1
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Ismi DP, Pulungan R, Afiahayati. Deep learning for protein secondary structure prediction: Pre and post-AlphaFold. Comput Struct Biotechnol J 2022; 20:6271-6286. [PMID: 36420164 PMCID: PMC9678802 DOI: 10.1016/j.csbj.2022.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/05/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022] Open
Abstract
This paper aims to provide a comprehensive review of the trends and challenges of deep neural networks for protein secondary structure prediction (PSSP). In recent years, deep neural networks have become the primary method for protein secondary structure prediction. Previous studies showed that deep neural networks had uplifted the accuracy of three-state secondary structure prediction to more than 80%. Favored deep learning methods, such as convolutional neural networks, recurrent neural networks, inception networks, and graph neural networks, have been implemented in protein secondary structure prediction. Methods adapted from natural language processing (NLP) and computer vision are also employed, including attention mechanism, ResNet, and U-shape networks. In the post-AlphaFold era, PSSP studies focus on different objectives, such as enhancing the quality of evolutionary information and exploiting protein language models as the PSSP input. The recent trend to utilize pre-trained language models as input features for secondary structure prediction provides a new direction for PSSP studies. Moreover, the state-of-the-art accuracy achieved by previous PSSP models is still below its theoretical limit. There are still rooms for improvement to be made in the field.
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Affiliation(s)
- Dewi Pramudi Ismi
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Infomatics, Faculty of Industrial Technology, Universitas Ahmad Dahlan, Yogyakarta, Indonesia
| | - Reza Pulungan
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Afiahayati
- Department of Computer Science and Electronics, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
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2
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V HH Structural Modelling Approaches: A Critical Review. Int J Mol Sci 2022; 23:ijms23073721. [PMID: 35409081 PMCID: PMC8998791 DOI: 10.3390/ijms23073721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/20/2022] Open
Abstract
VHH, i.e., VH domains of camelid single-chain antibodies, are very promising therapeutic agents due to their significant physicochemical advantages compared to classical mammalian antibodies. The number of experimentally solved VHH structures has significantly improved recently, which is of great help, because it offers the ability to directly work on 3D structures to humanise or improve them. Unfortunately, most VHHs do not have 3D structures. Thus, it is essential to find alternative ways to get structural information. The methods of structure prediction from the primary amino acid sequence appear essential to bypass this limitation. This review presents the most extensive overview of structure prediction methods applied for the 3D modelling of a given VHH sequence (a total of 21). Besides the historical overview, it aims at showing how model software programs have been shaping the structural predictions of VHHs. A brief explanation of each methodology is supplied, and pertinent examples of their usage are provided. Finally, we present a structure prediction case study of a recently solved VHH structure. According to some recent studies and the present analysis, AlphaFold 2 and NanoNet appear to be the best tools to predict a structural model of VHH from its sequence.
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3
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Yadav NS, Kumar P, Singh I. Structural and functional analysis of protein. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00026-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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4
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Mortuza SM, Zheng W, Zhang C, Li Y, Pearce R, Zhang Y. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nat Commun 2021; 12:5011. [PMID: 34408149 PMCID: PMC8373938 DOI: 10.1038/s41467-021-25316-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/04/2021] [Indexed: 11/28/2022] Open
Abstract
Sequence-based contact prediction has shown considerable promise in assisting non-homologous structure modeling, but it often requires many homologous sequences and a sufficient number of correct contacts to achieve correct folds. Here, we developed a method, C-QUARK, that integrates multiple deep-learning and coevolution-based contact-maps to guide the replica-exchange Monte Carlo fragment assembly simulations. The method was tested on 247 non-redundant proteins, where C-QUARK could fold 75% of the cases with TM-scores (template-modeling scores) ≥0.5, which was 2.6 times more than that achieved by QUARK. For the 59 cases that had either low contact accuracy or few homologous sequences, C-QUARK correctly folded 6 times more proteins than other contact-based folding methods. C-QUARK was also tested on 64 free-modeling targets from the 13th CASP (critical assessment of protein structure prediction) experiment and had an average GDT_TS (global distance test) score that was 5% higher than the best CASP predictors. These data demonstrate, in a robust manner, the progress in modeling non-homologous protein structures using low-accuracy and sparse contact-map predictions.
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Affiliation(s)
- S M Mortuza
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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5
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Kinch LN, Pei J, Kryshtafovych A, Schaeffer RD, Grishin NV. Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction. Proteins 2021; 89:1673-1686. [PMID: 34240477 DOI: 10.1002/prot.26172] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 12/25/2022]
Abstract
This report describes the tertiary structure prediction assessment of difficult modeling targets in the 14th round of the Critical Assessment of Structure Prediction (CASP14). We implemented an official ranking scheme that used the same scores as the previous CASP topology-based assessment, but combined these scores with one that emphasized physically realistic models. The top performing AlphaFold2 group outperformed the rest of the prediction community on all but two of the difficult targets considered in this assessment. They provided high quality models for most of the targets (86% over GDT_TS 70), including larger targets above 150 residues, and they correctly predicted the topology of almost all the rest. AlphaFold2 performance was followed by two manual Baker methods, a Feig method that refined Zhang-server models, two notable automated Zhang server methods (QUARK and Zhang-server), and a Zhang manual group. Despite the remarkable progress in protein structure prediction of difficult targets, both the prediction community and AlphaFold2, to a lesser extent, faced challenges with flexible regions and obligate oligomeric assemblies. The official ranking of top-performing methods was supported by performance generated PCA and heatmap clusters that gave insight into target difficulties and the most successful state-of-the-art structure prediction methodologies.
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Affiliation(s)
- Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - R Dustin Schaeffer
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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6
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Abstract
For two decades, Rosetta has consistently been at the forefront of protein structure
prediction. While it has become a very large package comprising programs, scripts, and tools, for
different types of macromolecular modelling such as ligand docking, protein-protein docking,
protein design, and loop modelling, it started as the implementation of an algorithm for ab initio
protein structure prediction. The term ’Rosetta’ appeared for the first time twenty years ago in the
literature to describe that algorithm and its contribution to the third edition of the community wide
Critical Assessment of techniques for protein Structure Prediction (CASP3). Similar to the Rosetta
stone that allowed deciphering the ancient Egyptian civilisation, David Baker and his co-workers
have been contributing to deciphering ’the second half of the genetic code’. Although the focus of
Baker’s team has expended to de novo protein design in the past few years, Rosetta’s ‘fame’ is
associated with its fragment-assembly protein structure prediction approach. Following a
presentation of the main concepts underpinning its foundation, especially sequence-structure
correlation and usage of fragments, we review the main stages of its developments and highlight
the milestones it has achieved in terms of protein structure prediction, particularly in CASP.
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Affiliation(s)
- Jad Abbass
- Department of Computer Science, Lebanese International University, Bekaa, Lebanon
| | - Jean-Christophe Nebel
- Faculty of Science, Engineering and Computing, Kingston University, London, KT1 2EE, United Kingdom
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7
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Dhingra S, Sowdhamini R, Cadet F, Offmann B. A glance into the evolution of template-free protein structure prediction methodologies. Biochimie 2020; 175:85-92. [DOI: 10.1016/j.biochi.2020.04.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 11/26/2022]
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8
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Abbass J, Nebel JC. Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure. BMC Bioinformatics 2020; 21:170. [PMID: 32357827 PMCID: PMC7195757 DOI: 10.1186/s12859-020-3491-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whenever suitable template structures are not available, usage of fragment-based protein structure prediction becomes the only practical alternative as pure ab initio techniques require massive computational resources even for very small proteins. However, inaccuracy of their energy functions and their stochastic nature imposes generation of a large number of decoys to explore adequately the solution space, limiting their usage to small proteins. Taking advantage of the uneven complexity of the sequence-structure relationship of short fragments, we adjusted the fragment insertion process by customising the number of available fragment templates according to the expected complexity of the predicted local secondary structure. Whereas the number of fragments is kept to its default value for coil regions, important and dramatic reductions are proposed for beta sheet and alpha helical regions, respectively. RESULTS The evaluation of our fragment selection approach was conducted using an enhanced version of the popular Rosetta fragment-based protein structure prediction tool. It was modified so that the number of fragment candidates used in Rosetta could be adjusted based on the local secondary structure. Compared to Rosetta's standard predictions, our strategy delivered improved first models, + 24% and + 6% in terms of GDT, when using 2000 and 20,000 decoys, respectively, while reducing significantly the number of fragment candidates. Furthermore, our enhanced version of Rosetta is able to deliver with 2000 decoys a performance equivalent to that produced by standard Rosetta while using 20,000 decoys. We hypothesise that, as the fragment insertion process focuses on the most challenging regions, such as coils, fewer decoys are needed to explore satisfactorily conformation spaces. CONCLUSIONS Taking advantage of the high accuracy of sequence-based secondary structure predictions, we showed the value of that information to customise the number of candidates used during the fragment insertion process of fragment-based protein structure prediction. Experimentations conducted using standard Rosetta showed that, when using the recommended number of decoys, i.e. 20,000, our strategy produces better results. Alternatively, similar results can be achieved using only 2000 decoys. Consequently, we recommend the adoption of this strategy to either improve significantly model quality or reduce processing times by a factor 10.
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Affiliation(s)
- Jad Abbass
- Faculty of Science, Engineering and Computing, Kingston University, London, KT1 2EE UK
- Department of Computer Science, Lebanese International University, Bekaa, Lebanon
| | - Jean-Christophe Nebel
- Faculty of Science, Engineering and Computing, Kingston University, London, KT1 2EE UK
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9
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Karczyńska AS, Ziȩba K, Uciechowska U, Mozolewska MA, Krupa P, Lubecka EA, Lipska AG, Sikorska C, Samsonov SA, Sieradzan AK, Giełdoń A, Liwo A, Ślusarz R, Ślusarz M, Lee J, Joo K, Czaplewski C. Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. J Chem Inf Model 2020; 60:1844-1864. [PMID: 31999919 PMCID: PMC7588044 DOI: 10.1021/acs.jcim.9b00864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The method for protein-structure
prediction, which combines the
physics-based coarse-grained UNRES force field with knowledge-based
modeling, has been developed further and tested in the 13th Community
Wide Experiment on the Critical Assessment of Techniques for Protein
Structure Prediction (CASP13). The method implements restraints from
the consensus fragments common to server models. In this work, the
server models to derive fragments have been chosen on the basis of
quality assessment; a fully automatic fragment-selection procedure
has been introduced, and Dynamic Fragment Assembly pseudopotentials
have been fully implemented. The Global Distance Test Score (GDT_TS),
averaged over our “Model 1” predictions, increased by
over 10 units with respect to CASP12 for the free-modeling category
to reach 40.82. Our “Model 1” predictions ranked 20
and 14 for all and free-modeling targets, respectively (upper 20.2%
and 14.3% of all models submitted to CASP13 in these categories, respectively),
compared to 27 (upper 21.1%) and 24 (upper 18.9%) in CASP12, respectively.
For oligomeric targets, the Interface Patch Similarity (IPS) and Interface
Contact Similarity (ICS) averaged over our best oligomer models increased
from 0.28 to 0.36 and from 12.4 to 17.8, respectively, from CASP12
to CASP13, and top-ranking models of 2 targets (H0968 and T0997o)
were obtained (none in CASP12). The improvement of our method in CASP13
over CASP12 was ascribed to the combined effect of the overall enhancement
of server-model quality, our success in selecting server models and
fragments to derive restraints, and improvements of the restraint
and potential-energy functions.
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Affiliation(s)
| | - Karolina Ziȩba
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Urszula Uciechowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Magdalena A Mozolewska
- Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warsaw PL-02668, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, Warsaw PL-02668, Poland
| | - Emilia A Lubecka
- Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Wita Stwosza 57, Gdańsk 80-308, Poland
| | - Agnieszka G Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Celina Sikorska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.,School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland.,School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Rafał Ślusarz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Magdalena Ślusarz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Jooyoung Lee
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Keehyoung Joo
- Center for Advanced Computation, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 130-722, Republic of Korea
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
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10
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Energy propagation along polypeptide α-helix: Experimental data and ab initio zone structure. Biosystems 2019; 185:104016. [DOI: 10.1016/j.biosystems.2019.104016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/09/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022]
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11
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Abriata LA, Tamò GE, Dal Peraro M. A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments. Proteins 2019; 87:1100-1112. [PMID: 31344267 DOI: 10.1002/prot.25787] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/26/2019] [Accepted: 07/19/2019] [Indexed: 12/22/2022]
Abstract
We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores-aided visual inspection of models for each evaluation unit (EU); (b) ranking of predictors resulting from this evaluation and from global scores; and (c) evaluation of progress, state of the art, and current limitations of protein structure prediction. We witness a sizable improvement in tertiary structure prediction building on the progress observed from CASP11 to CASP12, with (a) top models reaching backbone RMSD <3 å for several EUs of size <150 residues, contributed by many groups; (b) at least one model that roughly captures global topology for all EUs, probably unprecedented in this track of CASP; and (c) even quite good models for full, unsplit targets. Better structure predictions are brought about mainly by improved residue-residue contact predictions, and since this CASP also by distance predictions, achieved through state-of-the-art machine learning methods which also progressed to work with slightly shallower alignments compared to CASP12. As we reach a new realm of tertiary structure prediction quality, new directions are proposed and explored for future CASPs: (a) dropping splitting into EUs, (b) rethinking difficulty metrics probably in terms of contact and distance predictions, (c) assessing also side chains for models of high backbone accuracy, and (d) assessing residue-wise and possibly residue-residue quality estimates.
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Affiliation(s)
- Luciano A Abriata
- School of Life Sciences, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Giorgio E Tamò
- School of Life Sciences, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Matteo Dal Peraro
- School of Life Sciences, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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12
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Geng H, Chen F, Ye J, Jiang F. Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins. Comput Struct Biotechnol J 2019; 17:1162-1170. [PMID: 31462972 PMCID: PMC6709365 DOI: 10.1016/j.csbj.2019.07.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/07/2019] [Accepted: 07/23/2019] [Indexed: 12/21/2022] Open
Abstract
Compared with rapid accumulation of protein sequences from high-throughput DNA sequencing, obtaining experimental 3D structures of proteins is still much more difficult, making protein structure prediction (PSP) potentially very useful. Currently, a vast majority of PSP efforts are based on data mining of known sequences, structures and their relationships (informatics-based). However, if closely related template is not available, these methods are usually much less reliable than experiments. They may also be problematic in predicting the structures of naturally occurring or designed peptides. On the other hand, physics-based methods including molecular dynamics (MD) can utilize our understanding of detailed atomic interactions determining biomolecular structures. In this mini-review, we show that all-atom MD can predict structures of cyclic peptides and other peptide foldamers with accuracy similar to experiments. Then, some notable successes in reproducing experimental 3D structures of small proteins through MD simulations (some with replica-exchange) of the folding were summarized. We also describe advancements of MD-based refinement of structure models, and the integration of limited experimental or bioinformatics data into MD-based structure modeling.
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Affiliation(s)
- Hao Geng
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Fangfang Chen
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China
| | - Jing Ye
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China
| | - Fan Jiang
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- NanoAI Biotech Co.,Ltd., Silicon Valley Compound, Longhua District, Shenzhen 518109, China
- Corresponding author at: Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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13
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Jing X, Dong Q, Lu R, Dong Q. Protein Inter-Residue Contacts Prediction: Methods, Performances and Applications. Curr Bioinform 2019. [DOI: 10.2174/1574893613666181109130430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Protein inter-residue contacts prediction play an important role in the field of protein structure and function research. As a low-dimensional representation of protein tertiary structure, protein inter-residue contacts could greatly help de novo protein structure prediction methods to reduce the conformational search space. Over the past two decades, various methods have been developed for protein inter-residue contacts prediction.Objective:We provide a comprehensive and systematic review of protein inter-residue contacts prediction methods.Results:Protein inter-residue contacts prediction methods are roughly classified into five categories: correlated mutations methods, machine-learning methods, fusion methods, templatebased methods and 3D model-based methods. In this paper, firstly we describe the common definition of protein inter-residue contacts and show the typical application of protein inter-residue contacts. Then, we present a comprehensive review of the three main categories for protein interresidue contacts prediction: correlated mutations methods, machine-learning methods and fusion methods. Besides, we analyze the constraints for each category. Furthermore, we compare several representative methods on the CASP11 dataset and discuss performances of these methods in detail.Conclusion:Correlated mutations methods achieve better performances for long-range contacts, while the machine-learning method performs well for short-range contacts. Fusion methods could take advantage of the machine-learning and correlated mutations methods. Employing more effective fusion strategy could be helpful to further improve the performances of fusion methods.
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Affiliation(s)
- Xiaoyang Jing
- School of Computer Science, Fudan University, Shanghai, China
| | - Qimin Dong
- Vocational and Technical Education Center of Linxi County, Chifeng, Inner Mongolia, China
| | - Ruqian Lu
- School of Computer Science, Fudan University, Shanghai, China
| | - Qiwen Dong
- Faculty of Education, East China Normal University, Shanghai, China
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14
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Dehghani T, Naghibzadeh M, Eghdami M. BetaDL: A protein beta-sheet predictor utilizing a deep learning model and independent set solution. Comput Biol Med 2019; 104:241-249. [PMID: 30530227 DOI: 10.1016/j.compbiomed.2018.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
Abstract
The sequence-based prediction of beta-residue contacts and beta-sheet structures contain key information for protein structure prediction. However, the determination of beta-sheet structures poses numerous challenges due to long-range beta-residue interactions and the huge number of possible beta-sheet structures. Recently gaining attention has been the prediction of residue contacts based on deep learning models whose results have led to improvement in protein structure prediction. In addition, to reduce the computational complexity of determining beta-sheet structures, it has been suggested that this problem be transformed into graph-based solutions. Consequently, the current work proposes BetaDL, a combination of a deep learning and a graph-based beta-sheet structure predictor. BetaDL adopts deep learning models to capture beta-residue contacts and improve beta-sheet structure predictions. In addition, a graph-based approach is presented to model the beta-sheets conformational space and a new score function is introduced to evaluate beta-sheets. Furthermore, the present study demonstrates that the beta-sheet structure can be predicted within an acceptable computational time by the utilization of a heuristic maximum weight independent set solution. When compared to state-of-the-art methods, experimental results from BetaSheet916 and BetaSheet1452 datasets indicate that BetaDL improves the accuracy of beta-residue contact and beta-sheet structure prediction. Using BetaDL, beta-sheet structures are predicted with a 4% and 6% improvement in the F1-score at the residue and strand levels, respectively. BetaDL's source code and data are available at http://kerg.um.ac.ir/index.php/datasets/#BetaDL.
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Affiliation(s)
- Toktam Dehghani
- Department of Computer Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahmoud Naghibzadeh
- Department of Computer Engineering, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mahdie Eghdami
- Department of Computer Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
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15
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Blaszczyk M, Gront D, Kmiecik S, Kurcinski M, Kolinski M, Ciemny MP, Ziolkowska K, Panek M, Kolinski A. Protein Structure Prediction Using Coarse-Grained Models. SPRINGER SERIES ON BIO- AND NEUROSYSTEMS 2019. [DOI: 10.1007/978-3-319-95843-9_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Studer G, Tauriello G, Bienert S, Waterhouse AM, Bertoni M, Bordoli L, Schwede T, Lepore R. Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information. Methods Mol Biol 2019; 1851:301-316. [PMID: 30298405 DOI: 10.1007/978-1-4939-8736-8_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins are subject to evolutionary forces that shape their three-dimensional structure to meet specific functional demands. The knowledge of the structure of a protein is therefore instrumental to gain information about the molecular basis of its function. However, experimental structure determination is inherently time consuming and expensive, making it impossible to follow the explosion of sequence data deriving from genome-scale projects. As a consequence, computational structural modeling techniques have received much attention and established themselves as a valuable complement to experimental structural biology efforts. Among these, comparative modeling remains the method of choice to model the three-dimensional structure of a protein when homology to a protein of known structure can be detected.The general strategy consists of using experimentally determined structures of proteins as templates for the generation of three-dimensional models of related family members (targets) of which the structure is unknown. This chapter provides a description of the individual steps needed to obtain a comparative model using SWISS-MODEL, one of the most widely used automated servers for protein structure homology modeling.
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Affiliation(s)
- Gabriel Studer
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Gerardo Tauriello
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Stefan Bienert
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Andrew Mark Waterhouse
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Martino Bertoni
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Lorenza Bordoli
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Rosalba Lepore
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
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17
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Kc DB. Recent advances in sequence-based protein structure prediction. Brief Bioinform 2018; 18:1021-1032. [PMID: 27562963 DOI: 10.1093/bib/bbw070] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 11/13/2022] Open
Abstract
The most accurate characterizations of the structure of proteins are provided by structural biology experiments. However, because of the high cost and labor-intensive nature of the structural experiments, the gap between the number of protein sequences and solved structures is widening rapidly. Development of computational methods to accurately model protein structures from sequences is becoming increasingly important to the biological community. In this article, we highlight some important progress in the field of protein structure prediction, especially those related to free modeling (FM) methods that generate structure models without using homologous templates. We also provide a short synopsis of some of the recent advances in FM approaches as demonstrated in the recent Computational Assessment of Structure Prediction competition as well as recent trends and outlook for FM approaches in protein structure prediction.
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18
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Deng H, Jia Y, Zhang Y. Protein structure prediction. INTERNATIONAL JOURNAL OF MODERN PHYSICS. B 2018; 32:1840009. [PMID: 30853739 PMCID: PMC6407873 DOI: 10.1142/s021797921840009x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Predicting 3D structure of protein from its amino acid sequence is one of the most important unsolved problems in biophysics and computational biology. This paper attempts to give a comprehensive introduction of the most recent effort and progress on protein structure prediction. Following the general flowchart of structure prediction, related concepts and methods are presented and discussed. Moreover, brief introductions are made to several widely-used prediction methods and the community-wide critical assessment of protein structure prediction (CASP) experiments.
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Affiliation(s)
- Haiyou Deng
- College of Science, Huazhong Agricultural University, Wuhan 4R0070, P. R. China
| | - Ya Jia
- College of Physical Science and Technology, Central China Normal University, Wuhan 430079, P. R. China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 45108, USA
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19
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Gao S, Song S, Cheng J, Todo Y, Zhou M. Incorporation of Solvent Effect into Multi-Objective Evolutionary Algorithm for Improved Protein Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1365-1378. [PMID: 28534784 DOI: 10.1109/tcbb.2017.2705094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The problem of predicting the three-dimensional (3-D) structure of a protein from its one-dimensional sequence has been called the "holy grail of molecular biology", and it has become an important part of structural genomics projects. Despite the rapid developments in computer technology and computational intelligence, it remains challenging and fascinating. In this paper, to solve it we propose a multi-objective evolutionary algorithm. We decompose the protein energy function Chemistry at HARvard Macromolecular Mechanics force fields into bond and non-bond energies as the first and second objectives. Considering the effect of solvent, we innovatively adopt a solvent-accessible surface area as the third objective. We use 66 benchmark proteins to verify the proposed method and obtain better or competitive results in comparison with the existing methods. The results suggest the necessity to incorporate the effect of solvent into a multi-objective evolutionary algorithm to improve protein structure prediction in terms of accuracy and efficiency.
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20
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Yang Y, Gao J, Wang J, Heffernan R, Hanson J, Paliwal K, Zhou Y. Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Brief Bioinform 2018; 19:482-494. [PMID: 28040746 PMCID: PMC5952956 DOI: 10.1093/bib/bbw129] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/15/2016] [Indexed: 11/13/2022] Open
Abstract
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted helical and sheet conformations for protein polypeptide backbone even before the first protein structure was determined. Sixty-five years later, powerful new methods breathe new life into this field. The highest three-state accuracy without relying on structure templates is now at 82-84%, a number unthinkable just a few years ago. These improvements came from increasingly larger databases of protein sequences and structures for training, the use of template secondary structure information and more powerful deep learning techniques. As we are approaching to the theoretical limit of three-state prediction (88-90%), alternative to secondary structure prediction (prediction of backbone torsion angles and Cα-atom-based angles and torsion angles) not only has more room for further improvement but also allows direct prediction of three-dimensional fragment structures with constantly improved accuracy. About 20% of all 40-residue fragments in a database of 1199 non-redundant proteins have <6 Å root-mean-squared distance from the native conformations by SPIDER2. More powerful deep learning methods with improved capability of capturing long-range interactions begin to emerge as the next generation of techniques for secondary structure prediction. The time has come to finish off the final stretch of the long march towards protein secondary structure prediction.
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Affiliation(s)
- Yuedong Yang
- Insitute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, QLD, Australia
| | - Jianzhao Gao
- School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Rhys Heffernan
- Signal Processing Laboratory, Griffith University, Brisbane, Australia
| | - Jack Hanson
- Signal Processing Laboratory, Griffith University, Brisbane, Australia
| | - Kuldip Paliwal
- Signal Processing Laboratory, Griffith University, Brisbane, Australia
| | - Yaoqi Zhou
- Insitute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, QLD, Australia
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
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21
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Correa L, Borguesan B, Farfan C, Inostroza-Ponta M, Dorn M. A Memetic Algorithm for 3-D Protein Structure Prediction Problem. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:690-704. [PMID: 27925594 DOI: 10.1109/tcbb.2016.2635143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Memetic Algorithms are population-based metaheuristics intrinsically concerned with exploiting all available knowledge about the problem under study. The incorporation of problem domain knowledge is not an optional mechanism, but a fundamental feature of the Memetic Algorithms. In this paper, we present a Memetic Algorithm to tackle the three-dimensional protein structure prediction problem. The method uses a structured population and incorporates a Simulated Annealing algorithm as a local search strategy, as well as ad-hoc crossover and mutation operators to deal with the problem. It takes advantage of structural knowledge stored in the Protein Data Bank, by using an Angle Probability List that helps to reduce the search space and to guide the search strategy. The proposed algorithm was tested on nineteen protein sequences of amino acid residues, and the results show the ability of the algorithm to find native-like protein structures. Experimental results have revealed that the proposed algorithm can find good solutions regarding root-mean-square deviation and global distance total score test in comparison with the experimental protein structures. We also show that our results are comparable in terms of folding organization with state-of-the-art prediction methods, corroborating the effectiveness of our proposal.
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22
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Kim SS, Seffernick JT, Lindert S. Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application. J Phys Chem B 2018; 122:3920-3930. [PMID: 29595057 DOI: 10.1021/acs.jpcb.8b01763] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although many proteins necessitate well-folded structures to properly instigate their biological functions, a large fraction of functioning proteins contain regions-known as intrinsically disordered protein regions-where stable structures are not likely to form. Notable functional roles of intrinsically disordered proteins are in transcriptional regulation, translation, and cellular signal transduction. Moreover, intrinsically disordered protein regions are highly abundant in many proteins associated with various human diseases, therefore these segments have become attractive drug targets for potential therapeutics. Over the past decades, numerous computational methods have been developed to accurately predict disordered regions of proteins. Here we introduce a user-friendly and reliable approach for the prediction of disordered protein regions using the structure prediction software Rosetta. Using 245 proteins from a benchmark data set (16 DisProt database proteins) and a test data set (229 proteins with NMR data), we use Rosetta to predict the global protein structures and then show that there is a statistically significant difference between Rosetta scores in disordered and ordered regions, with scores being less favorable in disordered regions. Furthermore, the difference in scores between ordered and disordered protein regions is sufficient to accurately identify disordered protein regions. As a result, our Rosetta ResidueDisorder method (benchmark data set prediction accuracy of 71.77% and independent test data set prediction accuracy of 65.37%) outperformed other established disorder prediction tools and did not exhibit a biased prediction toward either ordered or disordered regions. To facilitate usage, a Rosetta application has been developed for the Rosetta ResidueDisorder method.
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Affiliation(s)
- Stephanie S Kim
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
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23
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Structural and functional modeling of viral protein 5 of Infectious Bursal Disease Virus. Virus Res 2018; 247:55-60. [PMID: 29427596 DOI: 10.1016/j.virusres.2018.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/28/2018] [Accepted: 01/31/2018] [Indexed: 11/22/2022]
Abstract
Infectious Bursal Disease (IBD) is an acute, highly contagious and immunosuppressive disease of young chicken. The causative virus (IBDV) is a bi-segmented, double-stranded RNA virus. The virus encodes five major proteins, viral protein (VP) 1-5. VPs 1-3 have been characterized crystallographically. Albeit a rise in the number of studies reporting successful heterologous expression of VP5 in recent times, challenging the notion that rapid death of host cells overexpressing VP5 disallows obtaining sufficiently pure preparations of the protein for crystallographic studies, the structure of VP5 remains unknown and its function controversial. Our study describes the first 3D model of IBD VP5 obtained through an elaborate computational workflow. Based on the results of the study, IBD VP5 can be predicted to be a structural analog of the leucine-rich repeat (LRR) family of proteins. Functional implications arising from structural similarity of VP5 with host Toll-like receptor (Tlr) 3 also satisfy the previously reported opposing roles of the protein in first abolishing and later inducing host-cell apoptosis.
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24
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Li B, Fooksa M, Heinze S, Meiler J. Finding the needle in the haystack: towards solving the protein-folding problem computationally. Crit Rev Biochem Mol Biol 2018; 53:1-28. [PMID: 28976219 PMCID: PMC6790072 DOI: 10.1080/10409238.2017.1380596] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
Abstract
Prediction of protein tertiary structures from amino acid sequence and understanding the mechanisms of how proteins fold, collectively known as "the protein folding problem," has been a grand challenge in molecular biology for over half a century. Theories have been developed that provide us with an unprecedented understanding of protein folding mechanisms. However, computational simulation of protein folding is still difficult, and prediction of protein tertiary structure from amino acid sequence is an unsolved problem. Progress toward a satisfying solution has been slow due to challenges in sampling the vast conformational space and deriving sufficiently accurate energy functions. Nevertheless, several techniques and algorithms have been adopted to overcome these challenges, and the last two decades have seen exciting advances in enhanced sampling algorithms, computational power and tertiary structure prediction methodologies. This review aims at summarizing these computational techniques, specifically conformational sampling algorithms and energy approximations that have been frequently used to study protein-folding mechanisms or to de novo predict protein tertiary structures. We hope that this review can serve as an overview on how the protein-folding problem can be studied computationally and, in cases where experimental approaches are prohibitive, help the researcher choose the most relevant computational approach for the problem at hand. We conclude with a summary of current challenges faced and an outlook on potential future directions.
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Affiliation(s)
- Bian Li
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Michaela Fooksa
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, TN, USA
| | - Sten Heinze
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
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25
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Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12thCritical Assessment of protein Structure Prediction experiment. Proteins 2017; 86 Suppl 1:215-227. [DOI: 10.1002/prot.25442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 12/10/2017] [Indexed: 12/26/2022]
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26
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Thomas JMH, Simkovic F, Keegan R, Mayans O, Zhang C, Zhang Y, Rigden DJ. Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta Crystallogr D Struct Biol 2017; 73:985-996. [PMID: 29199978 PMCID: PMC5713875 DOI: 10.1107/s2059798317016436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/15/2017] [Indexed: 02/06/2023] Open
Abstract
α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.
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Affiliation(s)
- Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan Keegan
- Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Olga Mayans
- Fachbereich Biologie, Universität Konstanz, D-78457 Konstanz, Germany
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, Department of Biological Chemistry, Medical School, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, Department of Biological Chemistry, Medical School, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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27
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Abriata LA, Tamò GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods. Proteins 2017; 86 Suppl 1:97-112. [DOI: 10.1002/prot.25423] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Luciano A. Abriata
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB); Lausanne Switzerland
| | - Giorgio E. Tamò
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB); Lausanne Switzerland
| | | | | | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB); Lausanne Switzerland
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28
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Zhang C, Mortuza SM, He B, Wang Y, Zhang Y. Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins 2017; 86 Suppl 1:136-151. [PMID: 29082551 DOI: 10.1002/prot.25414] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/09/2017] [Accepted: 10/27/2017] [Indexed: 12/26/2022]
Abstract
We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successfully folds three medium-size FM targets that have more than 150 residues, even though the interplay between the two pipelines still awaits further optimization. Newly developed sequence-based contact prediction by NeBcon plays a critical role to enhance the quality of models, particularly for FM targets, by the new pipelines. The inclusion of NeBcon predicted contacts as restraints in the QUARK simulations results in an average TM-score of 0.41 for the best in top five predicted models, which is 37% higher than that by the QUARK simulations without contacts. In particular, there are seven targets that are converted from non-foldable to foldable (TM-score >0.5) due to the use of contact restraints in the simulations. Another additional feature in the current pipelines is the local structure quality prediction by ResQ, which provides a robust residue-level modeling error estimation. Despite the success, significant challenges still remain in ab initio modeling of multi-domain proteins and folding of β-proteins with complicated topologies bound by long-range strand-strand interactions. Improvements on domain boundary and long-range contact prediction, as well as optimal use of the predicted contacts and multiple threading alignments, are critical to address these issues seen in the CASP12 experiment.
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Affiliation(s)
- Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - S M Mortuza
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Baoji He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Yanting Wang
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan
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29
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Jing X, Dong Q, Lu R. RRCRank: a fusion method using rank strategy for residue-residue contact prediction. BMC Bioinformatics 2017; 18:390. [PMID: 28865433 PMCID: PMC5581475 DOI: 10.1186/s12859-017-1811-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background In structural biology area, protein residue-residue contacts play a crucial role in protein structure prediction. Some researchers have found that the predicted residue-residue contacts could effectively constrain the conformational search space, which is significant for de novo protein structure prediction. In the last few decades, related researchers have developed various methods to predict residue-residue contacts, especially, significant performance has been achieved by using fusion methods in recent years. In this work, a novel fusion method based on rank strategy has been proposed to predict contacts. Unlike the traditional regression or classification strategies, the contact prediction task is regarded as a ranking task. First, two kinds of features are extracted from correlated mutations methods and ensemble machine-learning classifiers, and then the proposed method uses the learning-to-rank algorithm to predict contact probability of each residue pair. Results First, we perform two benchmark tests for the proposed fusion method (RRCRank) on CASP11 dataset and CASP12 dataset respectively. The test results show that the RRCRank method outperforms other well-developed methods, especially for medium and short range contacts. Second, in order to verify the superiority of ranking strategy, we predict contacts by using the traditional regression and classification strategies based on the same features as ranking strategy. Compared with these two traditional strategies, the proposed ranking strategy shows better performance for three contact types, in particular for long range contacts. Third, the proposed RRCRank has been compared with several state-of-the-art methods in CASP11 and CASP12. The results show that the RRCRank could achieve comparable prediction precisions and is better than three methods in most assessment metrics. Conclusions The learning-to-rank algorithm is introduced to develop a novel rank-based method for the residue-residue contact prediction of proteins, which achieves state-of-the-art performance based on the extensive assessment. Electronic supplementary material The online version of this article (10.1186/s12859-017-1811-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoyang Jing
- School of Computer Science, Fudan University, Shanghai, 200433, People's Republic of China
| | - Qiwen Dong
- School of Data Science and Engineering, East China Normal University, Shanghai, 200062, People's Republic of China.
| | - Ruqian Lu
- School of Computer Science, Fudan University, Shanghai, 200433, People's Republic of China
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30
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Xiong D, Mao W, Gong H. Predicting the helix-helix interactions from correlated residue mutations. Proteins 2017; 85:2162-2169. [PMID: 28833538 DOI: 10.1002/prot.25370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/03/2017] [Accepted: 08/13/2017] [Indexed: 12/30/2022]
Abstract
Helix-helix interactions are crucial in the structure assembly, stability and function of helix-rich proteins including many membrane proteins. In spite of remarkable progresses over the past decades, the accuracy of predicting protein structures from their amino acid sequences is still far from satisfaction. In this work, we focused on a simpler problem, the prediction of helix-helix interactions, the results of which could facilitate practical protein structure prediction by constraining the sampling space. Specifically, we started from the noisy 2D residue contact maps derived from correlated residue mutations, and utilized ridge detection to identify the characteristic residue contact patterns for helix-helix interactions. The ridge information as well as a few additional features were then fed into a machine learning model HHConPred to predict interactions between helix pairs. In an independent test, our method achieved an F-measure of ∼60% for predicting helix-helix interactions. Moreover, although the model was trained mainly using soluble proteins, it could be extended to membrane proteins with at least comparable performance relatively to previous approaches that were generated purely using membrane proteins. All data and source codes are available at http://166.111.152.91/Downloads.html or https://github.com/dpxiong/HHConPred.
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Affiliation(s)
- Dapeng Xiong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Innovation Center of Structural Biology, Tsinghua University, Beijing, China
| | - Wenzhi Mao
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Innovation Center of Structural Biology, Tsinghua University, Beijing, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Innovation Center of Structural Biology, Tsinghua University, Beijing, China
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31
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Mackenzie CO, Grigoryan G. Protein structural motifs in prediction and design. Curr Opin Struct Biol 2017; 44:161-167. [PMID: 28460216 PMCID: PMC5513761 DOI: 10.1016/j.sbi.2017.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/18/2017] [Accepted: 03/28/2017] [Indexed: 01/11/2023]
Abstract
The Protein Data Bank (PDB) has been an integral resource for shaping our fundamental understanding of protein structure and for the advancement of such applications as protein design and structure prediction. Over the years, information from the PDB has been used to generate models ranging from specific structural mechanisms to general statistical potentials. With accumulating structural data, it has become possible to mine for more complete and complex structural observations, deducing more accurate generalizations. Motif libraries, which capture recurring structural features along with their sequence preferences, have exposed modularity in the structural universe and found successful application in various problems of structural biology. Here we summarize recent achievements in this arena, focusing on subdomain level structural patterns and their applications to protein design and structure prediction, and suggest promising future directions as the structural database continues to grow.
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Affiliation(s)
- Craig O Mackenzie
- Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, United States
| | - Gevorg Grigoryan
- Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, United States; Department of Computer Science, Dartmouth College, Hanover, NH 03755, United States.
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32
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Gadzała M, Kalinowska B, Banach M, Konieczny L, Roterman I. Determining protein similarity by comparing hydrophobic core structure. Heliyon 2017; 3:e00235. [PMID: 28217749 PMCID: PMC5300504 DOI: 10.1016/j.heliyon.2017.e00235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 12/06/2016] [Accepted: 01/19/2017] [Indexed: 12/19/2022] Open
Abstract
Formal assessment of structural similarity is - next to protein structure prediction - arguably the most important unsolved problem in proteomics. In this paper we propose a similarity criterion based on commonalities between the proteins' hydrophobic cores. The hydrophobic core emerges as a result of conformational changes through which each residue reaches its intended position in the protein body. A quantitative criterion based on this phenomenon has been proposed in the framework of the CASP challenge. The structure of the hydrophobic core - including the placement and scope of any deviations from the idealized model - may indirectly point to areas of importance from the point of view of the protein's biological function. Our analysis focuses on an arbitrarily selected target from the CASP11 challenge. The proposed measure, while compliant with CASP criteria (70-80% correlation), involves certain adjustments which acknowledge the presence of factors other than simple spatial arrangement of solids.
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Affiliation(s)
- M. Gadzała
- AGH - Academic Computer Center − Cyfronet, Nawojki 11, Kraków 30-950, Poland
| | - B. Kalinowska
- Faculty of Physics, Astronomy, Applied Computer Science − Jagiellonian University, Łojasiewicza 11, Kraków 30-348, Poland
| | - M. Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University − Medical College, Łazarza 16, Krakow 31-530, Poland
| | - L. Konieczny
- Chair of Medical Biochemistry, Jagiellonian University − Medical College, Kopernika 7, Kraków 31-034, Poland
| | - I. Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University − Medical College, Łazarza 16, Krakow 31-530, Poland
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33
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Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP11 statistics and the prediction center evaluation system. Proteins 2016; 84 Suppl 1:15-9. [PMID: 26857434 PMCID: PMC5479680 DOI: 10.1002/prot.25005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/18/2016] [Accepted: 02/04/2016] [Indexed: 01/10/2023]
Abstract
We outline the role of the Protein Structure Prediction Center (predictioncenter.org) in conducting the CASP11 and CASP ROLL experiments, discuss the experiment statistics, and provide an overview of the present CASP infrastructure. The biggest changes compared to the previous CASPs are the implementation of the evaluation system incorporating practically all evaluation measures, statistical tests, and visualization tools historically used by the CASP assessors, the expansion of the infrastructure to incorporate new categories of contact-assisted and multimeric predictions, and the redesign of the assessors' web-workspace enabling assessments based on multiple measures for different group categories and target sets. Proteins 2016; 84(Suppl 1):15-19. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, 95616
| | - Bohdan Monastyrskyy
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, 95616
| | - Krzysztof Fidelis
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, 95616.
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Gao J, Yang Y, Zhou Y. Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks. Bioinformatics 2016; 32:3768-3773. [DOI: 10.1093/bioinformatics/btw549] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/29/2016] [Accepted: 08/18/2016] [Indexed: 11/14/2022] Open
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Yu J, Guerois R. PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets. Bioinformatics 2016; 32:3760-3767. [PMID: 27551106 DOI: 10.1093/bioinformatics/btw533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/22/2016] [Accepted: 08/10/2016] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Protein-protein docking methods are of great importance for understanding interactomes at the structural level. It has become increasingly appealing to use not only experimental structures but also homology models of unbound subunits as input for docking simulations. So far we are missing a large scale assessment of the success of rigid-body free docking methods on homology models. RESULTS We explored how we could benefit from comparative modelling of unbound subunits to expand docking benchmark datasets. Starting from a collection of 3157 non-redundant, high X-ray resolution heterodimers, we developed the PPI4DOCK benchmark containing 1417 docking targets based on unbound homology models. Rigid-body docking by Zdock showed that for 1208 cases (85.2%), at least one correct decoy was generated, emphasizing the efficiency of rigid-body docking in generating correct assemblies. Overall, the PPI4DOCK benchmark contains a large set of realistic cases and provides new ground for assessing docking and scoring methodologies. AVAILABILITY AND IMPLEMENTATION Benchmark sets can be downloaded from http://biodev.cea.fr/interevol/ppi4dock/ CONTACT: guerois@cea.frSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jinchao Yu
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette, France
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Simkovic F, Thomas JMH, Keegan RM, Winn MD, Mayans O, Rigden DJ. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. IUCRJ 2016; 3:259-70. [PMID: 27437113 PMCID: PMC4937781 DOI: 10.1107/s2052252516008113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/18/2016] [Indexed: 05/05/2023]
Abstract
For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.
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Affiliation(s)
- Felix Simkovic
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Jens M. H. Thomas
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Ronan M. Keegan
- Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - Martyn D. Winn
- Science and Technology Facilities Council, Daresbury Laboratory, Warrington WA4 4AD, England
| | - Olga Mayans
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, England
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Lindert S, McCammon JA. Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. J Chem Theory Comput 2016; 11:1337-46. [PMID: 25883538 PMCID: PMC4393324 DOI: 10.1021/ct500995d] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Indexed: 12/13/2022]
Abstract
![]()
Many excellent methods exist that
incorporate cryo-electron microscopy
(cryoEM) data to constrain computational protein structure prediction
and refinement. Previously, it was shown that iteration of two such
orthogonal sampling and scoring methods – Rosetta and molecular
dynamics (MD) simulations – facilitated exploration of conformational
space in principle. Here, we go beyond a proof-of-concept study and
address significant remaining limitations of the iterative MD–Rosetta
protein structure refinement protocol. Specifically, all parts of
the iterative refinement protocol are now guided by medium-resolution
cryoEM density maps, and previous knowledge about the native structure
of the protein is no longer necessary. Models are identified solely
based on score or simulation time. All four benchmark proteins showed
substantial improvement through three rounds of the iterative refinement
protocol. The best-scoring final models of two proteins had sub-Ångstrom
RMSD to the native structure over residues in secondary structure
elements. Molecular dynamics was most efficient in refining secondary
structure elements and was thus highly complementary to the Rosetta
refinement which is most powerful in refining side chains and loop
regions.
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38
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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39
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Calvaresi M, Eckhart L, Alibardi L. The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments. J Struct Biol 2016; 194:282-91. [DOI: 10.1016/j.jsb.2016.03.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 02/29/2016] [Accepted: 03/05/2016] [Indexed: 11/17/2022]
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40
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Figueroa M, Sleutel M, Vandevenne M, Parvizi G, Attout S, Jacquin O, Vandenameele J, Fischer AW, Damblon C, Goormaghtigh E, Valerio-Lepiniec M, Urvoas A, Durand D, Pardon E, Steyaert J, Minard P, Maes D, Meiler J, Matagne A, Martial JA, Van de Weerdt C. The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools. J Struct Biol 2016; 195:19-30. [PMID: 27181418 DOI: 10.1016/j.jsb.2016.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/19/2016] [Accepted: 05/12/2016] [Indexed: 12/26/2022]
Abstract
Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (αβα) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features.
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Affiliation(s)
- Maximiliano Figueroa
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
| | - Mike Sleutel
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marylene Vandevenne
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Gregory Parvizi
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Sophie Attout
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Olivier Jacquin
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Julie Vandenameele
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Axel W Fischer
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | | | - Erik Goormaghtigh
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Joseph A Martial
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium
| | - Cécile Van de Weerdt
- GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
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41
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Wang Y, Virtanen J, Xue Z, Tesmer JJG, Zhang Y. Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Crystallogr D Struct Biol 2016; 72:616-28. [PMID: 27139625 PMCID: PMC4931812 DOI: 10.1107/s2059798316003016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 02/19/2016] [Indexed: 04/15/2023] Open
Abstract
Molecular replacement (MR) often requires templates with high homology to solve the phase problem in X-ray crystallography. I-TASSER-MR has been developed to test whether the success rate for structure determination of distant-homology proteins could be improved by a combination of iterative fragmental structure-assembly simulations with progressive sequence truncation designed to trim regions with high variation. The pipeline was tested on two independent protein sets consisting of 61 proteins from CASP8 and 100 high-resolution proteins from the PDB. After excluding homologous templates, I-TASSER generated full-length models with an average TM-score of 0.773, which is 12% higher than the best threading templates. Using these as search models, I-TASSER-MR found correct MR solutions for 95 of 161 targets as judged by having a TFZ of >8 or with the final structure closer to the native than the initial search models. The success rate was 16% higher than when using the best threading templates. I-TASSER-MR was also applied to 14 protein targets from structure genomics centers. Seven of these were successfully solved by I-TASSER-MR. These results confirm that advanced structure assembly and progressive structural editing can significantly improve the success rate of MR for targets with distant homology to proteins of known structure.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, People’s Republic of China
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jouko Virtanen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhidong Xue
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- School of Software Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, People’s Republic of China
| | - John J. G. Tesmer
- Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, MI 41809, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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42
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Amyloid-like ribbons of amelogenins in enamel mineralization. Sci Rep 2016; 6:23105. [PMID: 27009419 PMCID: PMC4806362 DOI: 10.1038/srep23105] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/29/2016] [Indexed: 12/27/2022] Open
Abstract
Enamel, the outermost layer of teeth, is an acellular mineralized tissue that cannot regenerate; the mature tissue is composed of high aspect ratio apatite nanocrystals organized into rods and inter-rod regions. Amelogenin constitutes 90% of the protein matrix in developing enamel and plays a central role in guiding the hierarchical organization of apatite crystals observed in mature enamel. To date, a convincing link between amelogenin supramolecular structures and mature enamel has yet to be described, in part because the protein matrix is degraded during tissue maturation. Here we show compelling evidence that amelogenin self-assembles into an amyloid-like structure in vitro and in vivo. We show that enamel matrices stain positive for amyloids and we identify a specific region within amelogenin that self-assembles into β-sheets. We propose that amelogenin nanoribbons template the growth of apatite mineral in human enamel. This is a paradigm shift from the current model of enamel development.
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43
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Karakas E, Taveneau C, Bressanelli S, Marchi M, Robert B, Abel S. Derivation of original RESP atomic partial charges for MD simulations of the LDAO surfactant with AMBER: applications to a model of micelle and a fragment of the lipid kinase PI4KA. J Biomol Struct Dyn 2016; 35:159-181. [DOI: 10.1080/07391102.2015.1135822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Esra Karakas
- Maison de la Simulation, USR 3441, CEA – CNRS – INRIA – Univ. Paris-Sud – Univ. de Versailles, 91191, Gif sur Yvette, France
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DRF/IBITECS/SB2SM/LBMS & CNRS UMR 9198, Saclay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Cyntia Taveneau
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Massimo Marchi
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DRF/IBITECS/SB2SM/LBMS & CNRS UMR 9198, Saclay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Bruno Robert
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DRF/IBITECS/SB2SM/LBMS & CNRS UMR 9198, Saclay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Stéphane Abel
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DRF/IBITECS/SB2SM/LBMS & CNRS UMR 9198, Saclay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
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44
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Garza-Fabre M, Kandathil SM, Handl J, Knowles J, Lovell SC. Generating, Maintaining, and Exploiting Diversity in a Memetic Algorithm for Protein Structure Prediction. EVOLUTIONARY COMPUTATION 2016; 24:577-607. [PMID: 26908350 DOI: 10.1162/evco_a_00176] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Computational approaches to de novo protein tertiary structure prediction, including those based on the preeminent "fragment-assembly" technique, have failed to scale up fully to larger proteins (on the order of 100 residues and above). A number of limiting factors are thought to contribute to the scaling problem over and above the simple combinatorial explosion, but the key ones relate to the lack of exploration of properly diverse protein folds, and to an acute form of "deception" in the energy function, whereby low-energy conformations do not reliably equate with native structures. In this article, solutions to both of these problems are investigated through a multistage memetic algorithm incorporating the successful Rosetta method as a local search routine. We found that specialised genetic operators significantly add to structural diversity and that this translates well to reaching low energies. The use of a generalised stochastic ranking procedure for selection enables the memetic algorithm to handle and traverse deep energy wells that can be considered deceptive, which further adds to the ability of the algorithm to obtain a much-improved diversity of folds. The results should translate to a tangible improvement in the performance of protein structure prediction algorithms in blind experiments such as CASP, and potentially to a further step towards the more challenging problem of predicting the three-dimensional shape of large proteins.
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Affiliation(s)
- Mario Garza-Fabre
- Decision and Cognitive Sciences Research Centre, University of Manchester, Manchester, M15 6PB, UK
| | - Shaun M Kandathil
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Julia Handl
- Decision and Cognitive Sciences Research Centre, University of Manchester, Manchester, M15 6PB, UK
| | - Joshua Knowles
- School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK
| | - Simon C Lovell
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
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45
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Kinch LN, Li W, Monastyrskyy B, Kryshtafovych A, Grishin NV. Evaluation of free modeling targets in CASP11 and ROLL. Proteins 2016; 84 Suppl 1:51-66. [PMID: 26677002 DOI: 10.1002/prot.24973] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/12/2015] [Indexed: 12/25/2022]
Abstract
We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837-D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment-based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites. Proteins 2016; 84(Suppl 1):51-66. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9050.
| | - Wenlin Li
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9050
| | - Bohdan Monastyrskyy
- Genome Center, University of California, 451 Health Sciences Drive, Davis, California 95616
| | - Andriy Kryshtafovych
- Genome Center, University of California, 451 Health Sciences Drive, Davis, California 95616
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9050.,Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9050
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Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins. J Mol Biol 2016; 428:522-32. [DOI: 10.1016/j.jmb.2016.01.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/08/2016] [Accepted: 01/08/2016] [Indexed: 01/23/2023]
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Poleksic A. A polynomial time algorithm for computing the area under a GDT curve. Algorithms Mol Biol 2015; 10:27. [PMID: 26504491 PMCID: PMC4620747 DOI: 10.1186/s13015-015-0058-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Progress in the field of protein three-dimensional structure prediction depends on the development of new and improved algorithms for measuring the quality of protein models. Perhaps the best descriptor of the quality of a protein model is the GDT function that maps each distance cutoff θ to the number of atoms in the protein model that can be fit under the distance θ from the corresponding atoms in the experimentally determined structure. It has long been known that the area under the graph of this function (GDT_A) can serve as a reliable, single numerical measure of the model quality. Unfortunately, while the well-known GDT_TS metric provides a crude approximation of GDT_A, no algorithm currently exists that is capable of computing accurate estimates of GDT_A. METHODS We prove that GDT_A is well defined and that it can be approximated by the Riemann sums, using available methods for computing accurate (near-optimal) GDT function values. RESULTS In contrast to the GDT_TS metric, GDT_A is neither insensitive to large nor oversensitive to small changes in model's coordinates. Moreover, the problem of computing GDT_A is tractable. More specifically, GDT_A can be computed in cubic asymptotic time in the size of the protein model. CONCLUSIONS This paper presents the first algorithm capable of computing the near-optimal estimates of the area under the GDT function for a protein model. We believe that the techniques implemented in our algorithm will pave ways for the development of more practical and reliable procedures for estimating 3D model quality.
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Iacoangeli A, Marcatili P, Tramontano A. Exploiting Homology Information in Nontemplate Based Prediction of Protein Structures. J Chem Theory Comput 2015; 11:5045-51. [DOI: 10.1021/acs.jctc.5b00371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alfredo Iacoangeli
- Department
of Physics, Sapienza University of Rome, P.le A. Moro 4, 00185 Rome, Italy
| | - Paolo Marcatili
- Department
of Physics, Sapienza University of Rome, P.le A. Moro 4, 00185 Rome, Italy
| | - Anna Tramontano
- Department
of Physics, Sapienza University of Rome, P.le A. Moro 4, 00185 Rome, Italy
- Istituto
Pasteur Fondazione Cenci Bolognetti, Sapienza University of Rome, P.le
A. Moro 4, 00185 Rome, Italy
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Zhang W, Yang J, He B, Walker SE, Zhang H, Govindarajoo B, Virtanen J, Xue Z, Shen HB, Zhang Y. Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11. Proteins 2015; 84 Suppl 1:76-86. [PMID: 26370505 DOI: 10.1002/prot.24930] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/26/2015] [Accepted: 09/10/2015] [Indexed: 11/12/2022]
Abstract
We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Wenxuan Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Jianyi Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Baoji He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Sara Elizabeth Walker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Hongjiu Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Brandon Govindarajoo
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Jouko Virtanen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Zhidong Xue
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Hong-Bin Shen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109. .,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109.
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50
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Yuan J, Xue B. Role of structural flexibility in the evolution of emerin. J Theor Biol 2015; 385:102-11. [PMID: 26319992 DOI: 10.1016/j.jtbi.2015.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/07/2015] [Accepted: 08/17/2015] [Indexed: 02/07/2023]
Abstract
Emerin is a short inner nuclear membrane protein with an LEM-domain at the N-terminal end and a transmembrane domain at the C-terminal end. The middle region of human emerin contains multiple binding motifs. Since emerin is often found in evolutionarily newer species, the functional conservation of emerin becomes an interesting topic. In this study, we have demonstrated that most of the functional motifs of emerin are intrinsically disordered or highly flexible. Many post-translational modification sites and mutation sites are associated with these disordered regions. The averaged substitution rates of most functional motifs between species correlate positively with the averaged disorder scores of those functional motifs. Human emerin sequence may have acquired new functions on protein-protein interaction through the formation of hydrophobic motifs in the middle region, which is resulted from accumulated mutations during the evolution process.
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Affiliation(s)
- Jia Yuan
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, 4202 E. Fowler Ave, ISA 2015, Tampa, FL 33620, USA
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, 4202 E. Fowler Ave, ISA 2015, Tampa, FL 33620, USA.
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