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1.
Proteins ; 92(3): 317-328, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37864328

ABSTRACT

G protein-coupled receptors (GPCRs) are membrane-bound signaling proteins that play an essential role in cellular signaling processes. Due to their intrinsic function of transmitting internal signals in response to external cues, these receptors are adapted to be highly dynamic in nature. The ß2 -adrenergic receptor (ß2 AR) is a representative member of the family that has been extensively analyzed in terms of its structure and activation. Although the structure of the transmembrane domain has been characterized in the different functional states of the receptor, the conformational dynamics of the extramembrane domains, especially the intrinsically disordered regions are still emerging. In this study, we analyze the state-dependent dynamics of extramembrane domains of ß2 AR using atomistic molecular dynamics simulations. We introduce a parameter, the residue excess dynamics that allows us to better quantify receptor dynamics. Using this measure, we show that the dynamics of the extramembrane domains are sensitive to the receptor state. Interestingly, the ligand-bound intermediate R ' state shows the maximal dynamics compared to either the active R*G or inactive R states. Ligand binding appears to be correlated with high residue excess dynamics that are dampened upon G protein coupling. The intracellular loop-3 (ICL3) domain has a tendency to flip towards the membrane upon ligand binding, which could contribute to receptor "priming." We highlight an important ICL1-helix-8 interplay that is broken in the ligand-bound state but is retained in the active state. Overall, our study highlights the importance of characterizing the functional dynamics of the GPCR loop domains.


Subject(s)
Molecular Dynamics Simulation , Receptors, G-Protein-Coupled , Ligands , Receptors, G-Protein-Coupled/metabolism , Protein Domains , Membrane Proteins , Receptors, Adrenergic , Receptors, Adrenergic, beta-2/chemistry
2.
Biophys J ; 121(6): 1038-1055, 2022 03 15.
Article in English | MEDLINE | ID: mdl-35134335

ABSTRACT

Many double-stranded RNA-binding domains (dsRBDs) interact with topologically distinct dsRNAs in biological pathways pivotal to viral replication, cancer causation, neurodegeneration, and so on. We hypothesized that the adaptability of dsRBDs is essential to target different dsRNA substrates. A model dsRBD and a few dsRNAs, slightly different in shape from each other, were used to test the systematic shape dependence of RNA on the dsRBD-binding using nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. NMR-based titrations showed a distinct binding pattern for the dsRBD with the topologically distinct dsRNAs. The line broadening upon RNA binding was observed to cluster in the residues lying in close proximity, thereby suggesting an RNA-induced conformational exchange in the dsRBD. Further, while the intrinsic microsecond dynamics observed in the apo-dsRBD were found to quench upon binding with the dsRNA, the microsecond dynamics got induced at residues spatially proximal to quench sites upon binding with the dsRNA. This apparent relay of conformational exchange suggests the significance of intrinsic dynamics to help adapt the dsRBD to target various dsRNA-shapes. The conformational pool visualized in MD simulations for the apo-dsRBD reported here has also been observed to sample the conformations seen previously for various dsRBDs in apo- and in dsRNA-bound state structures, further suggesting the conformational adaptability of the dsRBDs. These investigations provide a dynamic basis for the substrate promiscuity for dsRBD proteins.


Subject(s)
RNA, Double-Stranded , Models, Molecular , Nucleic Acid Conformation
3.
PLoS Comput Biol ; 17(5): e1008593, 2021 05.
Article in English | MEDLINE | ID: mdl-34014914

ABSTRACT

The dynamic interactions between G protein-coupled receptors (GPCRs) and their cognate protein partners are central to several cell signaling pathways. For example, the association of CXC chemokine receptor 1 (CXCR1) with its cognate chemokine, interleukin-8 (IL8 or CXCL8) initiates pathways leading to neutrophil-mediated immune responses. The N-terminal domain of chemokine receptors confers ligand selectivity, but unfortunately the conformational dynamics of this intrinsically disordered region remains unresolved. In this work, we have explored the interaction of CXCR1 with IL8 by microsecond time scale coarse-grain simulations, complemented by atomistic models and NMR chemical shift predictions. We show that the conformational plasticity of the apo-receptor N-terminal domain is restricted upon ligand binding, driving it to an open C-shaped conformation. Importantly, we corroborated the dynamic complex sampled in our simulations against chemical shift perturbations reported by previous NMR studies and show that the trends are similar. Our results indicate that chemical shift perturbation is often not a reporter of residue contacts in such dynamic associations. We believe our results represent a step forward in devising a strategy to understand intrinsically disordered regions in GPCRs and how they acquire functionally important conformational ensembles in dynamic protein-protein interfaces.


Subject(s)
Receptors, Interleukin-8A/chemistry , Amino Acid Sequence , Computational Biology , Computer Simulation , Humans , Interleukin-8/chemistry , Interleukin-8/metabolism , Intrinsically Disordered Proteins/chemistry , Ligands , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Dynamics Simulation , Protein Binding , Protein Conformation , Protein Interaction Domains and Motifs , Protein Interaction Mapping , Receptors, Interleukin-8A/genetics , Receptors, Interleukin-8A/metabolism
4.
J Membr Biol ; 254(3): 311-319, 2021 06.
Article in English | MEDLINE | ID: mdl-33570689

ABSTRACT

Helicoverpa armigera is a devastating polyphagous and cosmopolitan crop pest. There are reports of this insect being resistant to a variety of pesticides raising concern worldwide. The Octopamine (OA) binding ß2-like receptor (OAR), a GPCR, is widely distributed in the nervous system of the insect and plays essential roles in the physiology and development and thus is an important target for insecticides. Yet, the molecular characterization of the H. armigera OAR (HarmOAR) and rational design of compounds based on this receptor is lacking. As a first step, we performed multiple sequence alignment of all insect OARs, which revealed that the sequences contained all conserved class A GPCR motifs. Phylogenetic studies showed clade-specific variations in the protein sequences primarily arising owing to differences in the ICL3 loop region. Further, a structural model of HarmOAR was built using the inactive human ß2AR as a template. 0.9 µs atomistic simulations revealed conserved inter helical contacts and water molecules of HarmOAR. The detailed binding of octopamine was studied using molecular docking and 0.3 µs atomistic simulations. Twenty-two insecticides active against octopamine receptors of other insects were compiled and docked to HarmOAR followed by rescoring with binding free energies to prioritize them for H. armigera. Our study suggests α-terpineol to be a good candidate as an insecticide or insect repellent for Helicoverpa armigera.


Subject(s)
Moths , Receptors, Biogenic Amine , Animals , Humans , Larva , Molecular Docking Simulation , Moths/genetics , Phylogeny , Receptors, Biogenic Amine/genetics
5.
Genet Med ; 23(10): 1933-1943, 2021 10.
Article in English | MEDLINE | ID: mdl-34172899

ABSTRACT

PURPOSE: Pathogenic variants in Lysyl-tRNA synthetase 1 (KARS1) have increasingly been recognized as a cause of early-onset complex neurological phenotypes. To advance the timely diagnosis of KARS1-related disorders, we sought to delineate its phenotype and generate a disease model to understand its function in vivo. METHODS: Through international collaboration, we identified 22 affected individuals from 16 unrelated families harboring biallelic likely pathogenic or pathogenic in KARS1 variants. Sequencing approaches ranged from disease-specific panels to genome sequencing. We generated loss-of-function alleles in zebrafish. RESULTS: We identify ten new and four known biallelic missense variants in KARS1 presenting with a moderate-to-severe developmental delay, progressive neurological and neurosensory abnormalities, and variable white matter involvement. We describe novel KARS1-associated signs such as autism, hyperactive behavior, pontine hypoplasia, and cerebellar atrophy with prevalent vermian involvement. Loss of kars1 leads to upregulation of p53, tissue-specific apoptosis, and downregulation of neurodevelopmental related genes, recapitulating key tissue-specific disease phenotypes of patients. Inhibition of p53 rescued several defects of kars1-/- knockouts. CONCLUSION: Our work delineates the clinical spectrum associated with KARS1 defects and provides a novel animal model for KARS1-related human diseases revealing p53 signaling components as potential therapeutic targets.


Subject(s)
Hearing Loss , Lysine-tRNA Ligase/genetics , Neurodevelopmental Disorders , Alleles , Animals , Disease Models, Animal , Hearing Loss/genetics , Humans , Neurodevelopmental Disorders/genetics , Phenotype , Zebrafish/genetics
6.
Proteins ; 88(1): 227-236, 2020 01.
Article in English | MEDLINE | ID: mdl-31365155

ABSTRACT

Thionins are small, cysteine-rich peptides that play an important role in plant defense, primarily through their interactions with membranes. Eight novel γ-thionin peptides (CanThio1-8) were isolated from the flower of Capsicum annuum. Sequence analysis revealed that the peptides cluster into three groups. A representative peptide from each group (CanThio1, 2, and 3) was used for experimental characterization. Interestingly, peptides were found to possess some cytotoxic activity against normal human embryonic kidney cell line but higher cytotoxicity against cancer cell line MCF-7. CanThio3 peptide was chosen as a representative peptide to study the molecular mechanism of action on membranes. Microsecond timescale atomistic simulations of CanThio3 were performed in the presence of a POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) lipid bilayer. Simulations revealed that CanThio3 interacts with the bilayer and causes lipid thinning in the vicinity. Nonpolar amino acids specific to the α-core region of CanThio3 along with nonpolar residues in the γ-core region are seen to interact with the lipid tails. The differences in the amino acid sequence of CanThio peptides in these regions explain the variability in cytotoxic activities. In summary, our results demonstrate the membrane-mediated activity of a novel series of γ-thionin peptides from C. annuum.


Subject(s)
Antineoplastic Agents, Phytogenic/pharmacology , Capsicum/chemistry , Lipid Bilayers/metabolism , Plant Proteins/pharmacology , Thionins/pharmacology , Amino Acid Sequence , Antineoplastic Agents, Phytogenic/chemistry , Cell Membrane/drug effects , Cell Membrane/metabolism , Cell Survival/drug effects , HEK293 Cells , Humans , MCF-7 Cells , Models, Molecular , Neoplasms/drug therapy , Plant Proteins/chemistry , Sequence Alignment , Structural Homology, Protein , Thionins/chemistry
7.
J Membr Biol ; 252(4-5): 499-507, 2019 10.
Article in English | MEDLINE | ID: mdl-31520159

ABSTRACT

The ß2-adrenergic receptor (ß2AR) is a membrane-bound G-protein-coupled receptor and an important drug target for asthma. Clinical studies report that the population variant Gln27Glu is associated with a differential response to common asthma drugs, such as albuterol, isoproterenol and terbutaline. Interestingly, the 27th amino acid is positioned on the N-terminal region that is the most flexible and consequently the least studied part of the receptor. In this study, we probe the molecular origin of the differential drug binding by performing structural modeling and simulations of the wild-type (Gln) and variant (Glu) receptors followed by ensemble docking with the ligands, albuterol, isoproterenol and terbutaline. In line with clinical studies, the ligands were observed to interact preferentially with the Glu variant. Our results indicate that the Glu residue at the 27th position perturbs the network of electrostatic interactions that connects the N-terminal region to the binding site in the wild-type receptor. As a result, the Glu variant is observed to bind better to the three ligands tested in this study. Our study provides a structural basis to explain the variable drug response associated with the 27th position polymorphism in the ß2AR and is a starting step to identify genotype-specific therapeutics.


Subject(s)
Glutamic Acid/chemistry , Glutamine/chemistry , Molecular Docking Simulation , Molecular Dynamics Simulation , Receptors, Adrenergic, beta-2/chemistry , Glutamic Acid/genetics , Glutamine/genetics , Humans , Protein Domains , Receptors, Adrenergic, beta-2/genetics
8.
PLoS Comput Biol ; 10(12): e1004006, 2014 Dec.
Article in English | MEDLINE | ID: mdl-25501358

ABSTRACT

The human ß2-adrenergic receptor (ß2AR), a member of the G-protein coupled receptor (GPCR) family, is expressed in bronchial smooth muscle cells. Upon activation by agonists, ß2AR causes bronchodilation and relief in asthma patients. The N-terminal polymorphism of ß2AR at the 16th position, Arg16Gly, has warranted a lot of attention since it is linked to variations in response to albuterol (agonist) treatment. Although the ß2AR is one of the well-studied GPCRs, the N-terminus which harbors this mutation, is absent in all available experimental structures. The goal of this work was to study the molecular level differences between the N-terminal variants using structural modeling and atomistic molecular dynamics simulations. Our simulations reveal that the N-terminal region of the Arg variant shows greater dynamics than the Gly variant, leading to differential placement. Further, the position and dynamics of the N-terminal region, further, affects the ligand binding-site accessibility. Interestingly, long-range effects are also seen at the ligand binding site, which is marginally larger in the Gly as compared to the Arg variant resulting in the preferential docking of albuterol to the Gly variant. This study thus reveals key differences between the variants providing a molecular framework towards understanding the variable drug response in asthma patients.


Subject(s)
Binding Sites/genetics , Polymorphism, Genetic/genetics , Receptors, Adrenergic, beta-2/chemistry , Receptors, Adrenergic, beta-2/genetics , Albuterol/chemistry , Albuterol/metabolism , Asthma/genetics , Humans , Molecular Dynamics Simulation , Pharmacogenetics , Receptors, Adrenergic, beta-2/metabolism
9.
Genome Med ; 15(1): 102, 2023 Nov 29.
Article in English | MEDLINE | ID: mdl-38031187

ABSTRACT

BACKGROUND: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship. METHODS: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity. RESULTS: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy. CONCLUSIONS: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as "OGDHL-related disorders".


Subject(s)
Proteins , Zebrafish , Animals , Humans , Gene Frequency , Ketoglutarate Dehydrogenase Complex/genetics , Ketoglutarate Dehydrogenase Complex/metabolism , Phenotype , Proteins/genetics , Zebrafish/genetics
10.
Adv Protein Chem Struct Biol ; 128: 361-396, 2022.
Article in English | MEDLINE | ID: mdl-35034724

ABSTRACT

G protein-coupled receptors (GPCRs) are membrane proteins that play a central role in cell signaling and constitute one of the largest classes of drug targets. The molecular mechanisms underlying GPCR function have been characterized by several experimental and computational methods and provide an understanding of their role in physiology and disease. Population variants arising from nsSNPs affect the native function of GPCRs and have been implicated in differential drug response. In this chapter, we provide an overview on GPCR structure and activation, with a special focus on the ß2-adrenergic receptor (ß2-AR). First, we discuss the current understanding of the structural and dynamic features of the wildtype receptor. Subsequently, the population variants identified in this receptor from clinical and large-scale genomic studies are described. We show how computational approaches such as bioinformatics tools and molecular dynamics simulations can be used to characterize the variant receptors in comparison to the wildtype receptor. In particular, we discuss three examples of clinically important variants and discuss how the structure and function of these variants differ from the wildtype receptor at a molecular level. Overall, the chapter provides an overview of structure and function of GPCR variants and is a step towards the study of inter-individual differences and personalized medicine.


Subject(s)
Molecular Dynamics Simulation , Signal Transduction , Computational Biology , Membrane Proteins , Precision Medicine
11.
Heliyon ; 7(3): e06564, 2021 Mar.
Article in English | MEDLINE | ID: mdl-33758785

ABSTRACT

The mortality rates due to COVID-19 have been found disproportionate globally and are currently being researched. India mortality rate with a population of 1.3 billion people is relatively lowest to other countries with high infection rates. Genetic composition of circulating isolates continues to be a key determinant of virulence and pathogenesis. This study aimed to analyse the extent of divergence between genomes of Indian isolates (n = 2525 as compared to reference Wuhan-1 strain and isolates from countries showing higher fatality rates including France, Italy, Belgium, and the USA. The study also analyses the impact of key mutations on interactions with angiotensin converting enzyme 2 (ACE2) and panel of neutralizing monoclonal antibodies. Using 1,44,605 spike protein sequences, global prevalence of mutations in spike protein was observed. The study suggests that SARS-CoV-2 genomes from India share consensus with global trends with respect to D614G as most prevalent mutational event (81.66% among 2525 Indian isolates). Indian isolates did not reported prevalence of N439K mutation in receptor binding motif (RBM) as compared to global isolates (0.54%). Computational docking and molecular dynamics simulation analysis of N439K mutation with respect to ACE 2 binding and reactivity with RBM targeted antibodies viz., B38, BD23, CB6, P2B-F26 and EY6A suggests that variant have relatively higher affinity with ACE 2 receptor which may support higher infectivity. The study warrants large scale monitoring of Indian isolates as SARS-CoV-2 virus is expected to evolve and mutations may appear in unpredictable way.

12.
Biochim Biophys Acta Proteins Proteom ; 1869(4): 140605, 2021 04.
Article in English | MEDLINE | ID: mdl-33453412

ABSTRACT

The ß2-adrenergic receptor (ß2AR) is a member of the G protein-coupled receptor (GPCR) family that is an important drug target for asthma and COPD. Clinical studies coupled with biochemical data have identified a critical receptor variant, Thr164Ile, to have a reduced response to agonist-based therapy, although the molecular mechanism underlying this seemingly "non-deleterious" substitution is not clear. Here, we couple molecular dynamics simulations with network analysis and free-energy calculations to identify the molecular determinants underlying the differential drug response. We are able to identify hydration sites in the transmembrane domain that are essential to maintain the integrity of the binding site but are absent in the variant. The loss of these hydration sites in the variant correlates with perturbations in the intra-protein interaction network and rearrangements in the orthosteric ligand binding site. In conjunction, we observe an altered binding and reduced free energy of a series of agonists, in line with experimental trends. Our work identifies a functional allosteric pathway connected by specific hydration sites in ß2AR that has not been reported before and provides insight into water-mediated networks in GPCRs in general. Overall, the work is one of the first step towards developing variant-specific potent and selective agonists.


Subject(s)
Adrenergic beta-Agonists/pharmacology , Receptors, Adrenergic, beta-2/drug effects , Water/chemistry , Humans , Protein Binding , Protein Conformation , Receptors, Adrenergic, beta-2/chemistry
13.
ACS Omega ; 6(46): 31236-31243, 2021 Nov 23.
Article in English | MEDLINE | ID: mdl-34841167

ABSTRACT

Mosquito control by personal protection is one of the most efficient ways of curtailing deadly diseases such as malaria and dengue with the potential to save millions of lives per year. DEET (N,N-diethyl-3-methyl benzamide) is currently considered as the gold standard for mosquito repellents, being used for the past several decades. Control by DEET, however, is being threatened by emerging resistance among mosquitoes. To address this concern and also to improve protection times, we synthesized a novel series of 25 silicon-containing acyl piperidines using acid-amine coupling protocol and tested their activity against Aedes aegypti in mosquito-repellent assays. Several compounds from this series appear to possess good mosquito-repellent properties. Most notably, at 0.5 mg/cm2 concentrations, the mean protection time for NDS100100 was 756 min, which was higher than that of DEET (616 min). The details of design, synthesis, and biological evaluation are discussed herein.

14.
PLoS One ; 16(6): e0248479, 2021.
Article in English | MEDLINE | ID: mdl-34115763

ABSTRACT

The Coronavirus disease (COVID-19) caused by the virus SARS-CoV-2 has become a global pandemic in a very short time span. Currently, there is no specific treatment or vaccine to counter this highly contagious disease. There is an urgent need to find a specific cure for the disease and global efforts are directed at developing SARS-CoV-2 specific antivirals and immunomodulators. Ayurvedic Rasayana therapy has been traditionally used in India for its immunomodulatory and adaptogenic effects, and more recently has been included as therapeutic adjuvant for several maladies. Amongst several others, Withania somnifera (Ashwagandha), Tinospora cordifolia (Guduchi) and Asparagus racemosus (Shatavari) play an important role in Rasayana therapy. The objective of this study was to explore the immunomodulatory and anti SARS-CoV2 potential of phytoconstituents from Ashwagandha, Guduchi and Shatavari using network pharmacology and docking. The plant extracts were prepared as per ayurvedic procedures and a total of 31 phytoconstituents were identified using UHPLC-PDA and mass spectrometry studies. To assess the immunomodulatory potential of these phytoconstituents an in-silico network pharmacology model was constructed. The model predicts that the phytoconstituents possess the potential to modulate several targets in immune pathways potentially providing a protective role. To explore if these phytoconstituents also possess antiviral activity, docking was performed with the Spike protein, Main Protease and RNA dependent RNA polymerase of the virus. Interestingly, several phytoconstituents are predicted to possess good affinity for the three targets, suggesting their application for the termination of viral life cycle. Further, predictive tools indicate that there would not be adverse herb-drug pharmacokinetic-pharmacodynamic interactions with concomitantly administered drug therapy. We thus make a compelling case to evaluate the potential of these Rasayana botanicals as therapeutic adjuvants in the management of COVID-19 following rigorous experimental validation.


Subject(s)
Antiviral Agents/metabolism , Asparagus Plant/chemistry , COVID-19/metabolism , Immunologic Factors/metabolism , Molecular Docking Simulation/methods , Plant Extracts/metabolism , SARS-CoV-2/enzymology , Tinospora/chemistry , Withania/chemistry , Antiviral Agents/pharmacokinetics , Binding Sites , COVID-19/virology , Coronavirus 3C Proteases/metabolism , Coronavirus RNA-Dependent RNA Polymerase/metabolism , Herb-Drug Interactions , Humans , Immunologic Factors/pharmacokinetics , India , Medicine, Ayurvedic/methods , Phytotherapy/methods , Plant Extracts/pharmacokinetics , Protein Binding , Spike Glycoprotein, Coronavirus/metabolism , COVID-19 Drug Treatment
15.
J Mol Model ; 26(10): 264, 2020 Sep 10.
Article in English | MEDLINE | ID: mdl-32914310

ABSTRACT

White spot disease caused by the white spot syndrome virus (WSSV) incurs a huge loss to the shrimp farming industry. Since no effective therapeutic measures are available, early detection and prevention of the disease are indispensable. Towards this goal, we previously identified a 12-mer phage displayed peptide (designated as pep28) with high affinity for VP28, the structural protein of the white spot syndrome virus (WSSV). The peptide pep28 was successfully used as a biorecognition probe in the lateral flow assay developed for rapid, on-site detection of WSSV. To unravel the structural determinants for the selective binding between VP28 and pep28, we used bioinformatics, structural modeling, protein-protein docking, and binding-free energy studies. We performed atomistic molecular dynamics simulations of pep28-pIII model totaling 300 ns timescale. The most representative pep28-pIII structure from the simulation was used for docking with the crystal structure of VP28. Our results reveal that pep28 binds in a surface groove of the monomeric VP28 ß-barrel and makes several hydrogen bonds and non-polar interactions. Ensemble-based binding-free energy studies reveal that the binding is dominated by non-polar interactions. Our studies provide molecular level insights into the binding mechanism of pep28 with VP28, which explain why the peptide is selective and can assist in modifying pep28 for its practical use, both as a biorecognition probe and a therapeutic.


Subject(s)
Cell Surface Display Techniques , Epitope Mapping , Molecular Docking Simulation , Molecular Dynamics Simulation , Peptides/chemistry , Protein Interaction Mapping , Viral Envelope Proteins/chemistry , Amino Acid Sequence , Binding Sites , Epitope Mapping/methods , Hydrogen Bonding , Peptides/metabolism , Protein Binding , Protein Conformation , Protein Interaction Mapping/methods , Protein Multimerization , Structure-Activity Relationship , Viral Envelope Proteins/metabolism
16.
Int J Biol Macromol ; 149: 1051-1058, 2020 Apr 15.
Article in English | MEDLINE | ID: mdl-32006583

ABSTRACT

Kainate receptors belong to the ionotropic glutamate receptor family and play critical roles in the regulation of synaptic networks. The kainate receptor subunit GluK3 has unique functional properties and contributes to presynaptic facilitation at the hippocampal mossy fiber synapses along with roles at the post-synapses. To gain structural insights into the unique functional properties and dynamics of GluK3 receptor, we imaged them via electron microscopy in the apo-state and in complex with either agonist kainate or antagonist UBP301. Our analysis of all the GluK3 full-length structures not only provides insights into the receptor transitions between desensitized and closed states but also reveals a "non-classical" conformation of neurotransmitter binding domain in the closed-state distinct from that observed in AMPA and other kainate receptor structures. We show by molecular dynamics simulations that Asp759 influences the stability of the LBD dimers and hence could be responsible for the observed conformational variability and dynamics of the GluK3 via electron microscopy. Lower dimer stability could explain faster desensitization and low agonist sensitivity of GluK3. In overview, our work helps to associate biochemistry and physiology of GluK3 receptors with their structural biology and offers structural insights into the unique functional properties of these atypical receptors.


Subject(s)
Cryoelectron Microscopy , Neurotransmitter Agents/metabolism , Receptors, Kainic Acid/chemistry , Receptors, Kainic Acid/ultrastructure , Aspartic Acid/chemistry , HEK293 Cells , Humans , Kainic Acid/metabolism , Ligands , Models, Molecular , Protein Domains , Protein Multimerization , Receptors, Kainic Acid/isolation & purification , GluK3 Kainate Receptor
17.
Proteins ; 75(2): 323-35, 2009 May 01.
Article in English | MEDLINE | ID: mdl-18831046

ABSTRACT

The anthrax lethal factor is a zinc metalloprotease toxin secreted by Bacillus anthracis which cleaves at the N-terminal region of six mitogen activated protein kinase kinases (MEKs) in the cell. Additionally, it is known to cleave a nine residue peptide "LF10," 50-fold more efficiently than nine residues of MEK1. There is very little sequence similarity between the MEK N-termini, thus, it is unclear how the lethal factor can accommodate and cleave the diverse N-termini of the MEKs and whether there is a hierarchy in this interaction, as there is between LF10 and MEK1. To investigate this problem, we carried out multiple molecular dynamics simulations of the lethal factor with nine residues of each of the substrates. Our simulations reveal that like LF10, certain MEK substrates have residue compositions that favor beta-sheet formation with the lethal factor over others. The formation of this secondary structure maintains a catalytic conformation. Binding energetics using the MM-PBSA method was used to rank-order the substrates for their affinity to LF (K(M)). On the basis of the results, we conclude that the LF does not equally accommodate the MEK substrates and further predict that there will be differences between rates of cleavage among the nine residue MEK N-termini.


Subject(s)
Antigens, Bacterial/chemistry , Antigens, Bacterial/metabolism , Bacillus anthracis/metabolism , Bacterial Toxins/chemistry , Bacterial Toxins/metabolism , Mitogen-Activated Protein Kinase Kinases/chemistry , Mitogen-Activated Protein Kinase Kinases/metabolism , Bacillus anthracis/chemistry , Computer Simulation , Models, Molecular , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , Substrate Specificity , Thermodynamics
19.
J Biomol Struct Dyn ; 37(7): 1715-1723, 2019 Apr.
Article in English | MEDLINE | ID: mdl-29663856

ABSTRACT

The Heme-Regulated Inhibitor (HRI) kinase regulates globin synthesis in a heme-dependent manner in reticulocytes and erythroid cells in bone marrow. Inhibitors of HRI have been proposed to lead to an increased amount of haemoglobin, benefitting anaemia patients. A series of indeno[1,2-c]pyrazoles were discovered to be the first known in vitro inhibitors of HRI. However, the structural mechanism of inhibition is yet to be understood. The aim of this study was to unravel the binding mechanism of these inhibitors using molecular dynamic simulations and docking. The docking scores were observed to correlate well with experimentally determined pIC50 values. The inhibitors were observed to bind in the ATP-binding site forming hydrogen bonds with the hinge region and van der Waals interactions with non-polar residues in the binding site. Further, quantitative structure-activity relationship (QSAR) studies were performed to correlate the structural features of the inhibitors with their biological activity. The developed QSAR models were found to be statistically significant in terms of internal and external predictabilities. The presence of chlorine atoms and the hydroxymethyl groups were found to correlate with higher activity. The identified binding modes and the descriptors can support future rational identification of more potent and selective small molecule inhibitors for this kinase which are of therapeutic importance in the context of various human pathological disorders.


Subject(s)
Binding Sites , Protein Interaction Domains and Motifs , Protein Kinase Inhibitors/chemistry , eIF-2 Kinase/chemistry , Humans , Molecular Conformation , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Interaction Domains and Motifs/drug effects , Protein Kinase Inhibitors/pharmacology , Quantitative Structure-Activity Relationship , eIF-2 Kinase/antagonists & inhibitors
20.
Chem Phys Lipids ; 210: 142-148, 2018 01.
Article in English | MEDLINE | ID: mdl-28939366

ABSTRACT

The CXC chemokine receptor 1 (CXCR1) is an important member of the G protein-coupled receptor (GPCR) family in which the extracellular N-terminal domain has been implicated in ligand binding and selectivity. The structure of this domain has not yet been elucidated due to its inherent dynamics, but experimental evidence points toward membrane-dependent organization and dynamics. To gain molecular insight into the interaction of the N-terminal domain with the membrane bilayer, we performed a series of microsecond time scale atomistic simulations of the N-terminal domain of CXCR1 in the presence and absence of POPC bilayers. Our results show that the peptide displays a high propensity to adopt a ß-sheet conformation in the presence of the membrane bilayer. The interaction of the peptide with the membrane bilayer was found to be transient in our simulations. Interestingly, a scrambled peptide, containing the same residues in a randomly varying sequence, did not exhibit membrane-modulated structural dynamics. These results suggest that sequence-dependent electrostatics, modulated by the membrane, could play an important role in folding of the N-terminal domain. We believe that our results reinforce the emerging paradigm that cellular membranes could be important modulators of function of G protein-coupled receptors such as CXCR1.


Subject(s)
Lipid Bilayers/chemistry , Molecular Dynamics Simulation , Receptors, Interleukin-8A/chemistry , Humans
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