1
|
Dehghani T, Naghibzadeh M, Sadri J. Enhancement of Protein β-Sheet Topology Prediction Using Maximum Weight Disjoint Path Cover. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1936-1947. [PMID: 29994539 DOI: 10.1109/tcbb.2018.2837753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Predicting β-sheet topology (β-topology) is one of the most critical intermediate steps towards protein structure and function prediction. The β-topology prediction problem is defined as the determination of the optimal arrangement of β-strand interactions within protein β-sheets. Significant efforts have been made to predict β-topologies. However, due to the inaccurate determination of interactions among β-strands and the huge topological space of proteins with a large number of β-strands, more efficient methods are required to improve both the accuracy and speed of β-topology prediction. In order to attain higher accuracy, the current paper introduces a bidirectional strand-strand interaction graph and considers all possible orientations (parallel and antiparallel) and orders of β-strand pairwise interactions. For the first time, the β-topology prediction is transformed into a maximum weight disjoint path cover solution by conserving all potential topologies. Moreover, to manage the computation time, a set of candidate β-sheets is generated and an optimization process is applied to select a subset of maximum score disjoint β-sheets as a predicted β-topology. The proposed method is comprehensively compared with state-of-the-art methods. The experimental results on the BetaSheet916 and BetaSheet1452 datasets reveal that the current study's approach enhances performance measurements as well as reduces the runtime.
Collapse
|
2
|
Ma B, Allard C, Bouchard L, Perron P, Mittleman MA, Hivert MF, Liang L. Locus-specific DNA methylation prediction in cord blood and placenta. Epigenetics 2019; 14:405-420. [PMID: 30885044 DOI: 10.1080/15592294.2019.1588685] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
DNA methylation is known to be responsive to prenatal exposures, which may be a part of the mechanism linking early developmental exposures to future chronic diseases. Many studies use blood to measure DNA methylation, yet we know that DNA methylation is tissue specific. Placenta is central to fetal growth and development, but it is rarely feasible to collect this tissue in large epidemiological studies; on the other hand, cord blood samples are more accessible. In this study, based on paired samples of both placenta and cord blood tissues from 169 individuals, we investigated the methylation concordance between placenta and cord blood. We then employed a machine-learning-based model to predict locus-specific DNA methylation levels in placenta using DNA methylation levels in cord blood. We found that methylation correlation between placenta and cord blood is lower than other tissue pairs, consistent with existing observations that placenta methylation has a distinct pattern. Nonetheless, there are still a number of CpG sites showing robust association between the two tissues. We built prediction models for placenta methylation based on cord blood data and documented a subset of 1,012 CpG sites with high correlation between measured and predicted placenta methylation levels. The resulting list of CpG sites and prediction models could help to reveal the loci where internal or external influences may affect DNA methylation in both placenta and cord blood, and provide a reference data to predict the effects on placenta in future study even when the tissue is not available in an epidemiological study.
Collapse
Affiliation(s)
- Baoshan Ma
- a College of Information Science and Technology , Dalian Maritime University , Dalian , Liaoning Province , China
| | - Catherine Allard
- b Centre de Recherche du Center Hospitalier Universitaire de Sherbrooke , Sherbrooke , Quebec , Canada
| | - Luigi Bouchard
- b Centre de Recherche du Center Hospitalier Universitaire de Sherbrooke , Sherbrooke , Quebec , Canada.,c Department of Biochemistry, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec , Canada.,d ECOGENE-21 Biocluster , CSSS de Chicoutimi , Chicoutimi , Quebec , Canada
| | - Patrice Perron
- b Centre de Recherche du Center Hospitalier Universitaire de Sherbrooke , Sherbrooke , Quebec , Canada.,e Department of Medicine, Faculty of Medicine and Life Sciences , Université de Sherbrooke , Sherbrooke , Quebec , Canada
| | - Murray A Mittleman
- f Department of Epidemiology , Harvard T.H. Chan School of Public Health , Boston , MA , USA.,g Cardiovascular Epidemiology Research Unit , Beth Israel Deaconess Medical Center , Boston , MA , USA
| | - Marie-France Hivert
- b Centre de Recherche du Center Hospitalier Universitaire de Sherbrooke , Sherbrooke , Quebec , Canada.,e Department of Medicine, Faculty of Medicine and Life Sciences , Université de Sherbrooke , Sherbrooke , Quebec , Canada.,h Department of Population Medicine , Harvard Pilgrim Health Care Institute, Harvard Medical School , Boston , MA , USA.,i Diabetes Unit , Massachusetts General Hospital , Boston , MA , USA
| | - Liming Liang
- f Department of Epidemiology , Harvard T.H. Chan School of Public Health , Boston , MA , USA.,j Department of Biostatistics , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| |
Collapse
|
3
|
MacCarthy E, Perry D, Kc DB. Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction. Methods Mol Biol 2019; 1958:15-45. [PMID: 30945212 DOI: 10.1007/978-1-4939-9161-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Due to the advancement in various sequencing technologies, the gap between the number of protein sequences and the number of experimental protein structures is ever increasing. Community-wide initiatives like CASP have resulted in considerable efforts in the development of computational methods to accurately model protein structures from sequences. Sequence-based prediction of super-secondary structure has direct application in protein structure prediction, and there have been significant efforts in the prediction of super-secondary structure in the last decade. In this chapter, we first introduce the protein structure prediction problem and highlight some of the important progress in the field of protein structure prediction. Next, we discuss recent methods for the prediction of super-secondary structures. Finally, we discuss applications of super-secondary structure prediction in structure prediction/analysis of proteins. We also discuss prediction of protein structures that are composed of simple super-secondary structure repeats and protein structures that are composed of complex super-secondary structure repeats. Finally, we also discuss the recent trends in the field.
Collapse
Affiliation(s)
- Elijah MacCarthy
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Derrick Perry
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Dukka B Kc
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA.
| |
Collapse
|
4
|
Comparative Analysis of TM and Cytoplasmic β-barrel Conformations Using Joint Descriptor. Sci Rep 2018; 8:14185. [PMID: 30242187 PMCID: PMC6155101 DOI: 10.1038/s41598-018-32136-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/16/2018] [Indexed: 01/01/2023] Open
Abstract
Macroscopic descriptors have become valuable as coarse-grained features of complex proteins and are complementary to microscopic descriptors. Proteins macroscopic geometric features provide effective clues in the quantification of distant similarity and close dissimilarity searches for structural comparisons. In this study, we performed a systematic comparison of β-barrels, one of the important classes of protein folds in various transmembrane (TM) proteins against cytoplasmic barrels to estimate the conformational features using a joint-based descriptor. The approach uses joint coordinates and dihedral angles (β and γ) based on the β-strand joints and loops to determine the arrangements and propensities at the local and global levels. We then confirmed that there is a clear preference in the overall β and γ distribution, arrangements of β-strands and loops, signature patterns, and the number of strand effects between TM and cytoplasmic β-barrel geometries. As a robust and simple approach, we determine that the joint-based descriptor could provide a reliable static structural comparison aimed at macroscopic level between complex protein conformations.
Collapse
|
5
|
Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015; 83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
Abstract
The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefited from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.
Collapse
Affiliation(s)
- Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Martin B. Ulmschneider
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
6
|
Moreira GMSG, Conceição FR, McBride AJA, Pinto LDS. Structure predictions of two Bauhinia variegata lectins reveal patterns of C-terminal properties in single chain legume lectins. PLoS One 2013; 8:e81338. [PMID: 24260572 PMCID: PMC3834338 DOI: 10.1371/journal.pone.0081338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
Bauhinia variegata lectins (BVL-I and BVL-II) are single chain lectins isolated from the plant Bauhinia variegata. Single chain lectins undergo post-translational processing on its N-terminal and C-terminal regions, which determines their physiological targeting, carbohydrate binding activity and pattern of quaternary association. These two lectins are isoforms, BVL-I being highly glycosylated, and thus far, it has not been possible to determine their structures. The present study used prediction and validation algorithms to elucidate the likely structures of BVL-I and -II. The program Bhageerath-H was chosen from among three different structure prediction programs due to its better overall reliability. In order to predict the C-terminal region cleavage sites, other lectins known to have this modification were analysed and three rules were created: (1) the first amino acid of the excised peptide is small or hydrophobic; (2) the cleavage occurs after an acid, polar, or hydrophobic residue, but not after a basic one; and (3) the cleavage spot is located 5-8 residues after a conserved Leu amino acid. These rules predicted that BVL-I and -II would have fifteen C-terminal residues cleaved, and this was confirmed experimentally by Edman degradation sequencing of BVL-I. Furthermore, the C-terminal analyses predicted that only BVL-II underwent α-helical folding in this region, similar to that seen in SBA and DBL. Conversely, BVL-I and -II contained four conserved regions of a GS-I association, providing evidence of a previously undescribed X4+unusual oligomerisation between the truncated BVL-I and the intact BVL-II. This is the first report on the structural analysis of lectins from Bauhinia spp. and therefore is important for the characterisation C-terminal cleavage and patterns of quaternary association of single chain lectins.
Collapse
Affiliation(s)
- Gustavo M. S. G. Moreira
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Fabricio R. Conceição
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Alan J. A. McBride
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Luciano da S. Pinto
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| |
Collapse
|