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Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
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2
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Li T, Li QZ. Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure. J Theor Biol 2012; 312:55-64. [PMID: 22874580 DOI: 10.1016/j.jtbi.2012.07.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 07/19/2012] [Accepted: 07/21/2012] [Indexed: 12/11/2022]
Abstract
RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.
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Affiliation(s)
- Tao Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
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3
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Abstract
Molecular modeling techniques have made significant advances in recent years and are becoming essential components of many chemical, physical and biological studies. Here we present three widely used techniques used in the simulation of biomolecular systems: structural and homology modeling, molecular dynamics and molecular docking. For each of these topics we present a brief discussion of the underlying scientific basis of the technique, some simple examples of how the method is commonly applied, and some discussion of the limitations and caveats of which the user should be aware. References for further reading as well as an extensive list of software resources are provided.
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Affiliation(s)
- Akansha Saxena
- Biomedical Engineering, Washington University, St Louis, Missouri, USA
| | - Diana Wong
- Biomedical Engineering, Washington University, St Louis, Missouri, USA
| | - Karthikeyan Diraviyam
- Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - David Sept
- Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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4
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Gopalasubramaniam SK, Kovacs F, Violante-Mota F, Twigg P, Arredondo-Peter R, Sarath G. Cloning and characterization of a caesalpinoid (Chamaecrista fasciculata) hemoglobin: the structural transition from a nonsymbiotic hemoglobin to a leghemoglobin. Proteins 2008; 72:252-60. [PMID: 18214970 DOI: 10.1002/prot.21917] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nonsymbiotic hemoglobins (nsHbs) and leghemoglobins (Lbs) are plant proteins that can reversibly bind O(2) and other ligands. The nsHbs are hexacoordinate and appear to modulate cellular concentrations of NO and maintain energy levels under hypoxic conditions. The Lbs are pentacoordinate and facilitate the diffusion of O(2) to symbiotic bacteroids within legume root nodules. Multiple lines of evidence suggest that all plant Hbs evolved from a common ancestor and that Lbs originated from nsHbs. However, little is known about the structural intermediates that occurred during the evolution of pentacoordinate Lbs from hexacoordinate nsHbs. We have cloned and characterized a Hb (ppHb) from the root nodules of the ancient caesalpinoid legume Chamaecrista fasciculata. Protein sequence, modeling data, and spectral analysis indicated that the properties of ppHb are intermediate between that of nsHb and Lb, suggesting that ppHb resembles a putative ancestral Lb. Predicted structural changes that appear to have occurred during the nsHb to Lb transition were a compaction of the CD-loop and decreased mobility of the distal His inhibiting its ability to coordinate directly with the heme-Fe, leading to a pentacoordinate protein. Other predicted changes include shortening of the N- and C-termini, compaction of the protein into a globular structure, disappearance of positive charges outside the heme pocket and appearance of negative charges in an area located between the N- and C-termini. A major consequence for some of these changes appears to be the decrease in O(2)-affinity of ancestral nsHb, which resulted in the origin of the symbiotic function of Lbs.
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Affiliation(s)
- Sabarinathan K Gopalasubramaniam
- Laboratorio de Biofísica y Biología Molecular, Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Morelos, México
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Gopalasubramaniam SK, Garrocho‐Villegas V, Rivera GB, Pastor N, Arredondo‐Peter R. Use of In Silico (Computer) Methods to Predict and Analyze the Tertiary Structure of Plant Hemoglobins. Methods Enzymol 2008; 436:393-410. [DOI: 10.1016/s0076-6879(08)36022-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Wang L, Donald BR. An efficient and accurate algorithm for assigning nuclear overhauser effect restraints using a rotamer library ensemble and residual dipolar couplings. PROCEEDINGS. IEEE COMPUTATIONAL SYSTEMS BIOINFORMATICS CONFERENCE 2007:189-202. [PMID: 16447976 DOI: 10.1109/csb.2005.13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nuclear Overhauser effect (NOE) distance restraints are the main experimental data from protein nuclear magnetic resonance (NMR) spectroscopy for computing a complete three dimensional solution structure including sidechain conformations. In general, NOE restraints must be assigned before they can be used in a structure determination program. NOE assignment is very time-consuming to do manually, challenging to fully automate, and has become a key bottleneck for high-throughput NMR structure determination. The difficulty in automated NOE assignment is ambiguity: there can be tens of possible different assignments for an NOE peak based solely on its chemical shifts. Previous automated NOE assignment approaches rely on an ensemble of structures, computed from a subset of all the NOEs, to iteratively filter ambiguous assignments. These algorithms are heuristic in nature, provide no guarantees on solution quality or running time, and are slow in practice. In this paper we present an accurate, efficient NOE assignment algorithm. The algorithm first invokes the algorithm in [30, 29] to compute an accurate backbone structure using only two backbone residual dipolar couplings (RDCs) per residue. The algorithm then filters ambiguous NOE assignments by merging an ensemble of intra-residue vectors from a protein rotamer database, together with internuclear vectors from the computed backbone structure. The protein rotamer database was built from ultra-high resolution structures (<1.0 A) in the Protein Data Bank (PDB). The algorithm has been successfully applied to assign more than 1,700 NOE distance restraints with better than 90% accuracy on the protein human ubiquitin using real experimentally-recorded NMR data. The algorithm assigns these NOE restraints in less than one second on a single-processor workstation.
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Affiliation(s)
- Lincong Wang
- Dartmouth Computer Science Department, Hanover, NH 03755, USA
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7
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Porwal G, Jain S, Babu SD, Singh D, Nanavati H, Noronha S. Protein structure prediction aided by geometrical and probabilistic constraints. J Comput Chem 2007; 28:1943-52. [PMID: 17450548 DOI: 10.1002/jcc.20736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Database-assisted ab initio protein structure prediction methods have exhibited considerable promise in the recent past, with several implementations being successful in community-wide experiments (CASP). We have employed combinatorial optimization techniques toward solving the protein structure prediction problem. A Monte Carlo minimization algorithm has been employed on a constrained search space to identify minimum energy configurations. The search space is constrained by using radius of gyration cutoffs, the loop backbone dihedral probability distributions, and various secondary structure packing conformations. Simulations have been carried out on several sequences and 1000 conformations have been initially generated. Of these, 50 best candidates have then been selected as probable conformations. The search for the optimum has been simplified by incorporating various geometrical constraints on secondary structural elements using distance restraint potential functions. The advantages of the reported methodology are its simplicity, and modifiability to include other geometric and probabilistic restraints.
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Affiliation(s)
- Gaurav Porwal
- Department of Chemical Engineering, IIT Bombay, Powai, Mumbai 400076, India
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Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J Mol Biol 2006; 363:835-57. [PMID: 16982067 DOI: 10.1016/j.jmb.2006.08.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Revised: 07/18/2006] [Accepted: 08/16/2006] [Indexed: 10/24/2022]
Abstract
In order to investigate the level of representation required to simulate folding and predict structure, we test the ability of a variety of reduced representations to identify native states in decoy libraries and to recover the native structure given the advanced knowledge of the very broad native Ramachandran basin assignments. Simplifications include the removal of the entire side-chain or the retention of only the Cbeta atoms. Scoring functions are derived from an all-atom statistical potential that distinguishes between atoms and different residue types. Structures are obtained by minimizing the scoring function with a computationally rapid simulated annealing algorithm. Results are compared for simulations in which backbone conformations are sampled from a Protein Data Bank-based backbone rotamer library generated by either ignoring or including a dependence on the identity and conformation of the neighboring residues. Only when the Cbeta atoms and nearest neighbor effects are included do the lowest energy structures generally fall within 4 A of the native backbone root-mean square deviation (RMSD), despite the initial configuration being highly expanded with an average RMSD > or = 10 A. The side-chains are reinserted into the Cbeta models with minimal steric clash. Therefore, the detailed, all-atom information lost in descending to a Cbeta-level representation is recaptured to a large measure using backbone dihedral angle sampling that includes nearest neighbor effects and an appropriate scoring function.
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Affiliation(s)
- Andrés Colubri
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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9
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Mosher RA, Durrant WE, Wang D, Song J, Dong X. A comprehensive structure-function analysis of Arabidopsis SNI1 defines essential regions and transcriptional repressor activity. THE PLANT CELL 2006; 18:1750-65. [PMID: 16766691 PMCID: PMC1488919 DOI: 10.1105/tpc.105.039677] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The expression of systemic acquired resistance (SAR) in plants involves the upregulation of many Pathogenesis-Related (PR) genes, which work in concert to confer resistance to a broad spectrum of pathogens. Because SAR is a costly process, SAR-associated transcription must be tightly regulated. Arabidopsis thaliana SNI1 (for Suppressor of NPR1, Inducible) is a negative regulator of SAR required to dampen the basal expression of PR genes. Whole genome transcriptional profiling showed that in the sni1 mutant, Nonexpresser of PR genes (NPR1)-dependent benzothiadiazole S-methylester-responsive genes were specifically derepressed. Interestingly, SNI1 also repressed transcription when expressed in yeast, suggesting that it functions as an active transcriptional repressor through a highly conserved mechanism. Chromatin immunoprecipitation indicated that histone modification may be involved in SNI1-mediated repression. Sequence comparison with orthologs in other plant species and a saturating NAAIRS-scanning mutagenesis of SNI1 identified regions in SNI1 that are required for its activity. The structural similarity of SNI1 to Armadillo repeat proteins implies that SNI1 may form a scaffold for interaction with proteins that modulate transcription.
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Affiliation(s)
- Rebecca A Mosher
- Developmental, Cell, and Molecular Biology Group, Department of Biology, Duke University, Durham, North Carolina 27708, USA
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10
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Fernandez-Fuentes N, Oliva B, Fiser A. A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res 2006; 34:2085-97. [PMID: 16617149 PMCID: PMC1440879 DOI: 10.1093/nar/gkl156] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105 950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed ϕ/ψ main chain dihedral angle propensities. Confidence Z-score cut-offs were determined for each loop length that identify those predicted fragments that outperform a competitive ab initio method. A web server implements the method, regularly updates the fragment library and performs prediction. Predicted segments are returned, or optionally, these can be completed with side chain reconstruction and subsequently annealed in the environment of the query protein by conjugate gradient minimization. The prediction method was tested on artificially prepared search datasets where all trivial sequence similarities on the SCOP superfamily level were removed. Under these conditions it is possible to predict loops of length 4, 8 and 12 with coverage of 98, 78 and 28% with at least of 0.22, 1.38 and 2.47 Å of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a ∼5:1 ratio an earlier developed database search method.
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Affiliation(s)
| | - Baldomero Oliva
- Structural Bioinformatics Group (GRIB), Universitat Pompeu FabraC/Doctor Aiguader,80. 08003, Barcelona, Catalonia, Spain
| | - András Fiser
- To whom correspondence should be addressed. Tel: +1 718 430 3233; Fax: +1 718 430 856;
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11
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Fernandez-Fuentes N, Querol E, Aviles FX, Sternberg MJE, Oliva B. Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops. Proteins 2006; 60:746-57. [PMID: 16021623 DOI: 10.1002/prot.20516] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In protein structure prediction, a central problem is defining the structure of a loop connecting 2 secondary structures. This problem frequently occurs in homology modeling, fold recognition, and in several strategies in ab initio structure prediction. In our previous work, we developed a classification database of structural motifs, ArchDB. The database contains 12,665 clustered loops in 451 structural classes with information about phi-psi angles in the loops and 1492 structural subclasses with the relative locations of the bracing secondary structures. Here we evaluate the extent to which sequence information in the loop database can be used to predict loop structure. Two sequence profiles were used, a HMM profile and a PSSM derived from PSI-BLAST. A jack-knife test was made removing homologous loops using SCOP superfamily definition and predicting afterwards against recalculated profiles that only take into account the sequence information. Two scenarios were considered: (1) prediction of structural class with application in comparative modeling and (2) prediction of structural subclass with application in fold recognition and ab initio. For the first scenario, structural class prediction was made directly over loops with X-ray secondary structure assignment, and if we consider the top 20 classes out of 451 possible classes, the best accuracy of prediction is 78.5%. In the second scenario, structural subclass prediction was made over loops using PSI-PRED (Jones, J Mol Biol 1999;292:195-202) secondary structure prediction to define loop boundaries, and if we take into account the top 20 subclasses out of 1492, the best accuracy is 46.7%. Accuracy of loop prediction was also evaluated by means of RMSD calculations.
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Affiliation(s)
- Narcis Fernandez-Fuentes
- Institute of Biomedicine and Biotechnology, Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain
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Centeno NB, Planas-Iglesias J, Oliva B. Comparative modelling of protein structure and its impact on microbial cell factories. Microb Cell Fact 2005; 4:20. [PMID: 15989691 PMCID: PMC1183243 DOI: 10.1186/1475-2859-4-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 06/30/2005] [Indexed: 11/22/2022] Open
Abstract
Comparative modeling is becoming an increasingly helpful technique in microbial cell factories as the knowledge of the three-dimensional structure of a protein would be an invaluable aid to solve problems on protein production. For this reason, an introduction to comparative modeling is presented, with special emphasis on the basic concepts, opportunities and challenges of protein structure prediction. This review is intended to serve as a guide for the biologist who has no special expertise and who is not involved in the determination of protein structure. Selected applications of comparative modeling in microbial cell factories are outlined, and the role of microbial cell factories in the structural genomics initiative is discussed.
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Affiliation(s)
- Nuria B Centeno
- Structural Bioinformatics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF. c/ Dr. Aiguader 80. 08003 Barcelona, Spain
| | - Joan Planas-Iglesias
- Structural Bioinformatics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF. c/ Dr. Aiguader 80. 08003 Barcelona, Spain
| | - Baldomero Oliva
- Structural Bioinformatics Laboratory, Research Group on Biomedical Informatics (GRIB), IMIM/UPF. c/ Dr. Aiguader 80. 08003 Barcelona, Spain
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13
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Affiliation(s)
- Roger E Ison
- Department of Computer Science and Engineering, University of Colorado at Denver, 80217-3364, USA.
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14
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KRETSINGER ROBERTH. Proteins and the Flow of Information in Cellular Function. Mol Imaging 2005. [DOI: 10.1016/b978-019517720-6.50010-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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