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1.
J Chem Theory Comput ; 16(10): 6383-6396, 2020 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-32905698

RESUMO

Molecular dynamics simulations are a popular means to study biomolecules, but it is often difficult to gain insights from the trajectories due to their large size, in both time and number of features. The Sapphire (States And Pathways Projected with HIgh REsolution) plot allows a direct visual inference of the dominant states visited by high-dimensional systems and how they are interconnected in time. Here, we extend this visual inference into a clustering algorithm. Specifically, the automatic procedure derives from the Sapphire plot states that are kinetically homogeneous, structurally annotated, and of tunable granularity. We provide a relative assessment of the kinetic fidelity of the Sapphire-based partitioning in comparison to popular clustering methods. This assessment is carried out on trajectories of n-butane, a ß-sheet peptide, and the small protein BPTI. We conclude with an application of our approach to a recent 100 µs trajectory of the main protease of SARS-CoV-2.


Assuntos
Butanos/química , Simulação de Dinâmica Molecular , Peptídeos/química , Proteínas/química , Algoritmos , Betacoronavirus/química , Análise por Conglomerados , Infecções por Coronavirus/virologia , Cisteína Endopeptidases/química , Humanos , Cinética , Pandemias , Pneumonia Viral/virologia , Conformação Proteica , Proteínas não Estruturais Virais/química
2.
PLoS Comput Biol ; 16(9): e1008103, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32956350

RESUMO

Highly coordinated water molecules are frequently an integral part of protein-protein and protein-ligand interfaces. We introduce an updated energy model that efficiently captures the energetic effects of these ordered water molecules on the surfaces of proteins. A two-stage method is developed in which polar groups arranged in geometries suitable for water placement are first identified, then a modified Monte Carlo simulation allows highly coordinated waters to be placed on the surface of a protein while simultaneously sampling amino acid side chain orientations. This "semi-explicit" water model is implemented in Rosetta and is suitable for both structure prediction and protein design. We show that our new approach and energy model yield significant improvements in native structure recovery of protein-protein and protein-ligand docking discrimination tests.


Assuntos
Sítios de Ligação/fisiologia , Simulação de Acoplamento Molecular , Ligação Proteica/fisiologia , Proteínas , Água , Algoritmos , Aminoácidos/química , Aminoácidos/metabolismo , Ligação de Hidrogênio , Ligantes , Método de Monte Carlo , Proteínas/química , Proteínas/metabolismo , Água/química , Água/metabolismo
3.
Nat Commun ; 11(1): 4768, 2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32958747

RESUMO

Detection and identification of proteins are typically achieved by analyzing protein size, charge, mobility and binding to antibodies, which are critical for biomedical research and disease diagnosis and treatment. Despite the importance, measuring these quantities with one technology and at the single-molecule level has not been possible. Here we tether a protein to a surface with a flexible polymer, drive it into oscillation with an electric field, and image the oscillation with a near field optical imaging method, from which we determine the size, charge, and mobility of the protein. We also measure antibody binding and conformation changes in the protein. The work demonstrates a capability for comprehensive protein analysis and precision protein biomarker detection at the single molecule level.


Assuntos
Proteínas/química , Proteínas/metabolismo , Imagem Individual de Molécula/métodos , Análise de Fourier , Ligantes , Polietilenoglicóis/química , Ligação Proteica , Conformação Proteica , Eletricidade Estática , Compostos de Estanho/química
4.
J Chem Inf Model ; 60(8): 3910-3934, 2020 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-32786511

RESUMO

Protein-protein interactions (PPIs) are attractive targets for drug design because of their essential role in numerous cellular processes and disease pathways. However, in general, PPIs display exposed binding pockets at the interface, and as such, have been largely unexploited for therapeutic interventions with low-molecular weight compounds. Here, we used docking and various rescoring strategies in an attempt to recover PPI inhibitors from a set of active and inactive molecules for 11 targets collected in ChEMBL and PubChem. Our focus is on the screening power of the various developed protocols and on using fast approaches so as to be able to apply such a strategy to the screening of ultralarge libraries in the future. First, we docked compounds into each target using the fast "pscreen" mode of the structure-based virtual screening (VS) package Surflex. Subsequently, the docking poses were postprocessed to derive a set of 3D topological descriptors: (i) shape similarity and (ii) interaction fingerprint similarity with a co-crystallized inhibitor, (iii) solvent-accessible surface area, and (iv) extent of deviation from the geometric center of a reference inhibitor. The derivatized descriptors, together with descriptor-scaled scoring functions, were utilized to investigate possible impacts on VS performance metrics. Moreover, four standalone scoring functions, RF-Score-VS (machine-learning), DLIGAND2 (knowledge-based), Vinardo (empirical), and X-SCORE (empirical), were employed to rescore the PPI compounds. Collectively, the results indicate that the topological scoring algorithms could be valuable both at a global level, with up to 79% increase in areas under the receiver operating characteristic curve for some targets, and in early stages, with up to a 4-fold increase in enrichment factors at 1% of the screened collections. Outstandingly, DLIGAND2 emerged as the best scoring function on this data set, outperforming all rescoring techniques in terms of VS metrics. The described methodology could help in the rational design of small-molecule PPI inhibitors and has direct applications in many therapeutic areas, including cancer, CNS, and infectious diseases such as COVID-19.


Assuntos
Desenho de Fármacos , Descoberta de Drogas , Mapas de Interação de Proteínas/efeitos dos fármacos , Bibliotecas de Moléculas Pequenas/farmacologia , Algoritmos , Betacoronavirus/efeitos dos fármacos , Betacoronavirus/metabolismo , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/metabolismo , Bases de Dados de Proteínas , Humanos , Ligantes , Aprendizado de Máquina , Simulação de Acoplamento Molecular , Terapia de Alvo Molecular , Pandemias , Pneumonia Viral/tratamento farmacológico , Pneumonia Viral/metabolismo , Proteínas/química , Proteínas/metabolismo , Bibliotecas de Moléculas Pequenas/química
5.
Phys Rev Lett ; 125(7): 078102, 2020 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-32857533

RESUMO

Diffusion-mediated surface phenomena are crucial for human life and industry, with examples ranging from oxygen capture by lung alveolar surface to heterogeneous catalysis, gene regulation, membrane permeation, and filtration processes. Their current description via diffusion equations with mixed boundary conditions is limited to simple surface reactions with infinite or constant reactivity. In this Letter, we propose a probabilistic approach based on the concept of boundary local time to investigate the intricate dynamics of diffusing particles near a reactive surface. Reformulating surface-particle interactions in terms of stopping conditions, we obtain in a unified way major diffusion-reaction characteristics such as the propagator, the survival probability, the first-passage time distribution, and the reaction rate. This general formalism allows us to describe new surface reaction mechanisms such as for instance surface reactivity depending on the number of encounters with the diffusing particle that can model the effects of catalyst fooling or membrane degradation. The disentanglement of the geometric structure of the medium from surface reactivity opens far-reaching perspectives for modeling, optimization, and control of diffusion-mediated surface phenomena.


Assuntos
Modelos Biológicos , Modelos Químicos , Membrana Celular/química , DNA/química , Difusão , Proteínas/química , Propriedades de Superfície , Termodinâmica
6.
Nat Commun ; 11(1): 4045, 2020 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-32792484

RESUMO

Monobodies are synthetic non-immunoglobulin customizable protein binders invaluable to basic and applied research, and of considerable potential as future therapeutics and diagnostic tools. The ability to reversibly control their binding activity to their targets on demand would significantly expand their applications in biotechnology, medicine, and research. Here we present, as proof-of-principle, the development of a light-controlled monobody (OptoMB) that works in vitro and in cells and whose affinity for its SH2-domain target exhibits a 330-fold shift in binding affinity upon illumination. We demonstrate that our αSH2-OptoMB can be used to purify SH2-tagged proteins directly from crude E. coli extract, achieving 99.8% purity and over 40% yield in a single purification step. By virtue of their ability to be designed to bind any protein of interest, OptoMBs have the potential to find new powerful applications as light-switchable binders of untagged proteins with the temporal and spatial precision afforded by light.


Assuntos
Luz , Optogenética/métodos , Cromatografia de Afinidade , Escherichia coli/genética , Escherichia coli/metabolismo , Células HEK293 , Humanos , Ligação Proteica/efeitos da radiação , Proteínas/química , Proteínas/metabolismo
7.
PLoS Comput Biol ; 16(8): e1007966, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32760072

RESUMO

Protein activity is often regulated by ligand binding or by post-translational modifications such as phosphorylation. Moreover, proteins that are regulated in this way often contain multiple ligand binding sites or modification sites, which can operate to create an ultrasensitive dose response. Here, we consider the contribution of the individual modification/binding sites to the activation process, and how their individual values affect the ultrasensitive behavior of the overall system. We use a generalized Monod-Wyman-Changeux (MWC) model that allows for variable conformational free energy contributions from distinct sites, and associate a so-called activation parameter to each site. Our analysis shows that the ultrasensitivity generally increases as the conformational free energy contribution from one or more sites is strengthened. Furthermore, ultrasensitivity depends on the mean of the activation parameters and not on their variability. In some cases, we find that the best way to maximize ultrasensitivity is to make the contribution from all sites as strong as possible. These results provide insights into the performance objectives of multiple modification/binding sites and thus help gain a greater understanding of signaling and its role in diseases.


Assuntos
Sítios de Ligação/fisiologia , Metabolismo Energético/fisiologia , Processamento de Proteína Pós-Traducional/fisiologia , Proteínas , Transdução de Sinais/fisiologia , Ligantes , Modelos Biológicos , Fosforilação/fisiologia , Conformação Proteica , Subunidades Proteicas , Proteínas/química , Proteínas/metabolismo , Termodinâmica
8.
PLoS Genet ; 16(8): e1008691, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32764743

RESUMO

Primary ciliary dyskinesia (PCD) is characterized by chronic airway disease, reduced fertility, and randomization of the left/right body axis. It is caused by defects of motile cilia and sperm flagella. We screened a cohort of affected individuals that lack an obvious axonemal defect for pathogenic variants using whole exome capture, next generation sequencing, and bioinformatic analysis assuming an autosomal recessive trait. We identified one subject with an apparently homozygous nonsense variant [(c.1762C>T), p.(Arg588*)] in the uncharacterized CFAP57 gene. Interestingly, the variant results in the skipping of exon 11 (58 amino acids), which may be due to disruption of an exonic splicing enhancer. In normal human nasal epithelial cells, CFAP57 localizes throughout the ciliary axoneme. Nasal cells from the PCD patient express a shorter, mutant version of CFAP57 and the protein is not incorporated into the axoneme. The missing 58 amino acids include portions of WD repeats that may be important for loading onto the intraflagellar transport (IFT) complexes for transport or docking onto the axoneme. A reduced beat frequency and an alteration in ciliary waveform was observed. Knockdown of CFAP57 in human tracheobronchial epithelial cells (hTECs) recapitulates these findings. Phylogenetic analysis showed that CFAP57 is highly conserved in organisms that assemble motile cilia. CFAP57 is allelic with the BOP2/IDA8/FAP57 gene identified previously in Chlamydomonas reinhardtii. Two independent, insertional fap57 Chlamydomonas mutant strains show reduced swimming velocity and altered waveforms. Tandem mass tag (TMT) mass spectroscopy shows that FAP57 is missing, and the "g" inner dyneins (DHC7 and DHC3) and the "d" inner dynein (DHC2) are reduced, but the FAP57 paralog FBB7 is increased. Together, our data identify a homozygous variant in CFAP57 that causes PCD that is likely due to a defect in the inner dynein arm assembly process.


Assuntos
Axonema/metabolismo , Transtornos da Motilidade Ciliar/genética , Códon sem Sentido , Dineínas/metabolismo , Proteínas/genética , Células 3T3 , Adulto , Animais , Axonema/fisiologia , Células Cultivadas , Chlamydomonas reinhardtii , Cílios/metabolismo , Cílios/fisiologia , Transtornos da Motilidade Ciliar/patologia , Sequência Conservada , Humanos , Masculino , Camundongos , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteínas/química , Proteínas/metabolismo , Mucosa Respiratória/metabolismo
9.
PLoS One ; 15(8): e0237814, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32804975

RESUMO

Schaaf-Yang syndrome (SYS) is a neurodevelopmental disorder caused by truncating variants in the paternal allele of MAGEL2, located in the Prader-Willi critical region, 15q11-q13. Although the phenotypes of SYS overlap those of Prader-Willi syndrome (PWS), including neonatal hypotonia, feeding problems, and developmental delay/intellectual disability, SYS patients show autism spectrum disorder and joint contractures, which are atypical phenotypes for PWS. Therefore, we hypothesized that the truncated Magel2 protein could potentially produce gain-of-function toxic effects. To test the hypothesis, we generated two engineered mouse models; one, an overexpression model that expressed the N-terminal region of Magel2 that was FLAG tagged with a strong ubiquitous promoter, and another, a genome-edited model that carried a truncating variant in Magel2 generated using the CRISPR/Cas9 system. In the overexpression model, all transgenic mice died in the fetal or neonatal period indicating embryonic or neonatal lethality of the transgene. Therefore, overexpression of the truncated Magel2 could show toxic effects. In the genome-edited model, we generated a mouse model carrying a frameshift variant (c.1690_1924del; p(Glu564Serfs*130)) in Magel2. Model mice carrying the frameshift variant in the paternal or maternal allele of Magel2 were termed Magel2P:fs and Magel2M:fs, respectively. The imprinted expression and spatial distribution of truncating Magel2 transcripts in the brain were maintained. Although neonatal Magel2P:fs mice were lighter than wildtype littermates, Magel2P:fs males and females weighed the same as their wildtype littermates by eight and four weeks of age, respectively. Collectively, the overexpression mouse model may recapitulate fetal or neonatal death, which are the severest phenotypes for SYS. In contrast, the genome-edited mouse model maintains genomic imprinting and distribution of truncated Magel2 transcripts in the brain, but only partially recapitulates SYS phenotypes. Therefore, our results imply that simple gain-of-function toxic effects may not explain the patho-mechanism of SYS, but rather suggest a range of effects due to Magel2 variants as in human SYS patients.


Assuntos
Antígenos de Neoplasias/genética , Mutação/genética , Proteínas/genética , Animais , Antígenos de Neoplasias/química , Antígenos de Neoplasias/metabolismo , Peso Corporal , Encéfalo/metabolismo , Modelos Animais de Doenças , Feminino , Edição de Genes , Regulação da Expressão Gênica , Células HEK293 , Humanos , Masculino , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Linhagem , Fenótipo , Proteínas/química , Proteínas/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
10.
PLoS One ; 15(8): e0236894, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32785279

RESUMO

High-quality three-dimensional structural data is of great value for the functional interpretation of biomacromolecules, especially proteins; however, structural quality varies greatly across the entries in the worldwide Protein Data Bank (wwPDB). Since 2008, the wwPDB has required the inclusion of structure factors with the deposition of x-ray crystallographic structures to support the independent evaluation of structures with respect to the underlying experimental data used to derive those structures. However, interpreting the discrepancies between the structural model and its underlying electron density data is difficult, since derived sigma-scaled electron density maps use arbitrary electron density units which are inconsistent between maps from different wwPDB entries. Therefore, we have developed a method that converts electron density values from sigma-scaled electron density maps into units of electrons. With this conversion, we have developed new methods that can evaluate specific regions of an x-ray crystallographic structure with respect to a physicochemical interpretation of its corresponding electron density map. We have systematically compared all deposited x-ray crystallographic protein models in the wwPDB with their underlying electron density maps, if available, and characterized the electron density in terms of expected numbers of electrons based on the structural model. The methods generated coherent evaluation metrics throughout all PDB entries with associated electron density data, which are consistent with visualization software that would normally be used for manual quality assessment. To our knowledge, this is the first attempt to derive units of electrons directly from electron density maps without the aid of the underlying structure factors. These new metrics are biochemically-informative and can be extremely useful for filtering out low-quality structural regions from inclusion into systematic analyses that span large numbers of PDB entries. Furthermore, these new metrics will improve the ability of non-crystallographers to evaluate regions of interest within PDB entries, since only the PDB structure and the associated electron density maps are needed. These new methods are available as a well-documented Python package on GitHub and the Python Package Index under a modified Clear BSD open source license.


Assuntos
Biologia Computacional , Bases de Dados de Proteínas , Elétrons , Proteínas/química
11.
BMC Bioinformatics ; 21(Suppl 4): 246, 2020 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-32631256

RESUMO

BACKGROUND: Protein model quality assessment (QA) is an essential procedure in protein structure prediction. QA methods can predict the qualities of protein models and identify good models from decoys. Clustering-based methods need a certain number of models as input. However, if a pool of models are not available, methods that only need a single model as input are indispensable. RESULTS: We developed MASS, a QA method to predict the global qualities of individual protein models using random forests and various novel energy functions. We designed six novel energy functions or statistical potentials that can capture the structural characteristics of a protein model, which can also be used in other protein-related bioinformatics research. MASS potentials demonstrated higher importance than the energy functions of RWplus, GOAP, DFIRE and Rosetta when the scores they generated are used as machine learning features. MASS outperforms almost all of the four CASP11 top-performing single-model methods for global quality assessment in terms of all of the four evaluation criteria officially used by CASP, which measure the abilities to assign relative and absolute scores, identify the best model from decoys, and distinguish between good and bad models. MASS has also achieved comparable performances with the leading QA methods in CASP12 and CASP13. CONCLUSIONS: MASS and the source code for all MASS potentials are publicly available at http://dna.cs.miami.edu/MASS/ .


Assuntos
Biologia Computacional/métodos , Proteínas/química , Modelos Moleculares
12.
BMC Bioinformatics ; 21(1): 286, 2020 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-32631216

RESUMO

BACKGROUND: Protein-ligand docking has emerged as a particularly important tool in drug design and development, and flexible ligand docking is a widely used method for docking simulations. Many docking software packages can simulate flexible ligand docking, and among them, Autodock is widely used. Focusing on the search algorithm used in Autodock, many new optimization approaches have been proposed over the last few decades. However, despite the large number of alternatives, we are still lacking a search method with high robustness and high performance. RESULTS: In this paper, in conjunction with the popular Autodock software, a novel hybrid version of the random drift particle swarm optimization (RDPSO) algorithm, called diversity-guided Lamarckian RDPSO (DGLRDPSO), is proposed to further enhance the performance and robustness of flexible ligand docking. In this algorithm, a novel two-phase diversity control (2PDC) strategy and an efficient local search strategy are used to improve the search ability and robustness of the RDPSO algorithm. By using the PDBbind coreset v.2016 and 24 complexes with apo-structures, the DGLRDPSO algorithm is compared with the Lamarckian genetic algorithm (LGA), Lamarckian particle swarm optimization (LPSO) and Lamarckian random drift particle swarm optimization (LRDPSO). The experimental results show that the 2PDC strategy is able to enhance the robustness and search performance of the proposed algorithm; for test cases with different numbers of torsions, the DGLRDPSO outperforms the LGA and LPSO in finding both low-energy and small-RMSD docking conformations with high robustness in most cases. CONCLUSION: The DGLRDPSO algorithm has good search performance and a high possibility of finding a conformation with both a low binding free energy and a small RMSD. Among all the tested algorithms, DGLRDPSO has the best robustness in solving both holo- and apo-structure docking problems with different numbers of torsions, which indicates that the proposed algorithm is a reliable choice for the flexible ligand docking in Autodock software.


Assuntos
Algoritmos , Desenho de Fármacos , Ligantes , Humanos , Proteínas/química
13.
BMC Bioinformatics ; 21(1): 289, 2020 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-32631222

RESUMO

BACKGROUND: The interaction between proteins and nucleic acids plays pivotal roles in various biological processes such as transcription, translation, and gene regulation. Hot spots are a small set of residues that contribute most to the binding affinity of a protein-nucleic acid interaction. Compared to the extensive studies of the hot spots on protein-protein interfaces, the hot spot residues within protein-nucleic acids interfaces remain less well-studied, in part because mutagenesis data for protein-nucleic acids interaction are not as abundant as that for protein-protein interactions. RESULTS: In this study, we built a new computational model, iPNHOT, to effectively predict hot spot residues on protein-nucleic acids interfaces. One training data set and an independent test set were collected from dbAMEPNI and some recent literature, respectively. To build our model, we generated 97 different sequential and structural features and used a two-step strategy to select the relevant features. The final model was built based only on 7 features using a support vector machine (SVM). The features include two unique features such as ∆SASsa1/2 and esp3, which are newly proposed in this study. Based on the cross validation results, our model gave F1 score and AUROC as 0.725 and 0.807 on the subset collected from ProNIT, respectively, compared to 0.407 and 0.670 of mCSM-NA, a state-of-the art model to predict the thermodynamic effects of protein-nucleic acid interaction. The iPNHOT model was further tested on the independent test set, which showed that our model outperformed other methods. CONCLUSION: In this study, by collecting data from a recently published database dbAMEPNI, we proposed a new model, iPNHOT, to predict hotspots on both protein-DNA and protein-RNA interfaces. The results show that our model outperforms the existing state-of-art models. Our model is available for users through a webserver: http://zhulab.ahu.edu.cn/iPNHOT/ .


Assuntos
Mapeamento de Interação de Proteínas/métodos , Proteínas/química , Humanos
14.
PLoS One ; 15(7): e0235263, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32639981

RESUMO

Dependent peptide searching is a method for discovering covalently-modified peptides-and therefore proteins-in mass-spectrometry-based proteomics experiments. Being more permissive than standard search methods, it has the potential to discover novel modifications (e.g., post-translational modifications occurring in vivo, or modifications introduced in vitro). However, few studies have explored dependent peptide search results in an untargeted way. In the present study, we sought to evaluate dependent peptide searching as a means of characterising proteins that have been modified in vitro. We generated a model data set by analysing N-ethylmaleimide-treated bovine serum albumin, and performed dependent peptide searches using the popular MaxQuant software. To facilitate interpretation of the search results (hundreds of dependent peptides), we developed a series of visualisation tools (R scripts). We used the tools to assess the diversity of putative modifications in the albumin, and to pinpoint hypothesised modifications. We went on to explore the tools' generality via analyses of public data from studies of rat and human proteomes. Of 19 expected sites of modification (one in rat cofilin-1 and 18 across six different human plasma proteins), eight were found and correctly localised. Apparently, some sites went undetected because chemical enrichment had depleted necessary analytes (potential 'base' peptides). Our results demonstrate (i) the ability of the tools to provide accurate and informative visualisations, and (ii) the usefulness of dependent peptide searching for characterising in vitro protein modifications. Our model data are available via PRIDE/ProteomeXchange (accession number PXD013040).


Assuntos
Peptídeos/análise , Proteínas/química , Proteômica/métodos , Animais , Proteínas Sanguíneas/química , Bovinos , Bases de Dados de Proteínas , Etilmaleimida/análogos & derivados , Humanos , Processamento de Proteína Pós-Traducional , Ratos , Soroalbumina Bovina/química
15.
BMC Bioinformatics ; 21(1): 275, 2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32611389

RESUMO

BACKGROUND: Protein engineering has many applications for industry, such as the development of new drugs, vaccines, treatment therapies, food, and biofuel production. A common way to engineer a protein is to perform mutations in functionally essential residues to optimize their function. However, the discovery of beneficial mutations for proteins is a complex task, with a time-consuming and high cost for experimental validation. Hence, computational approaches have been used to propose new insights for experiments narrowing the search space and reducing the costs. RESULTS: In this study, we developed Proteus (an acronym for Protein Engineering Supporter), a new algorithm for proposing mutation pairs in a target 3D structure. These suggestions are based on contacts observed in other known structures from Protein Data Bank (PDB). Proteus' basic assumption is that if a non-interacting pair of amino acid residues in the target structure is exchanged to an interacting pair, this could enhance protein stability. This trade is only allowed if the main-chain conformation of the residues involved in the contact is conserved. Furthermore, no steric impediment is expected between the proposed mutations and the surrounding protein atoms. To evaluate Proteus, we performed two case studies with proteins of industrial interests. In the first case study, we evaluated if the mutations suggested by Proteus for four protein structures enhance the number of inter-residue contacts. Our results suggest that most mutations proposed by Proteus increase the number of interactions into the protein. In the second case study, we used Proteus to suggest mutations for a lysozyme protein. Then, we compared Proteus' outcomes to mutations with available experimental evidence reported in the ProTherm database. Four mutations, in which our results agree with the experimental data, were found. This could be initial evidence that changes in the side-chain of some residues do not cause disturbances that harm protein structure stability. CONCLUSION: We believe that Proteus could be used combined with other methods to give new insights into the rational development of engineered proteins. Proteus user-friendly web-based tool is available at < http://proteus.dcc.ufmg.br >.


Assuntos
Proteínas/química , Interface Usuário-Computador , Algoritmos , Bases de Dados de Proteínas , Muramidase/química , Muramidase/genética , Muramidase/metabolismo , Mutagênese , Engenharia de Proteínas/métodos , Estrutura Terciária de Proteína , Proteínas/genética , Proteínas/metabolismo
16.
Nat Commun ; 11(1): 3336, 2020 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-32620782

RESUMO

We describe theory, experiments, and analyses of three-color Förster resonance energy transfer (FRET) spectroscopy for probing sub-millisecond conformational dynamics of protein folding and binding of disordered proteins. We devise a scheme that uses single continuous-wave laser excitation of the donor instead of alternating excitation of the donor and one of the acceptors. This scheme alleviates photophysical problems of acceptors such as rapid photobleaching, which is crucial for high time resolution experiments with elevated illumination intensity. Our method exploits the molecular species with one of the acceptors absent or photobleached, from which two-color FRET data is collected in the same experiment. We show that three FRET efficiencies and kinetic parameters can be determined without alternating excitation from a global maximum likelihood analysis of two-color and three-color photon trajectories. We implement co-parallelization of CPU-GPU processing, which leads to a significant reduction of the likelihood calculation time for efficient parameter determination.


Assuntos
Algoritmos , Transferência Ressonante de Energia de Fluorescência/métodos , Modelos Teóricos , Conformação Proteica , Dobramento de Proteína , Proteínas/química , Cor , Transferência Ressonante de Energia de Fluorescência/instrumentação , Transferência Ressonante de Energia de Fluorescência/estatística & dados numéricos , Proteínas Intrinsicamente Desordenadas/química , Proteínas Intrinsicamente Desordenadas/metabolismo , Cinética , Microscopia Confocal , Fotodegradação , Fótons , Ligação Proteica , Proteínas/metabolismo , Fatores de Tempo
17.
PLoS Comput Biol ; 16(7): e1007970, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32639954

RESUMO

Detection of protein structure similarity is a central challenge in structural bioinformatics. Comparisons are usually performed at the polypeptide chain level, however the functional form of a protein within the cell is often an oligomer. This fact, together with recent growth of oligomeric structures in the Protein Data Bank (PDB), demands more efficient approaches to oligomeric assembly alignment/retrieval. Traditional methods use atom level information, which can be complicated by the presence of topological permutations within a polypeptide chain and/or subunit rearrangements. These challenges can be overcome by comparing electron density volumes directly. But, brute force alignment of 3D data is a compute intensive search problem. We developed a 3D Zernike moment normalization procedure to orient electron density volumes and assess similarity with unprecedented speed. Similarity searching with this approach enables real-time retrieval of proteins/protein assemblies resembling a target, from PDB or user input, together with resulting alignments (http://shape.rcsb.org).


Assuntos
Biologia Computacional/métodos , Bases de Dados de Proteínas , Proteínas/química , Algoritmos , Internet , Modelos Moleculares , Modelos Estatísticos , Distribuição Normal , Peptídeos/química , Conformação Proteica , Software
18.
Nat Commun ; 11(1): 3714, 2020 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-32709852

RESUMO

The detailed understanding of the binding of small molecules to proteins is the key for the development of novel drugs or to increase the acceptance of substrates by enzymes. Nowadays, computer-aided design of protein-ligand binding is an important tool to accomplish this task. Current approaches typically rely on high-throughput docking essays or computationally expensive atomistic molecular dynamics simulations. Here, we present an approach to use the recently re-parametrized coarse-grained Martini model to perform unbiased millisecond sampling of protein-ligand interactions of small drug-like molecules. Remarkably, we achieve high accuracy without the need of any a priori knowledge of binding pockets or pathways. Our approach is applied to a range of systems from the well-characterized T4 lysozyme over members of the GPCR family and nuclear receptors to a variety of enzymes. The presented results open the way to high-throughput screening of ligand libraries or protein mutations using the coarse-grained Martini model.


Assuntos
Simulação de Dinâmica Molecular , Ligação Proteica , Proteínas/química , Bacteriófago T4/enzimologia , Biofísica , Biologia Computacional , Ensaios de Triagem em Larga Escala , Ligantes , Simulação de Acoplamento Molecular , Muramidase/química , Conformação Proteica , Termodinâmica
19.
J Chromatogr A ; 1625: 461298, 2020 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-32709341

RESUMO

This study has examined the batch binding behaviour of different thermo-responsive co-polymer grafted chromatographic materials under different temperature and protein loading conditions. The effect of molecular composition of poly(N-isopropylacrylamide) (PNIPAAm)-based co-polymers on the phase transition properties has been documented. Sixteen co-polymers of different compositions were synthesized by free radical polymerization methods. Most underwent relatively sharp phase transitions upon application of increasing temperature. However, the value of the lower critical solution temperature (LCST) varied due to differences in co-polymer compositions. In general, it was found that the LCST increased for co-polymers containing more hydrophilic moieties, but decreased for co-polymers with more hydrophobic moieties. Moreover, the LCST increased, together with increased width of the transition temperature, when highly branched monomeric moieties (i.e. N­tert­octyl groups) were present. When bulky side chains (octadecyl or triphenylmethyl groups) were located in the polymer structures the LCST transition was absent. Based on these findings, 6 thermo-responsive co-polymers of different compositions were individually immobilised onto cross-linked Sepharose 6 Fast Flow by a "grafting-from" method. Bovine holo-lactoferrin and bovine holo-transferrin at different concentrations in the range 1-100 mg/mL were then employed as target proteins to evaluate the adsorption behaviour under batch binding conditions with these different polymer grafted Sepharose 6 Fast Flow sorbents at two different temperatures. In general, all sorbents exhibited greater affinity and adsorption capacity for bovine holo-lactoferrin at 50 °C compared to 20 °C. In addition, the affinity and adsorption capacity of bovine holo-lactoferrin with positively charged copolymer grafted Sepharose 6 Fast Flow chromatographic sorbents at 20 °C and 50 °C were much lower than that found for negatively charged copolymer grafted Sepharose 6 Fast Flow sorbents, whilst the opposite trend was found with bovine holo-transferrin due to differences in the surface charge properties of these two proteins, indicative of different separation selectivity. Furthermore, the structure of the side chains present in the grafted copolymer structure was found to affect the adsorption performance of both proteins at 20 °C and 50 °C.


Assuntos
Polímeros/química , Proteínas/química , Reologia , Sefarose/química , Temperatura , Resinas Acrílicas/síntese química , Resinas Acrílicas/química , Adsorção , Animais , Bovinos , Interações Hidrofóbicas e Hidrofílicas , Lactoferrina/química , Polimerização , Polímeros/síntese química , Transferrina/química
20.
PLoS One ; 15(6): e0235153, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32603341

RESUMO

The secondary structure prediction of proteins is a classic topic of computational structural biology with a variety of applications. During the past decade, the accuracy of prediction achieved by state-of-the-art algorithms has been >80%; meanwhile, the time cost of prediction increased rapidly because of the exponential growth of fundamental protein sequence data. Based on literature studies and preliminary observations on the relationships between the size/homology of the fundamental protein dataset and the speed/accuracy of predictions, we raised two hypotheses that might be helpful to determine the main influence factors of the efficiency of secondary structure prediction. Experimental results of size and homology reductions of the fundamental protein dataset supported those hypotheses. They revealed that shrinking the size of the dataset could substantially cut down the time cost of prediction with a slight decrease of accuracy, which could be increased on the contrary by homology reduction of the dataset. Moreover, the Shannon information entropy could be applied to explain how accuracy was influenced by the size and homology of the dataset. Based on these findings, we proposed that a proper combination of size and homology reductions of the protein dataset could speed up the secondary structure prediction while preserving the high accuracy of state-of-the-art algorithms. Testing the proposed strategy with the fundamental protein dataset of the year 2018 provided by the Universal Protein Resource, the speed of prediction was enhanced over 20 folds while all accuracy measures remained equivalently high. These findings are supposed helpful for improving the efficiency of researches and applications depending on the secondary structure prediction of proteins. To make future implementations of the proposed strategy easy, we have established a database of size and homology reduced protein datasets at http://10.life.nctu.edu.tw/UniRefNR.


Assuntos
Estrutura Secundária de Proteína , Proteínas/química , Algoritmos , Biologia Computacional , Confiabilidade dos Dados , Bases de Dados de Proteínas , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos
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