The pathogenicity,structural and functional exploration of human HMGB1 single nucleotide polymorphisms using in silico study

Abstract

The human HMGB1 gene mutations have a major impact on several immune-related diseases and cancer. The detrimental effect of non-synonymous mutations of HMGB1 has not been investigated yet, hence the present study aims to examine single nucleotide polymorphisms and their implications on the structure-function of human HMGB1. The multifaceted HMGB1 protein acts as pleiotropic cytokine and regulates essential genes for coordinated cellular functions. The mutational effect on HMGB1 was analyzed by sequence-based homology methods, supervised learning methods, and structure-based methods. The study identified 58 non-synonymous mutations in human HMGB1, out of which only 2 mutations; R10T (rs61742222) and F103C (rs61733675) were classified as the SNPs with highest deleterious and disease-causing mutants. The effect of these mutations in structure of HMGB1 was scrutinized and the R10T mutant found to have a distinct structural behaviour in the B-box domain. In addition, R10T mutant predicted that it affects the MoRF function of HMGB1 and it could disrupt the DNA binding or/and protein partner interaction activity by HMGB1. F103C mutation takes place at the TLR binding and cytokine inducing region of HMGB1, hence it could affect the protein binding activity which involves in many cellular signaling. The study identified potent mutations R10T (a cancer-causing somatic mutation) and F103C (a novel mutation) and these mutations either directly or indirectly hinder DNA binding activity and TLR and cytokine binding of HMGB1. These findings will help in understanding the molecular basis of these promising mutations and functional role of human HMGB1 in cancer and immunological diseases.

Abbreviations AGER Advanced glycosylation end product-specific receptor

CXCL Chemokine (C-X-C motif) ligand

dbSNP The single nucleotide polymorphism database

HMGB1 High mobility group box 1

LINCS LINear Constraint Solver

MDS Molecular dynamics simulation

MoRF Molecular recognition features

NPT Number of particle, Pressure and Temperature

NVT Number of particle, Volume and Temperature

nsSNP Non-synonymous SNP

PBC Partial boundary condition

PCA Principal component analysis

PME Partial mesh Ewald

RMSD Root mean square deviation

RMSF Root mean square fluctuation

SNP Single nucleotide polymorphism

SPC Single-point charge

TLR Toll-like receptor

UTR Un-translated Region

Communicated by Ramaswamy H. Sarma     

Tolerance and Immobilization of Cobalt by Some Bacteria from Ferromanganese Crusts of the Afanasiy Nikitin Seamounts

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Synaptic drosophila UNC‐13 is regulated by antagonistic G‐protein pathways via a proteasome‐dependent degradation mechanism

UNC‐13 is a highly conserved plasma membrane‐associated synaptic protein implicated in the regulation of neurotransmitter release through the direct modulation of the SNARE exocytosis complex. Previously, we characterized the Drosophila homologue (DUNC‐13) and showed it to be essential for neurotransmitter release immediately upstream of vesicular fusion (“priming”) at the neuromuscular junction (NMJ). Here, we show that the abundance of DUNC‐13 in NMJ synaptic boutons is regulated downstream of GαS and Gαq pathways, which have inhibitory and facilitatory roles, respectively. Both cAMP modulation and PKA function are required for DUNC‐13 synaptic up‐regulation, suggesting that the cAMP pathway enhances synaptic efficacy via DUNC‐13. Similarly, PLC function and DAG modulation also regulate the synaptic levels of DUNC‐13, through a mechanism that appears independent of PKC. Our results suggest that proteasome‐mediated protein degradation is the primary mechanism regulating DUNC‐13 levels at the synapse. Both PLC‐ and PKA‐mediated pathways appear to regulate synaptic levels of DUNC‐13 through controlling the rate of proteasome‐dependent DUNC‐13 degradation. We conclude that the functional abundance of DUNC‐13 at the synapse, a key determinant of synaptic vesicle priming and neurotransmitter release probability, is primarily regulated by the rate of protein degradation, rather than translocation or transport, convergently controlled via both cAMP and DAG signal transduction pathways. © 2003 Wiley Periodicals, Inc. J Neurobiol 54: 417–438, 2003     

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Development and validation of a highly sensitive and robust LC-MS/MS with electrospray ionization method for simultaneous quantitation of itraconazole and hydroxyitraconazole in human plasma: application to a bioequivalence study

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Molecular mechanisms of anti-angiogenic effect of curcumin

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