1

Author(s):

David Winogradoff ◽

Shalini John ◽

Aleksei Aksimentiev

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Anionic Surfactant ◽

Protein Unfolding ◽

Protein Assembly ◽

Full Length ◽

Dynamics Simulations

Molecular dynamics simulations reveal how anionic surfactant SDS and heat unfold full-length proteins.

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Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis

Biochemical Journal ◽

10.1042/bcj20180874 ◽

2019 ◽

Vol 476 (6) ◽

pp. 991-1003 ◽

Cited By ~ 1

Author(s):

Vijaykumar Pillalamarri ◽

Tarun Arya ◽

Neshatul Haque ◽

Sandeep Chowdary Bala ◽

Anil Kumar Marapaka ◽

...

Keyword(s):

Natural Product ◽

Active Site ◽

Covalent Modification ◽

Structural Basis ◽

Wild Type ◽

Methionine Aminopeptidases ◽

Synthetic Derivative ◽

Dynamics Simulations

Abstract Natural product ovalicin and its synthetic derivative TNP-470 have been extensively studied for their antiangiogenic property, and the later reached phase 3 clinical trials. They covalently modify the conserved histidine in Type 2 methionine aminopeptidases (MetAPs) at nanomolar concentrations. Even though a similar mechanism is possible in Type 1 human MetAP, it is inhibited only at millimolar concentration. In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulations suggest that ovalicin is not stably placed in the active site of wild-type MetAP1b before the covalent modification. In the case of F309M mutant and human Type 2 MetAP, molecule spends more time in the active site providing time for covalent modification.

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