当前位置： SCI文献检索 > Computational and Structural Biotechnology Journal期刊下所有文献 > The impact of Gag non-cleavage site mutations on HIV-1 viral fitness from integrative modelling and simulations.

The impact of Gag non-cleavage site mutations on HIV-1 viral fitness from integrative modelling and simulations.

Abstract：

:The high mutation rate in retroviruses is one of the leading causes of drug resistance. In human immunodeficiency virus type-1 (HIV-1), synergistic mutations in its protease and the protease substrate - the Group-specific antigen (Gag) polyprotein - work together to confer drug resistance against protease inhibitors and compensate the mutations affecting viral fitness. Some Gag mutations can restore Gag-protease binding, yet most Gag-protease correlated mutations occur outside of the Gag cleavage site. To investigate the molecular basis for this, we now report multiscale modelling approaches to investigate various sequentially cleaved Gag products in the context of clinically relevant mutations that occur outside of the cleavage sites, including simulations of the largest Gag proteolytic product in its viral membrane-bound state. We found that some mutations, such as G123E and H219Q, involve direct interaction with cleavage site residues to influence their local environment, while certain mutations in the matrix domain lead to the enrichment of lipids important for Gag targeting and assembly. Collectively, our results reveal why non-cleavage site mutations have far-reaching implications outside of Gag proteolysis, with important consequences for drugging Gag maturation intermediates and tackling protease inhibitor resistance.

journal_name

Comput Struct Biotechnol J

journal_title

Computational and structural biotechnology journal

authors

Samsudin F,Gan SK,Bond PJ

doi

10.1016/j.csbj.2020.12.022

subject

Has Abstract

pub_date

2020-12-23 00:00:00

pages

330-342

issn

2001-0370

pii

S2001-0370(20)30547-X

journal_volume

19

pub_type

杂志文章

相关文献

Computational and Structural Biotechnology Journal文献大全
  • YaTCM: Yet another Traditional Chinese Medicine Database for Drug Discovery.

    abstract：:Traditional Chinese Medicine (TCM) has a long history of widespread clinical applications, especially in East Asia, and is becoming frequently used in Western countries. However, owing to extreme complicacy in both chemical ingredients and mechanism of action, a deep understanding of TCM is still difficult. To acceler...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2018.11.002

    authors： Li B,Ma C,Zhao X,Hu Z,Du T,Xu X,Wang Z,Lin J

    更新日期：2018-11-23 00:00:00

  • A metagenome-wide association study of gut microbiome and visceral fat accumulation.

    abstract：Purpose:Visceral fat is an independent risk factor for metabolic and cardiovascular disease. The study aimed to investigate the associations between gut microbiome and visceral fat. Methods:We recruited 32 obese adults and 30 healthy controls at baseline. Among the obese subjects, 14 subjects underwent laparoscopic sl...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.09.026

    authors： Nie X,Chen J,Ma X,Ni Y,Shen Y,Yu H,Panagiotou G,Bao Y

    更新日期：2020-09-20 00:00:00

  • Synthesis, LSD1 Inhibitory Activity, and LSD1 Binding Model of Optically Pure Lysine-PCPA Conjugates.

    abstract：:Compounds that inhibit the catalytic function of lysine-specific demethylase 1 (LSD1) are interesting as therapeutic agents. Recently, we identified three lysine-phenylcyclopropylamine conjugates, NCD18, NCD25, and NCD41, which are potent LSD1 inactivators. However, in our previous study, because we tested those compo...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.5936/csbj.201402002

    authors： Itoh Y,Ogasawara D,Ota Y,Mizukami T,Suzuki T

    更新日期：2014-02-15 00:00:00

  • PreMSIm: An R package for predicting microsatellite instability from the expression profiling of a gene panel in cancer.

    abstract：:Microsatellite instability (MSI) is a genomic property of the cancers with defective DNA mismatch repair and is a useful marker for cancer diagnosis and treatment in diverse cancer types. In particular, MSI has been associated with the active immune checkpoint blockade therapy response in cancer. Most of computational...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.03.007

    authors： Li L,Feng Q,Wang X

    更新日期：2020-03-19 00:00:00

  • A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments.

    abstract：:Metabonomics/metabolomics is an important science for the understanding of biological systems and the prediction of their behaviour, through the profiling of metabolites. Two technologies are routinely used in order to analyse metabolite profiles in biological fluids: nuclear magnetic resonance (NMR) spectroscopy and ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2016.02.005

    authors： Dona AC,Kyriakides M,Scott F,Shephard EA,Varshavi D,Veselkov K,Everett JR

    更新日期：2016-03-09 00:00:00

  • Learning distributed representations of RNA and protein sequences and its application for predicting lncRNA-protein interactions.

    abstract：:The long noncoding RNAs (lncRNAs) are ubiquitous in organisms and play crucial role in a variety of biological processes and complex diseases. Emerging evidences suggest that lncRNAs interact with corresponding proteins to perform their regulatory functions. Therefore, identifying interacting lncRNA-protein pairs is t...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2019.11.004

    authors： Yi HC,You ZH,Cheng L,Zhou X,Jiang TH,Li X,Wang YB

    更新日期：2019-11-30 00:00:00

  • Treatment According to Molecular Profiling in Relapsed/Refractory Cancer Patients: A Review Focusing on Latest Profiling Studies.

    abstract：:In this review we aim to summarize studies investigating the impact of a molecular profiling (MP)-guided treatment approach in heavily pretreated cancer patients. In summary, many independent single- and multicenter studies showed a significant benefit of MP-guided treatment regarding response rates and survival. Howe...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2019.03.012

    authors： Zimmer K,Kocher F,Spizzo G,Salem M,Gastl G,Seeber A

    更新日期：2019-03-26 00:00:00

  • Structure-based discovery of neoandrographolide as a novel inhibitor of Rab5 to suppress cancer growth.

    abstract：:Rab5 is a small GTPase that plays a crucial role in oncogenic signal transduction, which was considered as an attractive target for cancer therapy. Rapid GDP/GTP exchange in the packet of Rab5 sustains its high activity for promoting cancer progression. However, Rab5 currently remains undruggable due to the lack of sp...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.11.033

    authors： Zhang J,Sun Y,Zhong LY,Yu NN,Ouyang L,Fang RD,Wang Y,He QY

    更新日期：2020-11-30 00:00:00

  • Homology modeling in the time of collective and artificial intelligence.

    abstract：:Homology modeling is a method for building protein 3D structures using protein primary sequence and utilizing prior knowledge gained from structural similarities with other proteins. The homology modeling process is done in sequential steps where sequence/structure alignment is optimized, then a backbone is built and ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.11.007

    authors： Hameduh T,Haddad Y,Adam V,Heger Z

    更新日期：2020-11-14 00:00:00

  • Ethical issues related to research on genome editing in human embryos.

    abstract：:Although the potential advantages of clinical germline genome editing (GGE) over currently available methods are limited, the implementation of GGE in the clinic has been proposed and discussed. Ethical issues related to such an application have been extensively debated, meanwhile, seemingly less attention has been pa...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.03.014

    authors： Niemiec E,Howard HC

    更新日期：2020-03-21 00:00:00

  • Developing a mobile application to better inform patients and enable effective consultation in implant dentistry.

    abstract：:The field of dentistry lacks satisfactory tools to help visualize planned procedures and their potential results to patients. Dentists struggle to provide an effective image in their patient's mind of the end results of the planned treatment only through verbal explanations. Thus, verbal explanations alone often canno...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2016.06.006

    authors： Canbazoglu E,Salman YB,Yildirim ME,Merdenyan B,Ince IF

    更新日期：2016-06-29 00:00:00

  • Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs).

    abstract：:Appropriate development of the intestinal microbiota during infancy is known to be important for human health. In fact, aberrant alterations of the microbial composition during childhood may cause short- and/or long-term negative health effects. Many factors influence the initial assembly and subsequent progression of...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.08.028

    authors： Mancabelli L,Tarracchini C,Milani C,Lugli GA,Fontana F,Turroni F,van Sinderen D,Ventura M

    更新日期：2020-09-15 00:00:00

  • Disease, Models, Variants and Altered Pathways-Journeying RGD Through the Magnifying Glass.

    abstract：:Understanding the pathogenesis of disease is instrumental in delineating its progression mechanisms and for envisioning ways to counteract it. In the process, animal models represent invaluable tools for identifying disease-related loci and their genetic components. Amongst them, the laboratory rat is used extensively...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2015.11.006

    authors： Petri V,Hayman GT,Tutaj M,Smith JR,Laulederkind S,Wang SJ,Nigam R,De Pons J,Shimoyama M,Dwinell MR

    更新日期：2015-11-26 00:00:00

  • Microvesicles from indoxyl sulfate-treated endothelial cells induce vascular calcification in vitro.

    abstract：:Vascular calcification (VC), an unpredictable pathophysiological process and critical event in patients with cardiovascular diseases (CVDs), is the leading cause of morbi-mortality and disability in chronic kidney disease (CKD) patients worldwide. Currently, no diagnostic method is available for identifying patients a...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.04.006

    authors： Alique M,Bodega G,Corchete E,García-Menéndez E,de Sequera P,Luque R,Rodríguez-Padrón D,Marqués M,Portolés J,Carracedo J,Ramírez R

    更新日期：2020-04-09 00:00:00

  • A bird's-eye view of deep learning in bioimage analysis.

    abstract：:Deep learning of artificial neural networks has become the de facto standard approach to solving data analysis problems in virtually all fields of science and engineering. Also in biology and medicine, deep learning technologies are fundamentally transforming how we acquire, process, analyze, and interpret data, with ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.08.003

    authors： Meijering E

    更新日期：2020-08-07 00:00:00

  • News in livestock research - use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals.

    abstract：:Technical progress in the field of next-generation sequencing, mass spectrometry and bioinformatics facilitates the study of highly complex biological samples such as taxonomic and functional characterization of microbial communities that virtually colonize all present ecological niches. Compared to the structural inf...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2014.12.005

    authors： Deusch S,Tilocca B,Camarinha-Silva A,Seifert J

    更新日期：2014-12-24 00:00:00

  • Assessment of automated analyses of cell migration on flat and nanostructured surfaces.

    abstract：:Motility studies of cells often rely on computer software that analyzes time-lapse recorded movies and establishes cell trajectories fully automatically. This raises the question of reproducibility of results, since different programs could yield significantly different results of such automated analysis. The fact tha...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.5936/csbj.201207004

    authors： Grădinaru C,Lopacińska JM,Huth J,Kestler HA,Flyvbjerg H,Mølhave K

    更新日期：2012-11-21 00:00:00

  • Quantitative comparison of ABC membrane protein type I exporter structures in a standardized way.

    abstract：:An increasing number of ABC membrane protein structures are determined by cryo-electron microscopy and X-ray crystallography, consequently identifying differences between their conformations has become an arising issue. Therefore, we propose to define standardized measures for ABC Type I exporter structure characteriz...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2018.10.008

    authors： Csizmadia G,Farkas B,Spagina Z,Tordai H,Hegedűs T

    更新日期：2018-10-18 00:00:00

  • Dynamic exchange of two types of stator units in Bacillus subtilis flagellar motor in response to environmental changes.

    abstract：:Bacteria can migrate towards more suitable environments by rotating flagella that are under the control of sensory signal transduction networks. The bacterial flagellum is composed of the long helical filament functioning as a propeller, the flexible hook as a universal joint and the basal body as a rotary motor power...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.1016/j.csbj.2020.10.009

    authors： Terahara N,Namba K,Minamino T

    更新日期：2020-10-15 00:00:00

  • Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity.

    abstract：:SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by binding with the cell surface receptor - angiotensin converting enzyme (ACE2). We computationally contrasted the binding interactions between human ACE2 and coronavirus spike protein receptor binding domain (RBD) of the 2002 epidemic-ca...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.09.019

    authors： Chowdhury R,Boorla VS,Maranas CD

    更新日期：2020-01-01 00:00:00

  • AUDACITY: A comprehensive approach for the detection and classification of Runs of Homozygosity in medical and population genomics.

    abstract：:Runs of Homozygosity (RoHs) are popular among geneticists as the footprint of demographic processes, evolutionary forces and inbreeding in shaping our genome, and are known to confer risk of Mendelian and complex diseases. Notwithstanding growing interest in their study, there is unmet need for reliable and rapid meth...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.07.003

    authors： Magi A,Giangregorio T,Semeraro R,Carangelo G,Palombo F,Romeo G,Seri M,Pippucci T

    更新日期：2020-07-14 00:00:00

  • HiPR: High-throughput probabilistic RNA structure inference.

    abstract：:Recent high-throughput structure-sensitive genome-wide sequencing-based assays have enabled large-scale studies of RNA structure, and robust transcriptome-wide computational prediction of individual RNA structures across RNA classes from these assays has potential to further improve the prediction accuracy. Here, we d...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.06.004

    authors： Kuksa PP,Li F,Kannan S,Gregory BD,Leung YY,Wang LS

    更新日期：2020-06-08 00:00:00

  • Characterization of ENU-induced Mutations in Red Blood Cell Structural Proteins.

    abstract：:Murine models with modified gene function as a result of N-ethyl-N-nitrosourea (ENU) mutagenesis have been used to study phenotypes resulting from genetic change. This study investigated genetic factors associated with red blood cell (RBC) physiology and structural integrity that may impact on blood component storage ...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.5936/csbj.201303012

    authors： Kildey K,Flower RL,Tran TV,Tunningley R,Harris J,Dean MM

    更新日期：2013-09-23 00:00:00

  • Engineering microbes for plant polyketide biosynthesis.

    abstract：:Polyketides are an important group of secondary metabolites, many of which have important industrial applications in the food and pharmaceutical industries. Polyketides are synthesized from one of three classes of enzymes differentiated by their biochemical features and product structure: type I, type II or type III p...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章,评审

    doi：10.5936/csbj.201210020

    authors： Lussier FX,Colatriano D,Wiltshire Z,Page JE,Martin VJ

    更新日期：2013-02-22 00:00:00

  • Classification and substrate head-group specificity of membrane fatty acid desaturases.

    abstract：:Membrane fatty acid desaturases are a diverse superfamily of enzymes that catalyze the introduction of double bonds into fatty acids. They are essential in a range of metabolic processes, such as the production of omega-3 fatty acids. However, our structure-function understanding of this superfamily is still developin...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2016.08.003

    authors： Li D,Moorman R,Vanhercke T,Petrie J,Singh S,Jackson CJ

    更新日期：2016-09-12 00:00:00

  • Transcriptome and proteome analyses reveal the regulatory networks and metabolite biosynthesis pathways during the development of Tolypocladium guangdongense.

    abstract：:Tolypocladium guangdongense has a similar metabolite profile to Ophiocordyceps sinensis, a highly regarded fungus used for traditional Chinese medicine with high nutritional and medicinal value. Although the genome sequence of T. guangdongense has been reported, relatively little is known about the regulatory networks...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.07.014

    authors： Wang G,Li M,Zhang C,Cheng H,Gao Y,Deng W,Li T

    更新日期：2020-07-25 00:00:00

  • Leveraging biological replicates to improve analysis in ChIP-seq experiments.

    abstract：:ChIP-seq experiments identify genome-wide profiles of DNA-binding molecules including transcription factors, enzymes and epigenetic marks. Biological replicates are critical for reliable site discovery and are required for the deposition of data in the ENCODE and modENCODE projects. While early reports suggested two r...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.5936/csbj.201401002

    authors： Yang Y,Fear J,Hu J,Haecker I,Zhou L,Renne R,Bloom D,McIntyre LM

    更新日期：2014-01-31 00:00:00

  • Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods.

    abstract：Purpose:Mutation-induced variation of protein-ligand binding affinity is the key to many genetic diseases and the emergence of drug resistance, and therefore predicting such mutation impacts is of great importance. In this work, we aim to predict the mutation impacts on protein-ligand binding affinity using efficient s...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.02.007

    authors： Wang DD,Ou-Yang L,Xie H,Zhu M,Yan H

    更新日期：2020-02-20 00:00:00

  • ASJA: A Program for Assembling Splice Junctions Analysis.

    abstract：:RNA splicing may generate different kinds of splice junctions, such as linear, back-splice and fusion junctions. Only a limited number of programs are available for detection and quantification of splice junctions. Here, we present Assembling Splice Junctions Analysis (ASJA), a software package that identifies and cha...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2019.08.001

    authors： Zhao J,Li Q,Li Y,He X,Zheng Q,Huang S

    更新日期：2019-08-07 00:00:00

  • A molecular device: A DNA molecular lock driven by the nicking enzymes.

    abstract：:As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molec...

    journal_title：Computational and structural biotechnology journal

    pub_type： 杂志文章

    doi：10.1016/j.csbj.2020.08.004

    authors： Zhang X,Zhang Q,Liu Y,Wang B,Zhou S

    更新日期：2020-08-06 00:00:00