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1.
Braz. j. biol ; 84: e256732, 2024. tab, graf, ilus
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1364524

RESUMO

Germin-like proteins (GLPs) play an important role against various stresses. Vitis vinifera L. genome contains 7 GLPs; many of them are functionally unexplored. However, the computational analysis may provide important new insight into their function. Currently, physicochemical properties, subcellular localization, domain architectures, 3D structures, N-glycosylation & phosphorylation sites, and phylogeney of the VvGLPs were investigated using the latest computational tools. Their functions were predicted using the Search tool for the retrieval of interacting genes/proteins (STRING) and Blast2Go servers. Most of the VvGLPs were extracellular (43%) in nature but also showed periplasmic (29%), plasma membrane (14%), and mitochondrial- or chloroplast-specific (14%) expression. The functional analysis predicted unique enzymatic activities for these proteins including terpene synthase, isoprenoid synthase, lipoxygenase, phosphate permease, receptor kinase, and hydrolases generally mediated by Mn+ cation. VvGLPs showed similarity in the overall structure, shape, and position of the cupin domain. Functionally, VvGLPs control and regulate the production of secondary metabolites to cope with various stresses. Phylogenetically VvGLP1, -3, -4, -5, and VvGLP7 showed greater similarity due to duplication while VvGLP2 and VvGLP6 revealed a distant relationship. Promoter analysis revealed the presence of diverse cis-regulatory elements among which CAAT box, MYB, MYC, unnamed-4 were common to all of them. The analysis will help to utilize VvGLPs and their promoters in future food programs by developing resistant cultivars against various biotic (Erysiphe necator and in Powdery Mildew etc.) and abiotic (Salt, drought, heat, dehydration, etc.) stresses.


As proteínas do tipo germin (GLPs) desempenham um papel importante contra vários estresses. O genoma de Vitis vinifera L. contém 7 GLPs; muitos deles são funcionalmente inexplorados. No entanto, a análise computacional pode fornecer informações importantes sobre sua função. Atualmente, as propriedades físico-químicas, localização subcelular, arquitetura de domínio, estruturas 3D, sítios de N-glicosilação e fosforilação e estudos filogenéticos dos VvGLPs foram conduzidos usando as ferramentas computacionais mais recentes. Suas funções foram previstas usando a ferramenta Search para recuperação de genes/proteínas em interação (STRING) e servidores Blast2Go. A maioria dos VvGLPs são extracelulares (43%) na natureza, mas também mostraram expressão periplasmática (29%), na membrana plasmática (14%) e específica para mitocôndrias ou cloroplastos (14%). A análise funcional previu atividades enzimáticas únicas para essas proteínas, incluindo terpeno sintase, isoprenoide sintase, lipoxigenase, fosfato permease, receptor quinase e hidrolases geralmente mediadas por cátion Mn +. VvGLPs mostraram similaridade na estrutura geral, forma e posição do domínio cupin. Funcionalmente, os VvGLPs controlam e regulam a produção de metabólitos secundários para lidar com vários estresses. Filogeneticamente, VvGLP1, -3, -4, -5 e VvGLP7 mostraram maior similaridade devido à duplicação, enquanto VvGLP2 e VvGLP6 revelaram uma relação distante. A análise do promotor revelou a presença de diversos elementos cis-reguladores, entre os quais CAAT box, MYB, MYC, sem nome-4, sendo comum a todos eles. A análise ajudará a utilizar VvGLPs e seus promotores em programas alimentares futuros, desenvolvendo cultivares resistentes contra vários estresses bióticos (Erysiphe necator e no oídio, etc.) e abióticos (sal, seca, calor, estresse hídrico, etc.).


Assuntos
Estresse Fisiológico/genética , Proteínas , Vitis/genética
2.
Methods Mol Biol ; 2564: 1-45, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36107335

RESUMO

FPbase is a database of fluorescent proteins and their characteristics and a set of online tools that facilitate searching the database and performing experiments with fluorescent probes. This chapter serves as a general reference for using and searching the database and a guide to some of the more commonly used tools including the spectra viewer, custom microscope pages, and FRET calculator. Important caveats when evaluating the data are also discussed.


Assuntos
Corantes Fluorescentes , Proteínas , Bases de Dados de Proteínas
3.
Methods Mol Biol ; 2564: 47-52, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36107336

RESUMO

Many fluorescent proteins are available nowadays suitable for in vivo imaging experiments. Each fluorescent protein has unique biophysical properties, such as emission and excitation spectra, quantum yield, oligomerization state, pH sensitivity, fluorescence lifetime, and stability within the cellular environment. Even a small variation in fluorescent protein properties might result in significant differences in the experimental outcomes. This chapter discusses the aspects that need to be considered while selecting the fluorescent proteins for in vivo imaging experiment.


Assuntos
Diagnóstico por Imagem , Proteínas , Biofísica , Corantes , Diagnóstico por Imagem/métodos , Fluorescência
4.
Methods Mol Biol ; 2564: 53-74, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36107337

RESUMO

Fluorescent proteins are standard tools for addressing biological questions in a cell biology laboratory. The genetic tagging of protein of interest with fluorescent proteins opens the opportunity to follow them in vivo and to understand their interactions and dynamics. In addition, the latest advances in optical microscopy image acquisition and processing allow us to study many cellular processes in vivo. Techniques such as fluorescence lifetime microscopy and hyperspectral imaging provide valuable tools for understanding fluorescent protein interactions and their photophysics. Finally, fluorescence fluctuation analysis opens the possibility to address questions of molecular diffusion, protein-protein interactions, and oligomerization, among others, yielding quantitative information on the subject of study. This chapter will cover some of the more important advances in cutting-edge technologies and methods that, combined with fluorescent proteins, open new frontiers for biological studies.


Assuntos
Corantes , Proteínas , Fenômenos Fisiológicos Celulares , Microscopia de Fluorescência/métodos
5.
Methods Mol Biol ; 2564: 121-141, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36107340

RESUMO

Flavin-based fluorescent proteins (FbFPs) are small fluorescent proteins derived from light-oxygen-voltage (LOV) domains. The proteins bind ubiquitous endogenous flavins as chromophores and can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents the methodology to identify LOV domain sequences in genomic databases; design new FbFPs; characterize their biochemical, spectroscopic, photophysical, and photochemical properties; and conduct basic fluorescence microscopy experiments.


Assuntos
Dinitrocresóis , Flavinas , Flavinas/metabolismo , Oxigênio/metabolismo , Proteínas
6.
Methods Mol Biol ; 2564: 143-183, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36107341

RESUMO

Flavin-based fluorescent proteins (FbFPs), a class of small fluorescent proteins derived from light-oxygen-voltage (LOV) domains, bind ubiquitous endogenous flavins as chromophores. Due to their unique properties, they can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents methodologies for in-depth characterization of the biochemical, spectroscopic, photophysical, and photochemical properties of FbFPs.


Assuntos
Dinitrocresóis , Flavinas , Flavinas/metabolismo , Oxigênio/metabolismo , Proteínas
7.
Methods Mol Biol ; 2564: 247-258, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36107346

RESUMO

Citrate is a central intracellular metabolite with roles in a variety of normal and aberrant biological processes. The methods for quantifying citrate concentration in cells can enable the study of the molecular mechanisms of citrate-related biological processes and diseases. Compared to existing analytical methods such as enzymatic assays and mass spectrometry, genetically encoded biosensors based on fluorescent proteins (FPs) offer the advantage of noninvasively tracking intracellular ion and small molecule dynamics with high spatial-temporal resolution. These biosensors are less toxic than chemosensors and can be targeted to specific organelles for subcellular imaging. Here we present a protocol for quantification of cytosolic and mitochondrial citrate in mammalian cells with recently reported genetically encoded biosensors for citrate.


Assuntos
Técnicas Biossensoriais , Ácido Cítrico , Animais , Técnicas Biossensoriais/métodos , Citratos , Mamíferos , Proteínas
8.
Food Chem ; 398: 133874, 2023 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-35964567

RESUMO

The influence of ultrasound-assisted immersion freezing (UF), immersion freezing (IF), and air freezing (AF) on the protein oxidation, structure, and thermal stability of chicken breast during frozen storage was evaluated in this study. Compared to IF and AF samples, the UF samples had a lower carbonyl content, dityrosine content, and surface hydrophobicity of myofibrillar protein (MP) (P < 0.05), as well as a higher free amino group content and total and reactive sulfhydryl content (P < 0.05). Moreover, UF significantly delayed the deterioration of protein secondary and tertiary structures and the decrease in protein thermal stability during frozen storage (P < 0.05). Additionally, the UF samples at 180 days had similar protein structures and quality characteristics to the IF samples at 90 days or the AF samples at 60 days. Overall, UF treatment can effectively retard protein oxidation, protein structure deterioration, and protein thermal stability loss caused by frozen storage.


Assuntos
Galinhas , Proteínas , Animais , Congelamento , Interações Hidrofóbicas e Hidrofílicas , Estabilidade Proteica
9.
J. Health Biol. Sci. (Online) ; 10(1): 1-6, 01/jan./2022. tab, ilus
Artigo em Inglês | LILACS | ID: biblio-1370924

RESUMO

Objective: to evaluate the molecular interaction of silibinin with the targets ALS3 and SAP5. Methodology: Molecular docking protocols were conducted to analyze the binding interaction of silibinin with ALS3 and SAP5. Results: Eleven interactions of ALS3 with silibinin and four with fluconazole were found, while six interactions were observed of SAP5 with silibinin and four with fluconazole. Conclusion: Molecular docking between silibinin and ALS3 identified important interactions, but no significant interactions were observed with SAP5, even though silibinin can exhibit affinity and interactions with other SAP5 sites.


Objetivo: Avaliar a interação molecular da silibinina com os alvos ALS3 e SAP5. Metodologia: Protocolos de docking molecular foram conduzidos para analisar a interação de ligação da silibinina com ALS3 e SAP5. Resultados: Foram encontradas onze interações de ALS3 com silibinina e quatro com fluconazol, enquanto seis interações foram observadas de SAP5 com silibinina e quatro com fluconazol. Conclusão: Docking molecular entre silibinina e ALS3 identificou interações importantes, mas não foram observadas interações significativas com SAP5, embora a silibinina possa apresentar afinidade e interações com outros sítios SAP5.


Assuntos
Candida albicans , Silimarina , Proteínas , Infecções Fúngicas Invasivas
10.
PLoS One ; 17(9): e0270058, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36084098

RESUMO

The interaction among proteins is one of the most fundamental methods of information transfer in the living system. Many methods have been developed in order to identify the interaction pairs or groups either in vivo or in vitro. The in vitro pulldown/coprecipitation assay directly observes the protein that binds to the target. This method involves electrophoresis, which is a technique of a low resolution as well as a low throughput. As a better alternative, we wish to propose a new method that is based on the NMR spectroscopy. This method utilizes the aggregation of the target protein and the concomitant signal disappearance of the interacting partner. The aggregation is accomplished by the elastin-like polypeptide, which is fused to the target. If a protein binds to this supramolecular complex, its NMR signal then becomes too broadened in order to be observed, which is the basic phenomenon of the NMR spectroscopy. Thus, the protein that loses its signal is the one that binds to the target. A compound that interferes with these types of bindings among the proteins can be identified by observing the reappearance of the protein signals with the simultaneous disappearance of the signals of the compound. This technique will be applied in order to find an interaction pair in the information transfer pathway as well as a compound that disrupts it. This proposed method should be able to work with a mixture of proteins and provide a higher resolution in order to find the binding partner in a higher throughput fashion.


Assuntos
Agregados Proteicos , Proteínas , Espectroscopia de Ressonância Magnética/métodos , Proteínas/química
11.
PLoS One ; 17(9): e0268664, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36094910

RESUMO

The HEAT domains are a family of helical hairpin repeat domains, composed of four or more hairpins. HEAT is derived from the names of four family members: huntingtin, eukaryotic translation elongation factor 3 (eEF3), protein phosphatase 2 regulatory A subunit (PP2A), and mechanistic target of rapamycin (mTOR). HEAT domain-containing proteins play roles in a wide range of cellular processes, such as protein synthesis, nuclear transport and metabolism, and cell signaling. The PCI domains are a related group of helical hairpin domains, with a "winged-helix" (WH) subdomain at their C-terminus, which is responsible for multi-subunit complex formation with other PCI domains. The name is derived from the complexes, where these domains are found: the 26S Proteasome "lid" regulatory subcomplex, the COP9 signalosome (CSN), and eukaryotic translation initiation factor 3 (eIF3). We noted that in structure similarity searches using HEAT domains, sometimes PCI domains appeared in the search results ahead of other HEAT domains, which indicated that the PCI domains could be members of the HEAT domain family, and not a related but separate group, as currently thought. Here, we report extensive structure similarity analysis of HEAT and PCI domains, both within and between the two groups of proteins. We present evidence that the PCI domains as a group have greater structural similarity with individual groups of HEAT domains than some of the HEAT domain groups have among each other. Therefore, our results indicate that the PCI domains have evolved from a HEAT domain that acquired a WH subdomain. The WH subdomain in turn mediated self-association into a multi-subunit complex, which eventually evolved into the common ancestor of the Proteasome lid/CSN/eIF3.


Assuntos
Fator de Iniciação 3 em Eucariotos , Intervenção Coronária Percutânea , Complexo do Signalossomo COP9 , Fator de Iniciação 3 em Eucariotos/química , Temperatura Alta , Proteínas
12.
Phys Rev E ; 106(2-1): 024404, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-36109974

RESUMO

Acylphosphatase (AcP) is a small protein with 98 amino acid residues that catalyzes the hydrolysis of carboxyl-phosphate bonds. AcP is a typical two-state protein with slow folding rate due to its relatively large contact order in the native structure. The mechanical properties and unfolding behavior of AcP has been studied by atomic force microscope. Here using stable magnetic tweezers, we measured the force-dependent folding rates within a force range 1-3 pN, and unfolding rates 15-40 pN. The obtained unfolding rates show different force sensitivities at forces below and above ∼27 pN, which determines a free-energy landscape with two energy barriers. Our results indicate that the free-energy landscape of small globule proteins have general Bactrian camel shape, and large contact order of the native state produces a high barrier dominate at low forces.


Assuntos
Dobramento de Proteína , Proteínas , Hidrolases Anidrido Ácido , Aminoácidos , Fosfatos , Proteínas/química
13.
Methods Mol Biol ; 2569: 267-281, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36083453

RESUMO

Proteins have played a fundamental role throughout life's history on Earth. Despite their biological importance, ancient origin, early function, and evolution of proteins are seldom able to be directly studied because few of these attributes are preserved across geologic timescales. Ancestral sequence reconstruction (ASR) provides a method to infer ancestral amino acid sequences and determine the evolutionary predecessors of modern-day proteins using phylogenetic tools. Laboratory application of ASR allows ancient sequences to be deduced from genetic information available in extant organisms and then experimentally resurrected to elucidate ancestral characteristics. In this article, we provide a generalized, stepwise protocol that considers the major elements of a well-designed ASR study and details potential sources of reconstruction bias that can reduce the relevance of historical inferences. We underscore key stages in our approach so that it may be broadly utilized to reconstruct the evolutionary histories of proteins.


Assuntos
Evolução Molecular , Proteínas , Sequência de Aminoácidos , Filogenia , Proteínas/genética
14.
J Cell Biol ; 221(10)2022 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-36102907

RESUMO

Reversible protein phosphorylation by kinases controls a plethora of processes essential for the proper development and homeostasis of multicellular organisms. One main obstacle in studying the role of a defined kinase-substrate interaction is that kinases form complex signaling networks and most often phosphorylate multiple substrates involved in various cellular processes. In recent years, several new approaches have been developed to control the activity of a given kinase. However, most of them fail to regulate a single protein target, likely hiding the effect of a unique kinase-substrate interaction by pleiotropic effects. To overcome this limitation, we have created protein binder-based engineered kinases that permit a direct, robust, and tissue-specific phosphorylation of fluorescent fusion proteins in vivo. We show the detailed characterization of two engineered kinases based on Rho-associated protein kinase (ROCK) and Src. Expression of synthetic kinases in the developing fly embryo resulted in phosphorylation of their respective GFP-fusion targets, providing for the first time a means to direct the phosphorylation to a chosen and tagged target in vivo. We presume that after careful optimization, the novel approach we describe here can be adapted to other kinases and targets in various eukaryotic genetic systems to regulate specific downstream effectors.


Assuntos
Proteínas , Quinases Associadas a rho , Quinases da Família src , Animais , Drosophila , Fosforilação , Engenharia de Proteínas , Proteínas/metabolismo , Transdução de Sinais , Especificidade por Substrato , Quinases Associadas a rho/metabolismo , Quinases da Família src/metabolismo
15.
Eur Rev Med Pharmacol Sci ; 26(17): 6014-6026, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36111901

RESUMO

OBJECTIVE: Drug-target relationships provide the basis for network-based polypharmacology, and target deconvolution is a key step in phenotypic-screening based drug discovery. Due to the complexity of the mammalian proteomics and the often-limited affinity of the lead compound, it is challenging to identify the drug targets, especially when the goal is to identify all targets. This paper attempts to provide a brief and comprehensive introduction to the various methods in chemical proteomics for target deconvolution by categorizing them into two groups: the biochemical enrichment and the proteomics-screening methods. Moreover, a brief introduction of related Mass Spectrometry techniques is also provided, together with recent progress. MATERIALS AND METHODS: The data for this review were queried from Web of Science and PubMed, the keywords used were Drug targets, Target deconvolution, and Chemical Proteomics. A total of over 500 relevant articles, with a time limit from 1953 to 2022, were identified according to search strategy. Duplicate records and review articles were excluded by their titles and abstracts. Finally, we found about 120 articles matching our inclusion criteria, which covered representative research and reviews of various target discovery methods. RESULTS: Existing target discovery methods can be grouped into either biochemical enrichment or the proteomics-screening methods, with the recent emergence of a hybrid method combining these two such as lysine reactivity profiling. The advantage of the biochemical enrichment method is the ease of operation and the comprehensive target coverage. However, most biochemical enrichment methods require a high-affinity binding of the drug to the target proteins and cannot differentiate direct/indirect targets. The proteomics-screening methods do not require drug modification but have limited protein coverage, and most of them cannot differentiate direct/indirect targets. CONCLUSIONS: Although existing target discovery methods have greatly facilitated pharmacological research, each of these methods has advantages and disadvantages. New strategies/methods are needed to further improve both the coverage of the proteosome and the specificity.


Assuntos
Lisina , Proteômica , Animais , Descoberta de Drogas , Mamíferos , Espectrometria de Massas , Proteínas , Proteômica/métodos
16.
Prog Nucl Magn Reson Spectrosc ; 130-131: 62-105, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36113918

RESUMO

Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.


Assuntos
Proteínas , Dedos de Zinco , Sequência de Aminoácidos , Zinco/química , Zinco/metabolismo
17.
Nat Commun ; 13(1): 5438, 2022 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-36114175

RESUMO

The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the binding of Benzamidine to Trypsin which is a much studied and paradigmatic ligand-protein system. We use machine learning methods to determine efficient collective coordinates for the complex non-local network of water. These coordinates are used to perform On-the-fly Probability Enhanced Sampling simulations, which we adapt to calculate also the ligand residence time. Our results, both static and dynamic, are in good agreement with experiments. We find that the presence of a water molecule located at the bottom of the binding pocket allows via a network of hydrogen bonds the ligand to be released into the solution. On a finer scale, even when unbinding is allowed, another water molecule further modulates the exit time.


Assuntos
Benzamidinas , Água , Benzamidinas/química , Ligantes , Ligação Proteica , Proteínas/metabolismo , Tripsina/química
18.
Nat Commun ; 13(1): 5434, 2022 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-36114189

RESUMO

Despite the great promise of genetic code expansion technology to modulate structures and functions of proteins, external addition of ncAAs is required in most cases and it often limits the utility of genetic code expansion technology, especially to noncanonical amino acids (ncAAs) with poor membrane internalization. Here, we report the creation of autonomous cells, both prokaryotic and eukaryotic, with the ability to biosynthesize and genetically encode sulfotyrosine (sTyr), an important protein post-translational modification with low membrane permeability. These engineered cells can produce site-specifically sulfated proteins at a higher yield than cells fed exogenously with the highest level of sTyr reported in the literature. We use these autonomous cells to prepare highly potent thrombin inhibitors with site-specific sulfation. By enhancing ncAA incorporation efficiency, this added ability of cells to biosynthesize ncAAs and genetically incorporate them into proteins greatly extends the utility of genetic code expansion methods.


Assuntos
Código Genético , Trombina , Aminoácidos/química , Proteínas/metabolismo , Trombina/genética , Tirosina/metabolismo
19.
Sci Rep ; 12(1): 15616, 2022 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-36114358

RESUMO

In contrast to other domestic mammals, the embryo-derived signal(s) leading to maternal recognition of pregnancy (MRP) are still unknow in the mare. We hypothesize that these embryonic signals could be packed into uterine extracellular vesicles (uEVs), acting as multi-signal messengers between the conceptus and the maternal tract, and contributing to MRP. To unveil these signals, the RNA and protein cargos of uEVs isolated from uterine lavages collected from pregnant mares (P; day 10, 11, 12 and 13 after ovulation) and cyclic control mares (C; day 10 and 13 after ovulation) were analyzed. Our results showed a fine-tuned regulation of the uEV cargo (RNAs and proteins), by the day of pregnancy, the estrous cycle, and even the size of the embryo. A particular RNA pattern was identified with specific increase on P12 related to immune system and hormonal response. Besides, a set of proteins as well as RNAs was highly enriched in EVs on P12 and P13. Differential abundance of miRNAs was also identified in P13-derived uEVs. Their target genes were linked to down- or upregulated genes in the embryo and the endometrium, exposing their potential origin. Our study identified for first time specific molecules packed in uEVs, which were previously associated to MRP in the mare, and thus bringing added value to the current knowledge. Further integrative and functional analyses will help to confirm the role of these molecules in uEVs during MRP in the mare.


Assuntos
Vesículas Extracelulares , MicroRNAs , Animais , Embrião de Mamíferos/metabolismo , Endométrio/metabolismo , Vesículas Extracelulares/metabolismo , Feminino , Cavalos , Mamíferos/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Gravidez , Proteínas/metabolismo , Útero/metabolismo
20.
J Mol Biol ; 434(19): 167758, 2022 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-36116806

RESUMO

Predicting the various binding sites of a protein from its structure sheds light on its function and paves the way towards design of interaction inhibitors. Here, we report ScanNet, a freely available web server for prediction of protein-protein, protein - disordered protein and protein - antibody binding sites from structure. ScanNet (Spatio-Chemical Arrangement of Neighbors Network) is an end-to-end, interpretable geometric deep learning model that learns spatio-chemical patterns directly from 3D structures. ScanNet consistently outperforms Machine Learning models based on handcrafted features and comparative modeling approaches. The web server is linked to both the PDB and AlphaFoldDB, and supports user-provided structure files. Predictions can be readily visualized on the website via the Molstar web app and locally via ChimeraX. ScanNet is available at http://bioinfo3d.cs.tau.ac.il/ScanNet/.


Assuntos
Aprendizado Profundo , Software , Sítios de Ligação , Ligação Proteica , Proteínas/química
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