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1.
BMC Bioinformatics ; 22(1): 430, 2021 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-34496745

RESUMO

BACKGROUND: Essential proteins have great impacts on cell survival and development, and played important roles in disease analysis and new drug design. However, since it is inefficient and costly to identify essential proteins by using biological experiments, then there is an urgent need for automated and accurate detection methods. In recent years, the recognition of essential proteins in protein interaction networks (PPI) has become a research hotspot, and many computational models for predicting essential proteins have been proposed successively. RESULTS: In order to achieve higher prediction performance, in this paper, a new prediction model called TGSO is proposed. In TGSO, a protein aggregation degree network is constructed first by adopting the node density measurement method for complex networks. And simultaneously, a protein co-expression interactive network is constructed by combining the gene expression information with the network connectivity, and a protein co-localization interaction network is constructed based on the subcellular localization data. And then, through integrating these three kinds of newly constructed networks, a comprehensive protein-protein interaction network will be obtained. Finally, based on the homology information, scores can be calculated out iteratively for different proteins, which can be utilized to estimate the importance of proteins effectively. Moreover, in order to evaluate the identification performance of TGSO, we have compared TGSO with 13 different latest competitive methods based on three kinds of yeast databases. And experimental results show that TGSO can achieve identification accuracies of 94%, 82% and 72% out of the top 1%, 5% and 10% candidate proteins respectively, which are to some degree superior to these state-of-the-art competitive models. CONCLUSIONS: We constructed a comprehensive interactive network based on multi-source data to reduce the noise and errors in the initial PPI, and combined with iterative methods to improve the accuracy of necessary protein prediction, and means that TGSO may be conducive to the future development of essential protein recognition as well.


Assuntos
Biologia Computacional , Mapas de Interação de Proteínas , Algoritmos , Mapeamento de Interação de Proteínas , Proteínas/genética , Proteínas/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo
2.
Phys Rev Lett ; 127(9): 098103, 2021 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-34506164

RESUMO

The genotype-phenotype mapping of proteins is a fundamental question in structural biology. In this Letter, with the analysis of a large dataset of proteins from hundreds of protein families, we quantitatively demonstrate the correlations between the noise-induced protein dynamics and mutation-induced variations of native structures, indicating the dynamics-evolution correspondence of proteins. Based on the investigations of the linear responses of native proteins, the origin of such a correspondence is elucidated. It is essential that the noise- and mutation-induced deformations of the proteins are restricted on a common low-dimensional subspace, as confirmed from the data. These results suggest an evolutionary mechanism of the proteins gaining both dynamical flexibility and evolutionary structural variability.


Assuntos
Modelos Químicos , Proteínas/química , Proteínas/genética , Proteases 3C de Coronavírus/química , Proteases 3C de Coronavírus/genética , Evolução Molecular , Estudos de Associação Genética , Mutação , Conformação Proteica
3.
PLoS Comput Biol ; 17(8): e1009284, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34347784

RESUMO

Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial role in protein engineering and drug design. In this study, we develop GeoPPI, a novel structure-based deep-learning framework to predict the change of binding affinity upon mutations. Based on the three-dimensional structure of a protein, GeoPPI first learns a geometric representation that encodes topology features of the protein structure via a self-supervised learning scheme. These representations are then used as features for training gradient-boosting trees to predict the changes of protein-protein binding affinity upon mutations. We find that GeoPPI is able to learn meaningful features that characterize interactions between atoms in protein structures. In addition, through extensive experiments, we show that GeoPPI achieves new state-of-the-art performance in predicting the binding affinity changes upon both single- and multi-point mutations on six benchmark datasets. Moreover, we show that GeoPPI can accurately estimate the difference of binding affinities between a few recently identified SARS-CoV-2 antibodies and the receptor-binding domain (RBD) of the S protein. These results demonstrate the potential of GeoPPI as a powerful and useful computational tool in protein design and engineering. Our code and datasets are available at: https://github.com/Liuxg16/GeoPPI.


Assuntos
Substituição de Aminoácidos , Modelos Químicos , Proteínas/metabolismo , Mutação Puntual , Ligação Proteica , Proteínas/química , Proteínas/genética
4.
Nat Commun ; 12(1): 4917, 2021 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-34389714

RESUMO

APOBEC3A is a cytidine deaminase driving mutagenesis in tumors. While APOBEC3A-induced mutations are common, APOBEC3A expression is rarely detected in cancer cells. This discrepancy suggests a tightly controlled process to regulate episodic APOBEC3A expression in tumors. In this study, we find that both viral infection and genotoxic stress transiently up-regulate APOBEC3A and pro-inflammatory genes using two distinct mechanisms. First, we demonstrate that STAT2 promotes APOBEC3A expression in response to foreign nucleic acid via a RIG-I, MAVS, IRF3, and IFN-mediated signaling pathway. Second, we show that DNA damage and DNA replication stress trigger a NF-κB (p65/IkBα)-dependent response to induce expression of APOBEC3A and other innate immune genes, independently of DNA or RNA sensing pattern recognition receptors and the IFN-signaling response. These results not only reveal the mechanisms by which tumors could episodically up-regulate APOBEC3A but also highlight an alternative route to stimulate the immune response after DNA damage independently of cGAS/STING or RIG-I/MAVS.


Assuntos
Citidina Desaminase/genética , Dano ao DNA , Regulação da Expressão Gênica , Imunidade/genética , Proteínas/genética , Transdução de Sinais/fisiologia , Linhagem Celular , Linhagem Celular Tumoral , Citidina Desaminase/metabolismo , Interações Hospedeiro-Patógeno , Humanos , Proteínas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Células THP-1 , Fator de Transcrição RelA/metabolismo , Regulação para Cima , Vírus/crescimento & desenvolvimento
5.
Gene ; 802: 145868, 2021 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-34364911

RESUMO

The Honduran white bat, Ectophylla alba (Allen 1982), is one of eight species belonging to the family Phyllostomidae that exclusively roosts in tents. Due to its restricted distribution, habitat specificity, and diet requirements, E. alba has been strongly affected by habitat loss and fragmentation during the last decade. In this study, we developed the first genomic resource for this species; we assembled and analyzed in detail the complete mitochondrial genome of E. alba. The mitogenome of E. alba is 16,664 bp in length and is comprised of 13 protein coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes (tRNAs), and a putative Control Region (CR) 1,232 bp in length. Gene arrangement in the mitochondrial chromosome of E. alba is identical to that reported before in other species of co-familiar bats. All PCGs are under purifying selection, with atp8 experiencing the least selective pressure. In all PCGs, codons ending with adenine are preferred over others ending in thymine and cytosine. Except tRNA-Serine 1, all tRNAs exhibit a cloverleaf secondary structure. The CR of E. alba exhibits three domains commonly described in other mammals, including bats; extended terminal associated sequences (ETAS), central, and conserved sequence block (CSB). A ML phylogenetic reconstruction of the family Phyllostomidae based on all 13 mitochondrial PCGs confirms the monophyletic status of the subfamily Sternodermatinae and indicates the close relationship between E. alba and the genus Artibeus. This is the first genomic resource developed for E. alba and represents the first step to improving our understanding of the genomic underpinnings involved in the evolution of specialization as well as acclimatization and adaptation to local and global change of specialist bats.


Assuntos
Quirópteros/genética , Genoma Mitocondrial , Animais , Quirópteros/classificação , Uso do Códon , DNA Mitocondrial , Filogenia , Proteínas/genética , RNA de Transferência/genética
6.
Nat Commun ; 12(1): 5044, 2021 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-34413298

RESUMO

Indirect somatic genetic rescue (SGR) of a germline mutation is thought to be rare in inherited Mendelian disorders. Here, we establish that acquired mutations in the EIF6 gene are a frequent mechanism of SGR in Shwachman-Diamond syndrome (SDS), a leukemia predisposition disorder caused by a germline defect in ribosome assembly. Biallelic mutations in the SBDS or EFL1 genes in SDS impair release of the anti-association factor eIF6 from the 60S ribosomal subunit, a key step in the translational activation of ribosomes. Here, we identify diverse mosaic somatic genetic events (point mutations, interstitial deletion, reciprocal chromosomal translocation) in SDS hematopoietic cells that reduce eIF6 expression or disrupt its interaction with the 60S subunit, thereby conferring a selective advantage over non-modified cells. SDS-related somatic EIF6 missense mutations that reduce eIF6 dosage or eIF6 binding to the 60S subunit suppress the defects in ribosome assembly and protein synthesis across multiple SBDS-deficient species including yeast, Dictyostelium and Drosophila. Our data suggest that SGR is a universal phenomenon that may influence the clinical evolution of diverse Mendelian disorders and support eIF6 suppressor mimics as a therapeutic strategy in SDS.


Assuntos
Mutação , Subunidades Ribossômicas Maiores de Eucariotos/metabolismo , Ribossomos/genética , Ribossomos/patologia , Síndrome de Shwachman-Diamond/genética , Síndrome de Shwachman-Diamond/patologia , Adolescente , Adulto , Animais , Fenômenos Biológicos , Células Cultivadas , Criança , Pré-Escolar , Dictyostelium , Drosophila , Fatores de Iniciação em Eucariotos/genética , Fatores de Iniciação em Eucariotos/metabolismo , Células Germinativas , Humanos , Lactente , Simulação de Dinâmica Molecular , Fatores de Alongamento de Peptídeos/genética , Fatores de Alongamento de Peptídeos/metabolismo , Ligação Proteica , Biossíntese de Proteínas , Proteínas/genética , Proteínas/metabolismo , Ribonucleoproteína Nuclear Pequena U5/genética , Ribonucleoproteína Nuclear Pequena U5/metabolismo , Ribossomos/metabolismo , Saccharomyces cerevisiae , Homologia de Sequência de Aminoácidos , Síndrome de Shwachman-Diamond/metabolismo , Adulto Jovem
7.
Molecules ; 26(16)2021 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-34443538

RESUMO

Cytochrome c is a small globular protein whose main physiological role is to shuttle electrons within the mitochondrial electron transport chain. This protein has been widely investigated, especially as a paradigmatic system for understanding the fundamental aspects of biological electron transfer and protein folding. Nevertheless, cytochrome c can also be endowed with a non-native catalytic activity and be immobilized on an electrode surface for the development of third generation biosensors. Here, an overview is offered of the most significant examples of such a functional transformation, carried out by either point mutation(s) or controlled unfolding. The latter can be induced chemically or upon protein immobilization on hydrophobic self-assembled monolayers. We critically discuss the potential held by these systems as core constituents of amperometric biosensors, along with the issues that need to be addressed to optimize their applicability and response.


Assuntos
Técnicas Biossensoriais , Elétrons , Proteínas/metabolismo , Eletroquímica , Oxirredução , Mutação Puntual/genética , Dobramento de Proteína , Proteínas/química , Proteínas/genética
8.
Nat Commun ; 12(1): 5011, 2021 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-34408149

RESUMO

Sequence-based contact prediction has shown considerable promise in assisting non-homologous structure modeling, but it often requires many homologous sequences and a sufficient number of correct contacts to achieve correct folds. Here, we developed a method, C-QUARK, that integrates multiple deep-learning and coevolution-based contact-maps to guide the replica-exchange Monte Carlo fragment assembly simulations. The method was tested on 247 non-redundant proteins, where C-QUARK could fold 75% of the cases with TM-scores (template-modeling scores) ≥0.5, which was 2.6 times more than that achieved by QUARK. For the 59 cases that had either low contact accuracy or few homologous sequences, C-QUARK correctly folded 6 times more proteins than other contact-based folding methods. C-QUARK was also tested on 64 free-modeling targets from the 13th CASP (critical assessment of protein structure prediction) experiment and had an average GDT_TS (global distance test) score that was 5% higher than the best CASP predictors. These data demonstrate, in a robust manner, the progress in modeling non-homologous protein structures using low-accuracy and sparse contact-map predictions.


Assuntos
Biologia Computacional/métodos , Proteínas/química , Bases de Dados de Proteínas , Modelos Moleculares , Método de Monte Carlo , Conformação Proteica , Dobramento de Proteína , Proteínas/genética , Software
9.
Molecules ; 26(16)2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34443469

RESUMO

The classical genetic code maps nucleotide triplets to amino acids. The associated sequence composition is complex, representing many elaborations during evolution of form and function. Other genomic elements code for the expression and processing of RNA transcripts. However, over 50% of the human genome consists of widely dispersed repetitive sequences. Among these are simple sequence repeats (SSRs), representing a class of flipons, that under physiological conditions, form alternative nucleic acid conformations such as Z-DNA, G4 quartets, I-motifs, and triplexes. Proteins that bind in a structure-specific manner enable the seeding of condensates with the potential to regulate a wide range of biological processes. SSRs also encode the low complexity peptide repeats to patch condensates together, increasing the number of combinations possible. In situations where SSRs are transcribed, SSR-specific, single-stranded binding proteins may further impact condensate formation. Jointly, flipons and patches speed evolution by enhancing the functionality of condensates. Here, the focus is on the selection of SSR flipons and peptide patches that solve for survival under a wide range of environmental contexts, generating complexity with simple parts.


Assuntos
DNA Forma Z/química , DNA Forma Z/genética , Evolução Molecular , Conformação de Ácido Nucleico , Proteínas/química , Proteínas/genética , Animais , Códon , DNA Forma Z/metabolismo , Genética , Humanos , Repetições de Microssatélites/genética , Proteínas/metabolismo
10.
Nat Genet ; 53(8): 1260-1269, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34226706

RESUMO

Exome association studies to date have generally been underpowered to systematically evaluate the phenotypic impact of very rare coding variants. We leveraged extensive haplotype sharing between 49,960 exome-sequenced UK Biobank participants and the remainder of the cohort (total n ≈ 500,000) to impute exome-wide variants with accuracy R2 > 0.5 down to minor allele frequency (MAF) ~0.00005. Association and fine-mapping analyses of 54 quantitative traits identified 1,189 significant associations (P < 5 × 10-8) involving 675 distinct rare protein-altering variants (MAF < 0.01) that passed stringent filters for likely causality. Across all traits, 49% of associations (578/1,189) occurred in genes with two or more hits; follow-up analyses of these genes identified allelic series containing up to 45 distinct 'likely-causal' variants. Our results demonstrate the utility of within-cohort imputation in population-scale genome-wide association studies, provide a catalog of likely-causal, large-effect coding variant associations and foreshadow the insights that will be revealed as genetic biobank studies continue to grow.


Assuntos
Bancos de Espécimes Biológicos , Frequência do Gene , Proteínas/genética , Sequenciamento Completo do Exoma/estatística & dados numéricos , Pressão Sanguínea/genética , Mapeamento Cromossômico/métodos , Mapeamento Cromossômico/estatística & dados numéricos , Marcadores Genéticos , Estudo de Associação Genômica Ampla/estatística & dados numéricos , Humanos , Desequilíbrio de Ligação , Proteínas de Membrana/genética , Modelos Genéticos , Fenótipo , Polimorfismo de Nucleotídeo Único , Proteínas/metabolismo , Receptores do Fator Natriurético Atrial/genética , Reino Unido , Sequenciamento Completo do Exoma/métodos
11.
Nat Commun ; 12(1): 4339, 2021 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-34267198

RESUMO

Pleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs), but specific interaction with and regulation by PIPs for most PH domain-containing proteins are unclear. Here we employ a single-molecule pulldown assay to study interactions of lipid vesicles with full-length proteins in mammalian whole cell lysates. Of 67 human PH domain-containing proteins initially examined, 36 (54%) are found to have affinity for PIPs with various specificity, the majority of which have not been reported before. Further investigation of ARHGEF3 reveals distinct structural requirements for its binding to PI(4,5)P2 and PI(3,5)P2, and functional relevance of its PI(4,5)P2 binding. We generate a recursive-learning algorithm based on the assay results to analyze the sequences of 242 human PH domains, predicting that 49% of them bind PIPs. Twenty predicted binders and 11 predicted non-binders are assayed, yielding results highly consistent with the prediction. Taken together, our findings reveal unexpected lipid-binding specificity of PH domain-containing proteins.


Assuntos
Fosfatidilinositóis/metabolismo , Domínios de Homologia à Plecstrina , Proteínas/química , Proteínas/metabolismo , Algoritmos , Animais , Sítios de Ligação , Biologia Computacional/métodos , Células HEK293 , Humanos , Camundongos , Microscopia de Fluorescência , Células NIH 3T3 , Fosfatidilinositóis/química , Fosfatidilserinas/química , Fosfatidilserinas/metabolismo , Proteínas/genética , Fatores de Troca de Nucleotídeo Guanina Rho/química , Fatores de Troca de Nucleotídeo Guanina Rho/genética , Fatores de Troca de Nucleotídeo Guanina Rho/metabolismo , Sensibilidade e Especificidade , Proteína rhoA de Ligação ao GTP/metabolismo
12.
Nat Commun ; 12(1): 4368, 2021 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-34272383

RESUMO

Bioproduction of renewable chemicals is considered as an urgent solution for fossil energy crisis. However, despite tremendous efforts, it is still challenging to generate microbial strains that can produce target biochemical to high levels. Here, we report an example of biosynthesis of high-value and easy-recoverable derivatives built upon natural microbial pathways, leading to improvement in bioproduction efficiency. By leveraging pathways in solventogenic clostridia for co-producing acyl-CoAs, acids and alcohols as precursors, through rational screening for host strains and enzymes, systematic metabolic engineering-including elimination of putative prophages, we develop strains that can produce 20.3 g/L butyl acetate and 1.6 g/L butyl butyrate. Techno-economic analysis results suggest the economic competitiveness of our developed bioprocess. Our principles of selecting the most appropriate host for specific bioproduction and engineering microbial chassis to produce high-value and easy-separable end products may be applicable to other bioprocesses.


Assuntos
Acetatos/metabolismo , Butiratos/química , Clostridium/metabolismo , Ácidos Graxos/metabolismo , Fermentação/genética , Engenharia Metabólica/métodos , Acetilcoenzima A/metabolismo , Biocombustíveis/microbiologia , Biomassa , Clostridium/enzimologia , Clostridium/genética , Ésteres/metabolismo , Redes e Vias Metabólicas/genética , NAD/metabolismo , Proteínas/genética , Proteínas/metabolismo , Proteínas Recombinantes
13.
BMC Bioinformatics ; 22(Suppl 7): 345, 2021 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-34225665

RESUMO

BACKGROUND: Despite decades on developing dedicated Web tools, it is still difficult to predict correctly the changes of the thermodynamic stability of proteins caused by mutations. Here, we assessed the reliability of five recently developed Web tools, in order to evaluate the progresses in the field. RESULTS: The results show that, although there are improvements in the field, the assessed predictors are still far from ideal. Prevailing problems include the bias towards destabilizing mutations, and, in general, the results are unreliable when the mutation causes a ΔΔG within the interval ± 0.5 kcal/mol. We found that using several predictors and combining their results into a consensus is a rough, but effective way to increase reliability of the predictions. CONCLUSIONS: We suggest all developers to consider in their future tools the usage of balanced data sets for training of predictors, and all users to combine the results of multiple tools to increase the chances of having correct predictions about the effect of mutations on the thermodynamic stability of a protein.


Assuntos
Proteínas , Mutação , Estabilidade Proteica , Proteínas/genética , Reprodutibilidade dos Testes , Termodinâmica
14.
Nat Genet ; 53(8): 1125-1134, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34312540

RESUMO

Autism is a highly heritable complex disorder in which de novo mutation (DNM) variation contributes significantly to risk. Using whole-genome sequencing data from 3,474 families, we investigate another source of large-effect risk variation, ultra-rare variants. We report and replicate a transmission disequilibrium of private, likely gene-disruptive (LGD) variants in probands but find that 95% of this burden resides outside of known DNM-enriched genes. This variant class more strongly affects multiplex family probands and supports a multi-hit model for autism. Candidate genes with private LGD variants preferentially transmitted to probands converge on the E3 ubiquitin-protein ligase complex, intracellular transport and Erb signaling protein networks. We estimate that these variants are approximately 2.5 generations old and significantly younger than other variants of similar type and frequency in siblings. Overall, private LGD variants are under strong purifying selection and appear to act on a distinct set of genes not yet associated with autism.


Assuntos
Transtorno do Espectro Autista/genética , Predisposição Genética para Doença , Proteínas/genética , Transtorno Autístico/genética , Evolução Molecular , Dosagem de Genes , Haplótipos , Humanos , Desequilíbrio de Ligação , Modelos Genéticos , Mutação , Linhagem , Polimorfismo de Nucleotídeo Único , Mapas de Interação de Proteínas/genética , Irmãos , Sequenciamento Completo do Genoma
15.
Methods Mol Biol ; 2328: 115-138, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34251622

RESUMO

With the popularity of high-throughput transcriptomic techniques like RNAseq, models of gene regulatory networks have been important tools for understanding how genes are regulated. These transcriptomic datasets are usually assumed to reflect their associated proteins. This assumption, however, ignores post-transcriptional, translational, and post-translational regulatory mechanisms that regulate protein abundance but not transcript abundance. Here we describe a method to model cross-regulatory influences between the transcripts and proteins of a set of genes using abundance data collected from a series of transgenic experiments. The developed model can capture the effects of regulation that impacts transcription as well as regulatory mechanisms occurring after transcription. This approach uses a sparse maximum likelihood algorithm to determine relationships that influence transcript and protein abundance. An example of how to explore the network topology of this type of model is also presented. This model can be used to predict how the transcript and protein abundances will change in novel transgenic modification strategies.


Assuntos
Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica/genética , Redes Reguladoras de Genes/genética , Metabolômica/métodos , Proteínas/metabolismo , Proteômica/métodos , Transcriptoma/genética , Algoritmos , Biologia Computacional/métodos , Modelos Teóricos , Populus/genética , Populus/metabolismo , Proteínas/genética
16.
Mol Genet Genomics ; 296(5): 1161-1173, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34259913

RESUMO

Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation amongst the human population and are key to personalized medicine. New tests are presented to distinguish pathogenic/malign (i.e., likely to contribute to or cause a disease) from nonpathogenic/benign SNPs, regardless of whether they occur in coding (exon) or noncoding (intron) regions in the human genome. The tests are based on the nearest neighbor (NN) model of Gibbs free energy landscapes of DNA hybridization and on deep structural properties of DNA revealed by an approximating metric (the h-distance) in DNA spaces of oligonucleotides of a common size. The quality assessments show that the newly defined PNPG test can classify a SNP with an accuracy about 73% for the required parameters. The best performance among machine learning models is a feed-forward neural network with fivefold cross-validation accuracy of at least 73%. These results may provide valuable tools to solve the SNP classification problem, where tools are lacking, to assess the likelihood of disease causing in unclassified SNPs. These tests highlight the significance of hybridization chemistry in SNPs. They can be applied to further the effectiveness of research in the areas of genomics and metabolomics.


Assuntos
Modelos Genéticos , Polimorfismo de Nucleotídeo Único , Proteínas/genética , Genoma Humano , Humanos , Aprendizado de Máquina , Proteínas/metabolismo
17.
Int J Mol Sci ; 22(14)2021 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-34299007

RESUMO

Ubiquitin fold modifier 1 (UFM1) is a member of the ubiquitin-like protein family. UFM1 undergoes a cascade of enzymatic reactions including activation by UBA5 (E1), transfer to UFC1 (E2) and selective conjugation to a number of target proteins via UFL1 (E3) enzymes. Despite the importance of ufmylation in a variety of cellular processes and its role in the pathogenicity of many human diseases, the molecular mechanisms of the ufmylation cascade remains unclear. In this study we focused on the biophysical and biochemical characterization of the interaction between UBA5 and UFC1. We explored the hypothesis that the unstructured C-terminal region of UBA5 serves as a regulatory region, controlling cellular localization of the elements of the ufmylation cascade and effective interaction between them. We found that the last 20 residues in UBA5 are pivotal for binding to UFC1 and can accelerate the transfer of UFM1 to UFC1. We solved the structure of a complex of UFC1 and a peptide spanning the last 20 residues of UBA5 by NMR spectroscopy. This structure in combination with additional NMR titration and isothermal titration calorimetry experiments revealed the mechanism of interaction and confirmed the importance of the C-terminal unstructured region in UBA5 for the ufmylation cascade.


Assuntos
Proteínas/química , Enzimas Ativadoras de Ubiquitina/química , Enzimas de Conjugação de Ubiquitina/química , Varredura Diferencial de Calorimetria , Expressão Gênica , Espectroscopia de Ressonância Magnética , Mutação , Peptídeos/química , Ligação Proteica , Domínios Proteicos , Proteínas/genética , Proteínas/metabolismo , Proteínas Recombinantes , Termodinâmica , Enzimas Ativadoras de Ubiquitina/genética , Enzimas Ativadoras de Ubiquitina/metabolismo , Enzimas de Conjugação de Ubiquitina/genética , Enzimas de Conjugação de Ubiquitina/metabolismo
18.
Neuron ; 109(14): 2203-2204, 2021 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-34293287

RESUMO

Expansions in C9ORF72, which cause frontotemporal dementia and amyotrophic lateral sclerosis, result in formation of aberrant peptide and RNA species and decreased expression of the normal gene. In this issue of Neuron, Lall et al. (2021) report the consequences of microglial C9ORF72 deficiency in mouse models of aging and Alzheimer's disease.


Assuntos
Esclerose Amiotrófica Lateral , Demência Frontotemporal , Doenças Neurodegenerativas , Esclerose Amiotrófica Lateral/genética , Proteína C9orf72/genética , Expansão das Repetições de DNA/genética , Demência Frontotemporal/genética , Humanos , Microglia , Doenças Neurodegenerativas/genética , Proteínas/genética
19.
Adv Exp Med Biol ; 1315: 1-16, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34302686

RESUMO

Hydrogen sulfide, a small molecule, produced by endogenous enzymes, such as CTH, CBS, and MPST using L-cysteine as substrates, has been reported to have numerous protective effects. However, the key problem that the target of H2S and how it can affect the structure and activity of biological molecules is still unknown. Till now, there are two main theories of its working mechanism. One is that H2S can modify the free thiol in cysteine to produce the persulfide state of the thiol and the sulfhydration of cysteine can significantly change the structure and activity of target proteins. The other theory is that H2S, as an antioxidant molecule, can directly break the disulfide bond in target proteins, and the persulfide state of thiol can be an intermediate product during the reaction. Both phenomena exit for no doubt since they are both supported by large amounts of experiments. Here, we will summarize both theories and try to discuss which one is the more effective or direct mechanism for H2S and what is the relationship between them. Therefore, we will discover more protein targets of H2S with the mechanism and understand more about the effect of this small molecule.


Assuntos
Sulfeto de Hidrogênio , Cisteína , Proteínas/genética , Compostos de Sulfidrila
20.
Medicine (Baltimore) ; 100(28): e26632, 2021 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-34260555

RESUMO

ABSTRACT: BCL7B plays a potential role in the progression of various cancers, while its role in sarcomas is unknown. We aimed to evaluate BCL7B's diagnostic and prognostic value, and potential BCL7B-related mechanisms in sarcomas based on The Cancer Genome Atlas (TCGA) database. We collected patients with sarcoma from TCGA. Wilcoxon rank sum test was used to compare the expression of BCL7B in sarcoma samples with different clinical-pathologic features. Univariate Cox regression analysis and multivariate Cox regression analysis were used to evaluate prognosis factors for sarcoma. Gene set enrichment analysis (GSEA) was conducted to elucidate the significant functions and pathways associated with BCL7B. BCL7B was a potential biomarker for distinguishing normal and tumor tissues with the analysis of ROC curve (AUC = 0.588). Low BCL7B expression was significantly correlated with tumor multifocal (OR = 0.39 for yes vs no), larger residual tumor (OR = 0.40 for R1,R2 vs RO), male gender (OR = 0.48 for male vs female) and White race (OR = 0.29 for White vs Asian, Black or African American). High BCL7B expression was correlated with leiomyosarcoma histological type (OR = 6.08 for leiomyosarcoma vs dedifferentiated liposarcoma, pleomorphic sarcoma). Univariate and multivariate Cox regression analysis showed that low BCL7B expression was independently associated with poor overall survival (P = .008). GSEA showed that GPCR (G protein-coupled receptors) ligand binding, secreted factors, class A1 rhodopsin-like receptors, extracellular matrix organization, core matrisome, Fc epsilon receptor I mediated NF-κB activation, and WNT signaling pathway were differentially enriched in BCL7B low expression phenotype (|NES| > 1, adjusted P value <.05, and FDR value <0.25). BCL7B may play an important role in sarcoma progression and may be a potential biomarker for prognosis and diagnosis in sarcomas.


Assuntos
Proteínas/genética , Sarcoma/genética , Sarcoma/patologia , Idoso , Biomarcadores Tumorais , Biologia Computacional , Grupos de Populações Continentais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Prognóstico , Análise de Regressão , Sarcoma/diagnóstico , Fatores Sexuais
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