1
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Mufassirin MMM, Newton MAH, Sattar A. Artificial intelligence for template-free protein structure prediction: a comprehensive review. Artif Intell Rev 2022. [DOI: 10.1007/s10462-022-10350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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2
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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3
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Feng SH, Xia CQ, Shen HB. CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks. Bioinformatics 2022; 38:720-729. [PMID: 34718416 DOI: 10.1093/bioinformatics/btab744] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/08/2021] [Accepted: 10/27/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Coiled-coil is composed of two or more helices that are wound around each other. It widely exists in proteins and has been discovered to play a variety of critical roles in biology processes. Generally, there are three types of structural features in coiled-coil: coiled-coil domain (CCD), oligomeric state and register. However, most of the existing computational tools only focus on one of them. RESULTS Here, we describe a new deep learning model, CoCoPRED, which is based on convolutional layers, bidirectional long short-term memory, and attention mechanism. It has three networks, i.e. CCD network, oligomeric state network, and register network, corresponding to the three types of structural features in coiled-coil. This means CoCoPRED has the ability of fulfilling comprehensive prediction for coiled-coil proteins. Through the 5-fold cross-validation experiment, we demonstrate that CoCoPRED can achieve better performance than the state-of-the-art models on both CCD prediction and oligomeric state prediction. Further analysis suggests the CCD prediction may be a performance indicator of the oligomeric state prediction in CoCoPRED. The attention heads in CoCoPRED indicate that registers a, b and e are more crucial for the oligomeric state prediction. AVAILABILITY AND IMPLEMENTATION CoCoPRED is available at http://www.csbio.sjtu.edu.cn/bioinf/CoCoPRED. The datasets used in this research can also be downloaded from the website. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shi-Hao Feng
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Chun-Qiu Xia
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.,Department of Computer Science, Shanghai Jiao Tong University, Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai 200240, China
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4
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Simm D, Hatje K, Waack S, Kollmar M. Critical assessment of coiled-coil predictions based on protein structure data. Sci Rep 2021; 11:12439. [PMID: 34127723 PMCID: PMC8203680 DOI: 10.1038/s41598-021-91886-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
Coiled-coil regions were among the first protein motifs described structurally and theoretically. The simplicity of the motif promises that coiled-coil regions can be detected with reasonable accuracy and precision in any protein sequence. Here, we re-evaluated the most commonly used coiled-coil prediction tools with respect to the most comprehensive reference data set available, the entire Protein Data Bank, down to each amino acid and its secondary structure. Apart from the 30-fold difference in minimum and maximum number of coiled coils predicted the tools strongly vary in where they predict coiled-coil regions. Accordingly, there is a high number of false predictions and missed, true coiled-coil regions. The evaluation of the binary classification metrics in comparison with naïve coin-flip models and the calculation of the Matthews correlation coefficient, the most reliable performance metric for imbalanced data sets, suggests that the tested tools' performance is close to random. This implicates that the tools' predictions have only limited informative value. Coiled-coil predictions are often used to interpret biochemical data and are part of in-silico functional genome annotation. Our results indicate that these predictions should be treated very cautiously and need to be supported and validated by experimental evidence.
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Affiliation(s)
- Dominic Simm
- grid.418140.80000 0001 2104 4211Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany ,grid.7450.60000 0001 2364 4210Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Göttingen, Germany
| | - Klas Hatje
- grid.418140.80000 0001 2104 4211Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany ,grid.417570.00000 0004 0374 1269Present Address: Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Stephan Waack
- grid.7450.60000 0001 2364 4210Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Kollmar
- grid.418140.80000 0001 2104 4211Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany ,grid.7450.60000 0001 2364 4210Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Göttingen, Germany
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5
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RF-MaloSite and DL-Malosite: Methods based on random forest and deep learning to identify malonylation sites. Comput Struct Biotechnol J 2020; 18:852-860. [PMID: 32322367 PMCID: PMC7160427 DOI: 10.1016/j.csbj.2020.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/27/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Malonylation, which has recently emerged as an important lysine modification, regulates diverse biological activities and has been implicated in several pervasive disorders, including cardiovascular disease and cancer. However, conventional global proteomics analysis using tandem mass spectrometry can be time-consuming, expensive and technically challenging. Therefore, to complement and extend existing experimental methods for malonylation site identification, we developed two novel computational methods for malonylation site prediction based on random forest and deep learning machine learning algorithms, RF-MaloSite and DL-MaloSite, respectively. DL-MaloSite requires the primary amino acid sequence as an input and RF-MaloSite utilizes a diverse set of biochemical, physiochemical and sequence-based features. While systematic assessment of performance metrics suggests that both ‘RF-MaloSite’ and ‘DL-MaloSite’ perform well in all metrics tested, our methods perform particularly well in the areas of accuracy, sensitivity and overall method performance (assessed by the Matthew’s Correlation Coefficient). For instance, RF-MaloSite exhibited MCC scores of 0.42 and 0.40 using 10-fold cross-validation and an independent test set, respectively. Meanwhile, DL-MaloSite was characterized by MCC scores of 0.51 and 0.49 based on 10-fold cross-validation and an independent set, respectively. Importantly, both methods exhibited efficiency scores that were on par or better than those achieved by existing malonylation site prediction methods. The identification of these sites may also provide important insights into the mechanisms of crosstalk between malonylation and other lysine modifications, such as acetylation, glutarylation and succinylation. To facilitate their use, both methods have been made freely available to the research community at https://github.com/dukkakc/DL-MaloSite-and-RF-MaloSite.
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6
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Ludwiczak J, Winski A, Szczepaniak K, Alva V, Dunin-Horkawicz S. DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences. Bioinformatics 2019; 35:2790-2795. [DOI: 10.1093/bioinformatics/bty1062] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/19/2018] [Accepted: 12/27/2018] [Indexed: 01/30/2023] Open
Abstract
Abstract
Motivation
Coiled coils are protein structural domains that mediate a plethora of biological interactions, and thus their reliable annotation is crucial for studies of protein structure and function.
Results
Here, we report DeepCoil, a new neural network-based tool for the detection of coiled-coil domains in protein sequences. In our benchmarks, DeepCoil significantly outperformed current state-of-the-art tools, such as PCOILS and Marcoil, both in the prediction of canonical and non-canonical coiled coils. Furthermore, in a scan of the human genome with DeepCoil, we detected many coiled-coil domains that remained undetected by other methods. This higher sensitivity of DeepCoil should make it a method of choice for accurate genome-wide detection of coiled-coil domains.
Availability and implementation
DeepCoil is written in Python and utilizes the Keras machine learning library. A web server is freely available at https://toolkit.tuebingen.mpg.de/#/tools/deepcoil and a standalone version can be downloaded at https://github.com/labstructbioinf/DeepCoil.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jan Ludwiczak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Aleksander Winski
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Szczepaniak
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
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7
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MacCarthy E, Perry D, Kc DB. Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction. Methods Mol Biol 2019; 1958:15-45. [PMID: 30945212 DOI: 10.1007/978-1-4939-9161-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Due to the advancement in various sequencing technologies, the gap between the number of protein sequences and the number of experimental protein structures is ever increasing. Community-wide initiatives like CASP have resulted in considerable efforts in the development of computational methods to accurately model protein structures from sequences. Sequence-based prediction of super-secondary structure has direct application in protein structure prediction, and there have been significant efforts in the prediction of super-secondary structure in the last decade. In this chapter, we first introduce the protein structure prediction problem and highlight some of the important progress in the field of protein structure prediction. Next, we discuss recent methods for the prediction of super-secondary structures. Finally, we discuss applications of super-secondary structure prediction in structure prediction/analysis of proteins. We also discuss prediction of protein structures that are composed of simple super-secondary structure repeats and protein structures that are composed of complex super-secondary structure repeats. Finally, we also discuss the recent trends in the field.
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Affiliation(s)
- Elijah MacCarthy
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Derrick Perry
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Dukka B Kc
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA.
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8
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Using a Classifier Fusion Strategy to Identify Anti-angiogenic Peptides. Sci Rep 2018; 8:14062. [PMID: 30218091 PMCID: PMC6138733 DOI: 10.1038/s41598-018-32443-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/07/2018] [Indexed: 12/27/2022] Open
Abstract
Anti-angiogenic peptides perform distinct physiological functions and potential therapies for angiogenesis-related diseases. Accurate identification of anti-angiogenic peptides may provide significant clues to understand the essential angiogenic homeostasis within tissues and develop antineoplastic therapies. In this study, an ensemble predictor is proposed for anti-angiogenic peptide prediction by fusing an individual classifier with the best sensitivity and another individual one with the best specificity. We investigate predictive capabilities of various feature spaces with respect to the corresponding optimal individual classifiers and ensemble classifiers. The accuracy and Matthew’s Correlation Coefficient (MCC) of the ensemble classifier trained by Bi-profile Bayes (BpB) features are 0.822 and 0.649, respectively, which represents the highest prediction results among the investigated prediction models. Discriminative features are obtained from BpB using the Relief algorithm followed by the Incremental Feature Selection (IFS) method. The sensitivity, specificity, accuracy, and MCC of the ensemble classifier trained by the discriminative features reach up to 0.776, 0.888, 0.832, and 0.668, respectively. Experimental results indicate that the proposed method is far superior to the previous study for anti-angiogenic peptide prediction.
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9
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Drobnak I, Ljubetič A, Gradišar H, Pisanski T, Jerala R. Designed Protein Origami. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 940:7-27. [PMID: 27677507 DOI: 10.1007/978-3-319-39196-0_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Proteins are highly perfected natural molecular machines, owing their properties to the complex tertiary structures with precise spatial positioning of different functional groups that have been honed through millennia of evolutionary selection. The prospects of designing new molecular machines and structural scaffolds beyond the limits of natural proteins make design of new protein folds a very attractive prospect. However, de novo design of new protein folds based on optimization of multiple cooperative interactions is very demanding. As a new alternative approach to design new protein folds unseen in nature, folds can be designed as a mathematical graph, by the self-assembly of interacting polypeptide modules within the single chain. Orthogonal coiled-coil dimers seem like an ideal building module due to their shape, adjustable length, and above all their designability. Similar to the approach of DNA nanotechnology, where complex tertiary structures are designed from complementary nucleotide segments, a polypeptide chain composed of a precisely specified sequence of coiled-coil forming segments can be designed to self-assemble into polyhedral scaffolds. This modular approach encompasses long-range interactions that define complex tertiary structures. We envision that by expansion of the toolkit of building blocks and design strategies of the folding pathways protein origami technology will be able to construct diverse molecular machines.
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Affiliation(s)
- Igor Drobnak
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Helena Gradišar
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tomaž Pisanski
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.,University of Primorska, Koper, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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10
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Li C, Ching Han Chang C, Nagel J, Porebski BT, Hayashida M, Akutsu T, Song J, Buckle AM. Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Brief Bioinform 2016; 17:270-82. [PMID: 26177815 PMCID: PMC6078162 DOI: 10.1093/bib/bbv047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Indexed: 12/19/2022] Open
Abstract
Coiled-coils refer to a bundle of helices coiled together like strands of a rope. It has been estimated that nearly 3% of protein-encoding regions of genes harbour coiled-coil domains (CCDs). Experimental studies have confirmed that CCDs play a fundamental role in subcellular infrastructure and controlling trafficking of eukaryotic cells. Given the importance of coiled-coils, multiple bioinformatics tools have been developed to facilitate the systematic and high-throughput prediction of CCDs in proteins. In this article, we review and compare 12 sequence-based bioinformatics approaches and tools for coiled-coil prediction. These approaches can be categorized into two classes: coiled-coil detection and coiled-coil oligomeric state prediction. We evaluated and compared these methods in terms of their input/output, algorithm, prediction performance, validation methods and software utility. All the independent testing data sets are available at http://lightning.med.monash.edu/coiledcoil/. In addition, we conducted a case study of nine human polyglutamine (PolyQ) disease-related proteins and predicted CCDs and oligomeric states using various predictors. Prediction results for CCDs were highly variable among different predictors. Only two peptides from two proteins were confirmed to be CCDs by majority voting. Both domains were predicted to form dimeric coiled-coils using oligomeric state prediction. We anticipate that this comprehensive analysis will be an insightful resource for structural biologists with limited prior experience in bioinformatics tools, and for bioinformaticians who are interested in designing novel approaches for coiled-coil and its oligomeric state prediction.
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11
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Hasan MM, Yang S, Zhou Y, Mollah MNH. SuccinSite: a computational tool for the prediction of protein succinylation sites by exploiting the amino acid patterns and properties. MOLECULAR BIOSYSTEMS 2016; 12:786-95. [DOI: 10.1039/c5mb00853k] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel computational tool termed SuccinSite has been developed to predict protein succinylation sites using the amino acid patterns and properties based on a random forest classifier.
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Affiliation(s)
- Md. Mehedi Hasan
- State Key Laboratory of Agrobiotechnology
- College of Biological Sciences
- China Agricultural University
- Beijing
- China
| | - Shiping Yang
- State Key Laboratory of Agrobiotechnology
- College of Biological Sciences
- China Agricultural University
- Beijing
- China
| | - Yuan Zhou
- State Key Laboratory of Agrobiotechnology
- College of Biological Sciences
- China Agricultural University
- Beijing
- China
| | - Md. Nurul Haque Mollah
- Laboratory of Bioinformatics
- Department of Statistics
- University of Rajshahi
- Rajshahi 6205
- Bangladesh
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12
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Wang X, Yan R, Li J, Song J. SOHPRED: a new bioinformatics tool for the characterization and prediction of human S-sulfenylation sites. MOLECULAR BIOSYSTEMS 2016; 12:2849-58. [DOI: 10.1039/c6mb00314a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SOHPRED is a new and competitive bioinformatics tool for characterizing and predicting human S-sulfenylation sites.
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Affiliation(s)
- Xiaofeng Wang
- College of Mathematics and Computer Science
- Shanxi Normal University
- Linfen 041004
- China
| | - Renxiang Yan
- Institute of Applied Genomics
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350002
- China
| | - Jinyan Li
- Advanced Analytics Institute and Centre for Health Technologies
- University of Technology Sydney
- Ultimo
- Australia
| | - Jiangning Song
- Infection and Immunity Program
- Biomedicine Discovery Institute and The Department of Biochemistry and Molecular Biology
- Monash University
- Clayton
- Australia
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13
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Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties. Sci Rep 2015; 5:14063. [PMID: 26370878 PMCID: PMC4570195 DOI: 10.1038/srep14063] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/17/2015] [Indexed: 01/23/2023] Open
Abstract
Coiled coils with defined assembly properties and dissociation constants are highly attractive components in synthetic biology and for fabrication of peptide-based hybrid nanomaterials and nanostructures. Complex assemblies based on multiple different peptides typically require orthogonal peptides obtained by negative design. Negative design does not necessarily exclude formation of undesired species and may eventually compromise the stability of the desired coiled coils. This work describe a set of four promiscuous 28-residue de novo designed peptides that heterodimerize and fold into parallel coiled coils. The peptides are non-orthogonal and can form four different heterodimers albeit with large differences in affinities. The peptides display dissociation constants for dimerization spanning from the micromolar to the picomolar range. The significant differences in affinities for dimerization make the peptides prone to thermodynamic social self-sorting as shown by thermal unfolding and fluorescence experiments, and confirmed by simulations. The peptides self-sort with high fidelity to form the two coiled coils with the highest and lowest affinities for heterodimerization. The possibility to exploit self-sorting of mutually complementary peptides could hence be a viable approach to guide the assembly of higher order architectures and a powerful strategy for fabrication of dynamic and tuneable nanostructured materials.
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14
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Wang X, Zhou Y, Yan R. AAFreqCoil: a new classifier to distinguish parallel dimeric and trimeric coiled coils. MOLECULAR BIOSYSTEMS 2015; 11:1794-801. [DOI: 10.1039/c5mb00119f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coiled coils are characteristic rope-like protein structures, constituted by one or more heptad repeats.
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Affiliation(s)
- Xiaofeng Wang
- School of Mathematics and Computer Science
- Shanxi Normal University
- Linfen 041004
- China
| | - Yuan Zhou
- College of Biological Sciences
- China Agricultural University
- Beijing 100193
- China
| | - Renxiang Yan
- Institute of Applied Genomics
- School of Biological Sciences and Engineering
- Fuzhou University
- Fuzhou 350108
- China
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