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Ebhohimen IE, Okolie NP, Okpeku M, Unweator M, Adeleke VT, Edemhanria L. Evaluation of the Antioxidant Properties of Carvacrol as a Prospective Replacement for Crude Essential Oils and Synthetic Antioxidants in Food Storage. Molecules 2023; 28:molecules28031315. [PMID: 36770981 PMCID: PMC9921622 DOI: 10.3390/molecules28031315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
The phenolic structural analogues of synthetic antioxidants such as butylated hydroxytoluene (BHT) in essential oils have been reported to exhibit antioxidant properties. Additionally, their lipophilicity makes them suitable for use in lipid-rich foods. This study evaluated the antioxidant capacity of carvacrol, a monoterpenoid antioxidant compound in the Monodora myristica (Gaertn.) seed essential oil, compared to the seed essential oil and BHT. In vitro studies (ferric reducing antioxidant power (FRAP), metal chelating activity (MCA), and nitric oxide scavenging activity (NOSA)) were conducted to ascertain if the antioxidant capacity of carvacrol was comparable to that of the seed essential oil. The potential binding affinity and molecular interactions between carvacrol and lipoxygenase (LOX) and its homologous model were investigated in silico. The molecular docking was performed using Autodock Vina, and the best poses were subjected to molecular dynamics simulation. The IC50 for MCA and NOSA were: carvacrol 50.29 µL/mL, seed essential oil (SEO) 71.06 µL/mL; and carvacrol 127.61 µL/mL, SEO 165.18 µL/mL, respectively. The LOX model was Ramachandran favoured (97.75%) and the overall quality factor in the ERRAT plot was 95.392. The results of the molecular docking and molecular dynamics simulations revealed that lipoxygenase has a higher affinity (-22.79 kcal/mol) for carvacrol compared to BHT. In the LOX-BHT and LOX-carvacrol complexes, the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and the radius of gyration (RoG) were not significantly different, indicating similar molecular interactions. The results obtained from this study suggest that carvacrol exhibits an antioxidant capacity that may be explored as an alternative for crude essential oils and synthetic compounds during the storage of lipid-rich foods.
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Affiliation(s)
| | - Ngozi P. Okolie
- Department of Biochemistry, University of Benin, Benin City 300213, Nigeria
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- Correspondence:
| | - Mfon Unweator
- Department of Chemical Sciences, Glorious Vision University, Ogwa 310107, Nigeria
| | - Victoria T. Adeleke
- Department of Chemical Engineering, Mangosuthu University of Technology, Umlazi 4031, South Africa
| | - Lawrence Edemhanria
- Department of Chemical Sciences, Glorious Vision University, Ogwa 310107, Nigeria
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2
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Criteria for Engineering Cutinases: Bioinformatics Analysis of Catalophores. Catalysts 2021. [DOI: 10.3390/catal11070784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cutinases are bacterial and fungal enzymes that catalyze the hydrolysis of natural cutin, a three-dimensional inter-esterified polyester with epoxy-hydroxy fatty acids with chain lengths between 16 and 18 carbon atoms. Due to their ability to accept long chain substrates, cutinases are also effective in catalyzing in vitro both the degradation and synthesis of several synthetic polyesters and polyamides. Here, we present a bioinformatics study that intends to correlate the structural features of cutinases with their catalytic properties to provide rational basis for their effective exploitation, particularly in polymer synthesis and biodegradation. The bioinformatics study used the BioGPS method (Global Positioning System in Biological Space) that computed molecular descriptors based on Molecular Interaction Fields (MIFs) described in the GRID force field. The information was used to generate catalophores, spatial representations of the ability of each enzymatic active site to establish hydrophobic and electrostatic interactions. These tools were exploited for comparing cutinases to other serine-hydrolases enzymes, namely lipases, esterases, amidases and proteases, and for highlighting differences and similarities that might guide rational engineering strategies. Structural features of cutinases with their catalytic properties were correlated. The “catalophore” of cutinases indicate shared features with lipases and esterases.
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Gress A, Kalinina OV. SphereCon-a method for precise estimation of residue relative solvent accessible area from limited structural information. Bioinformatics 2020; 36:3372-3378. [PMID: 32154837 DOI: 10.1093/bioinformatics/btaa159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. RESULTS We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. AVAILABILITY AND IMPLEMENTATION https://github.com/kalininalab/spherecon. CONTACT alexander.gress@helmholtz-hips.de. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexander Gress
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken 66123, Germany.,Graduate School of Computer Science, Saarland University, Saarbrücken 66123, Germany
| | - Olga V Kalinina
- Department of Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, Saarbrücken 66123, Germany.,Medical Faculty, Saarland University, Homburg 66421, Germany
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Studer G, Biasini M, Schwede T. Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). ACTA ACUST UNITED AC 2015; 30:i505-11. [PMID: 25161240 PMCID: PMC4147910 DOI: 10.1093/bioinformatics/btu457] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Motivation: Membrane proteins are an important class of biological macromolecules involved in many cellular key processes including signalling and transport. They account for one third of genes in the human genome and >50% of current drug targets. Despite their importance, experimental structural data are sparse, resulting in high expectations for computational modelling tools to help fill this gap. However, as many empirical methods have been trained on experimental structural data, which is biased towards soluble globular proteins, their accuracy for transmembrane proteins is often limited. Results: We developed a local model quality estimation method for membrane proteins (‘QMEANBrane’) by combining statistical potentials trained on membrane protein structures with a per-residue weighting scheme. The increasing number of available experimental membrane protein structures allowed us to train membrane-specific statistical potentials that approach statistical saturation. We show that reliable local quality estimation of membrane protein models is possible, thereby extending local quality estimation to these biologically relevant molecules. Availability and implementation: Source code and datasets are available on request. Contact:torsten.schwede@unibas.ch Supplementary Information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gabriel Studer
- Biozentrum, University of Basel, Basel, 4056, Switzerland and SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland Biozentrum, University of Basel, Basel, 4056, Switzerland and SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland
| | - Marco Biasini
- Biozentrum, University of Basel, Basel, 4056, Switzerland and SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland Biozentrum, University of Basel, Basel, 4056, Switzerland and SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, 4056, Switzerland and SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland Biozentrum, University of Basel, Basel, 4056, Switzerland and SIB Swiss Institute of Bioinformatics, Basel, 4056, Switzerland
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5
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Johari A, Moosavi-Movahedi AA, Amanlou M. Computational investigation of inhibitory mechanism of flavonoids as bovine serum albumin anti-glycation agents. ACTA ACUST UNITED AC 2014; 22:79. [PMID: 25498599 PMCID: PMC4272557 DOI: 10.1186/s40199-014-0079-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 11/26/2014] [Indexed: 01/04/2023]
Abstract
Background Glycation of serum albumin and its consequence products were considered as an important factor in drug distribution and diabetic complications, therefore finding the glycation inhibitors and their inhibitory mechanisms became a valuable field of study. In this work, bovine serum albumin (BSA) became a subject as a model protein for analyzing the inhibitory mechanism of flavonoids, known as natural BSA glycation inhibitors in the early stage of glycation. Methods Firstly, for theoretical study, the three-dimensional model of BSA structure was generated by homology modeling and refined through molecular dynamic simulation. Secondly, several validation methods (statistical assessment methods and also neural network methods) by simultaneous docking study were employed for insurance about accuracy of our simulation. Then docking studies were performed for visualizing the relation between flavonoids’ binding sites and BSA glycation sites besides, the correlation analyzes between calculated binding energy and reported experimental inhibitory IC50 values of the flavonoids set, was considered to explore their molecular inhibitory mechanism. Results The quality assessment methods and simultaneous docking studies on interaction of quercetin (as the most studied flavonoids) with BSA and Human serum albumin (HAS), confirm the accuracy of simulation and the second stage of docking results which were in close agreement with experimental observations, suggest that the potential residues in flavonoids binding sites (which were place neighbor of tryptophan 212 within 5Ǻ) cannot be considered as one of glycation sites. Conclusions Based on the results, flavonoids don’t participate in inhibitory interference mechanism, and also, the differentiation between complexes of flavonoids with BSA and HSA could destroy the speculation of using them as an exchangeable model protein in study of serum albumin and flavonoids interactions.
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Affiliation(s)
- Anahita Johari
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran. .,Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | | | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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6
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Schlessinger A, Khuri N, Giacomini KM, Sali A. Molecular modeling and ligand docking for solute carrier (SLC) transporters. Curr Top Med Chem 2014; 13:843-56. [PMID: 23578028 DOI: 10.2174/1568026611313070007] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/29/2013] [Accepted: 02/01/2013] [Indexed: 12/21/2022]
Abstract
Solute Carrier (SLC) transporters are membrane proteins that transport solutes, such as ions, metabolites, peptides, and drugs, across biological membranes, using diverse energy coupling mechanisms. In human, there are 386 SLC transporters, many of which contribute to the absorption, distribution, metabolism, and excretion of drugs and/or can be targeted directly by therapeutics. Recent atomic structures of SLC transporters determined by X-ray crystallography and NMR spectroscopy have significantly expanded the applicability of structure-based prediction of SLC transporter ligands, by enabling both comparative modeling of additional SLC transporters and virtual screening of small molecules libraries against experimental structures as well as comparative models. In this review, we begin by describing computational tools, including sequence analysis, comparative modeling, and virtual screening, that are used to predict the structures and functions of membrane proteins such as SLC transporters. We then illustrate the applications of these tools to predicting ligand specificities of select SLC transporters, followed by experimental validation using uptake kinetic measurements and other assays. We conclude by discussing future directions in the discovery of the SLC transporter ligands.
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Affiliation(s)
- Avner Schlessinger
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
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7
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Cao R, Wang Z, Wang Y, Cheng J. SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines. BMC Bioinformatics 2014; 15:120. [PMID: 24776231 PMCID: PMC4013430 DOI: 10.1186/1471-2105-15-120] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/15/2014] [Indexed: 01/19/2023] Open
Abstract
Background It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models. Results We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to make predictions. We also trained a SVM model with two new additional features (profiles and SOV scores) on 20 CASP8 targets and found that including them can only improve the performance when real deviations between native and model are higher than 5Å. The SMOQ tool finally released uses the basic feature set trained on 85 CASP8 targets. Moreover, SMOQ implemented a way to convert predicted local quality scores into a global quality score. SMOQ was tested on the 84 CASP9 single-domain targets. The average difference between the residue-specific distance deviation predicted by our method and the actual distance deviation on the test data is 2.637Å. The global quality prediction accuracy of the tool is comparable to other good tools on the same benchmark. Conclusion SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/.
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Affiliation(s)
| | | | | | - Jianlin Cheng
- Department of Computer Science, Informatics Institute, Christopher S, Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA.
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8
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Johansson KE, Hamelryck T. A simple probabilistic model of multibody interactions in proteins. Proteins 2013; 81:1340-50. [DOI: 10.1002/prot.24277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 01/31/2013] [Accepted: 02/18/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Kristoffer Enøe Johansson
- Section for Biomolecular Sciences; Department of Biology, University of Copenhagen; Ole Maal⊘es Vej 5, DK-2200 Copenhagen N Denmark
| | - Thomas Hamelryck
- Section for Computational and RNA biology; Department of Biology, University of Copenhagen; Room 1.2.22, Ole Maal⊘es Vej 5 DK-2200 Copenhagen N Denmark
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9
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Ray A, Lindahl E, Wallner B. Improved model quality assessment using ProQ2. BMC Bioinformatics 2012; 13:224. [PMID: 22963006 PMCID: PMC3584948 DOI: 10.1186/1471-2105-13-224] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/07/2012] [Indexed: 11/19/2022] Open
Abstract
Background Employing methods to assess the quality of modeled protein structures is now standard practice in bioinformatics. In a broad sense, the techniques can be divided into methods relying on consensus prediction on the one hand, and single-model methods on the other. Consensus methods frequently perform very well when there is a clear consensus, but this is not always the case. In particular, they frequently fail in selecting the best possible model in the hard cases (lacking consensus) or in the easy cases where models are very similar. In contrast, single-model methods do not suffer from these drawbacks and could potentially be applied on any protein of interest to assess quality or as a scoring function for sampling-based refinement. Results Here, we present a new single-model method, ProQ2, based on ideas from its predecessor, ProQ. ProQ2 is a model quality assessment algorithm that uses support vector machines to predict local as well as global quality of protein models. Improved performance is obtained by combining previously used features with updated structural and predicted features. The most important contribution can be attributed to the use of profile weighting of the residue specific features and the use features averaged over the whole model even though the prediction is still local. Conclusions ProQ2 is significantly better than its predecessors at detecting high quality models, improving the sum of Z-scores for the selected first-ranked models by 20% and 32% compared to the second-best single-model method in CASP8 and CASP9, respectively. The absolute quality assessment of the models at both local and global level is also improved. The Pearson’s correlation between the correct and local predicted score is improved from 0.59 to 0.70 on CASP8 and from 0.62 to 0.68 on CASP9; for global score to the correct GDT_TS from 0.75 to 0.80 and from 0.77 to 0.80 again compared to the second-best single methods in CASP8 and CASP9, respectively. ProQ2 is available at http://proq2.wallnerlab.org.
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Affiliation(s)
- Arjun Ray
- Department of Theoretical Physics & Swedish eScience Research Center, Royal Institute of Technology, Stockholm, Sweden
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10
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Jackson SA, Hinds MG, Eaton-Rye JJ. Solution structure of CyanoP from Synechocystis sp. PCC 6803: new insights on the structural basis for functional specialization amongst PsbP family proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1331-8. [PMID: 22414666 DOI: 10.1016/j.bbabio.2012.02.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 02/19/2012] [Accepted: 02/27/2012] [Indexed: 11/26/2022]
Abstract
The structure of the CyanoP subunit of photosystem II from the cyanobacterium Synechocystis sp. PCC 6803 has been determined in solution by Nuclear Magnetic Resonance spectroscopy. Combined with homology modeling of PsbP-like structures we have identified distinct structural differences between PsbP homologues which may account for the functional differences apparent between members of this protein family. A surface cleft containing a large number of conserved residues found only in CyanoP and PsbP-like homologues has been identified and our findings suggest that one of the potential cation binding sites found in CyanoP may be functionally significant. Evidence for the evolution and divergence of the PsbP super family is presented from a structural perspective including identification of residues which distinguish the PsbP family from unrelated proteins with a similar domain fold. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
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Affiliation(s)
- Simon A Jackson
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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11
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Brothers MC, Nesbitt AE, Hallock MJ, Rupasinghe SG, Tang M, Harris J, Baudry J, Schuler MA, Rienstra CM. VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy. JOURNAL OF BIOMOLECULAR NMR 2012; 52:41-56. [PMID: 22183804 DOI: 10.1007/s10858-011-9576-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 09/28/2011] [Indexed: 05/31/2023]
Abstract
Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.
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Affiliation(s)
- Michael C Brothers
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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12
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Abstract
Molecular dynamics (MD) simulation holds the promise of revealing the mechanisms of biological processes in their ultimate detail. It is carried out by computing the interaction forces acting on each atom and then propagating the velocities and positions of the atoms by numerical integration of Newton's equations of motion. In this review, we present an overview of how the MD simulation can be conducted to address computational toxicity problems. The study cases will cover a standard MD simulation performed to investigate the overall flexibility of a cytochrome P450 (CYP) enzyme and a set of more advanced MD simulations to examine the barrier to ion conduction in a human α7 nicotinic acetylcholine receptor (nAChR).
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13
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Morita M, Kakuta M, Shimizu K, Nakamura S. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates. ACTA ACUST UNITED AC 2012. [DOI: 10.7243/2050-2273-1-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Lee J, Lee J, Sasaki TN, Sasai M, Seok C, Lee J. De novo
protein structure prediction by dynamic fragment assembly and conformational space annealing. Proteins 2011; 79:2403-17. [DOI: 10.1002/prot.23059] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/24/2011] [Accepted: 04/12/2011] [Indexed: 12/25/2022]
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15
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Stary A, Wacker SJ, Boukharta L, Zachariae U, Karimi-Nejad Y, Aqvist J, Vriend G, de Groot BL. Toward a consensus model of the HERG potassium channel. ChemMedChem 2010; 5:455-67. [PMID: 20104563 DOI: 10.1002/cmdc.200900461] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Malfunction of hERG potassium channels, due to inherited mutations or inhibition by drugs, can cause long QT syndrome, which can lead to life-threatening arrhythmias. A three-dimensional structure of hERG is a prerequisite to understand the molecular basis of hERG malfunction. To achieve a consensus model, we carried out an extensive analysis of hERG models based on various alignments of helix S5. We analyzed seven models using a combination of conventional geometry/packing/normality validation methods as well as molecular dynamics simulations and molecular docking. A synthetic test set with the X-ray crystal structure of K(v)1.2 with artificially shifted S5 sequences modeled into the structure served as a reference case. We docked the known hERG inhibitors (+)-cisapride, (S)-terfenadine, and MK-499 into the hERG models and simulation snapshots. None of the single analyses unambiguously identified a preferred model, but the combination of all three revealed that there is only one model that fulfils all quality criteria. This model is confirmed by a recent mutation scanning experiment (P. Ju, G. Pages, R. P. Riek, P. C. Chen, A. M. Torres, P. S. Bansal, S. Kuyucak, P. W. Kuchel, J. I. Vandenberg, J. Biol. Chem. 2009, 284, 1000-1008). We expect the modeled structure to be useful as a basis both for computational studies of channel function and kinetics as well as the design of experiments.
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Affiliation(s)
- Anna Stary
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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16
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Kalman M, Ben-Tal N. Quality assessment of protein model-structures using evolutionary conservation. ACTA ACUST UNITED AC 2010; 26:1299-307. [PMID: 20385730 PMCID: PMC2865859 DOI: 10.1093/bioinformatics/btq114] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Motivation: Programs that evaluate the quality of a protein structural model are important both for validating the structure determination procedure and for guiding the model-building process. Such programs are based on properties of native structures that are generally not expected for faulty models. One such property, which is rarely used for automatic structure quality assessment, is the tendency for conserved residues to be located at the structural core and for variable residues to be located at the surface. Results: We present ConQuass, a novel quality assessment program based on the consistency between the model structure and the protein's conservation pattern. We show that it can identify problematic structural models, and that the scores it assigns to the server models in CASP8 correlate with the similarity of the models to the native structure. We also show that when the conservation information is reliable, the method's performance is comparable and complementary to that of the other single-structure quality assessment methods that participated in CASP8 and that do not use additional structural information from homologs. Availability: A perl implementation of the method, as well as the various perl and R scripts used for the analysis are available at http://bental.tau.ac.il/ConQuass/. Contact:nirb@tauex.tau.ac.il Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matan Kalman
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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17
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Benkert P, Tosatto SCE, Schwede T. Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins 2010; 77 Suppl 9:173-80. [PMID: 19705484 DOI: 10.1002/prot.22532] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Identifying the best candidate model among an ensemble of alternatives is crucial in protein structure prediction. For this purpose, scoring functions have been developed which either calculate a quality estimate on the basis of a single model or derive a score from the information contained in the ensemble of models generated for a given sequence (i.e., consensus methods). At CASP7, consensus methods have performed considerably better than scoring functions operating on single models. However, consensus methods tend to fail if the best models are far from the center of the dominant structural cluster. At CASP8, we investigated whether our hybrid method QMEANclust may overcome this limitation by combining the QMEAN composite scoring function operating on single models with consensus information. We participated with four different scoring functions in the quality assessment category. The QMEANclust consensus scoring function turned out to be a successful method both for the ranking of entire models but especially for the estimation of the per-residue model quality. In this article, we briefly describe the two scoring functions QMEAN and QMEANclust and discuss their performance in the context of what went right and wrong at CASP8. Both scoring functions are publicly available at http://swissmodel.expasy.org/qmean/.
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Affiliation(s)
- Pascal Benkert
- Biozentrum, University of Basel, Basel 4056, Switzerland
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18
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Abstract
Functional characterization of a protein is often facilitated by its 3D structure. However, the fraction of experimentally known 3D models is currently less than 1% due to the inherently time-consuming and complicated nature of structure determination techniques. Computational approaches are employed to bridge the gap between the number of known sequences and that of 3D models. Template-based protein structure modeling techniques rely on the study of principles that dictate the 3D structure of natural proteins from the theory of evolution viewpoint. Strategies for template-based structure modeling will be discussed with a focus on comparative modeling, by reviewing techniques available for all the major steps involved in the comparative modeling pipeline.
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Affiliation(s)
- Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
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Gao X, Xu J, Li SC, Li M. Predicting local quality of a sequence-structure alignment. J Bioinform Comput Biol 2009; 7:789-810. [PMID: 19785046 DOI: 10.1142/s0219720009004345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 04/06/2009] [Accepted: 04/07/2009] [Indexed: 11/18/2022]
Abstract
Although protein structure prediction has made great progress in recent years, a protein model derived from automated prediction methods is subject to various errors. As methods for structure prediction develop, a continuing problem is how to evaluate the quality of a protein model, especially to identify some well-predicted regions of the model, so that the structural biology community can benefit from the automated structure prediction. It is also important to identify badly-predicted regions in a model so that some refinement measurements can be applied to it. We present two complementary techniques, FragQA and PosQA, to accurately predict local quality of a sequence-structure (i.e. sequence-template) alignment generated by comparative modeling (i.e. homology modeling and threading). FragQA and PosQA predict local quality from two different perspectives. Different from existing methods, FragQA directly predicts cRMSD between a continuously aligned fragment determined by an alignment and the corresponding fragment in the native structure, while PosQA predicts the quality of an individual aligned position. Both FragQA and PosQA use an SVM (Support Vector Machine) regression method to perform prediction using similar information extracted from a single given alignment. Experimental results demonstrate that FragQA performs well on predicting local fragment quality, and PosQA outperforms two top-notch methods, ProQres and ProQprof. Our results indicate that (1) local quality can be predicted well; (2) local sequence evolutionary information (i.e. sequence similarity) is the major factor in predicting local quality; and (3) structural information such as solvent accessibility and secondary structure helps to improve the prediction performance.
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Affiliation(s)
- Xin Gao
- David R. Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
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Benkert P, Schwede T, Tosatto SC. QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC STRUCTURAL BIOLOGY 2009; 9:35. [PMID: 19457232 PMCID: PMC2709111 DOI: 10.1186/1472-6807-9-35] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 05/20/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND The selection of the most accurate protein model from a set of alternatives is a crucial step in protein structure prediction both in template-based and ab initio approaches. Scoring functions have been developed which can either return a quality estimate for a single model or derive a score from the information contained in the ensemble of models for a given sequence. Local structural features occurring more frequently in the ensemble have a greater probability of being correct. Within the context of the CASP experiment, these so called consensus methods have been shown to perform considerably better in selecting good candidate models, but tend to fail if the best models are far from the dominant structural cluster. In this paper we show that model selection can be improved if both approaches are combined by pre-filtering the models used during the calculation of the structural consensus. RESULTS Our recently published QMEAN composite scoring function has been improved by including an all-atom interaction potential term. The preliminary model ranking based on the new QMEAN score is used to select a subset of reliable models against which the structural consensus score is calculated. This scoring function called QMEANclust achieves a correlation coefficient of predicted quality score and GDT_TS of 0.9 averaged over the 98 CASP7 targets and perform significantly better in selecting good models from the ensemble of server models than any other groups participating in the quality estimation category of CASP7. Both scoring functions are also benchmarked on the MOULDER test set consisting of 20 target proteins each with 300 alternatives models generated by MODELLER. QMEAN outperforms all other tested scoring functions operating on individual models, while the consensus method QMEANclust only works properly on decoy sets containing a certain fraction of near-native conformations. We also present a local version of QMEAN for the per-residue estimation of model quality (QMEANlocal) and compare it to a new local consensus-based approach. CONCLUSION Improved model selection is obtained by using a composite scoring function operating on single models in order to enrich higher quality models which are subsequently used to calculate the structural consensus. The performance of consensus-based methods such as QMEANclust highly depends on the composition and quality of the model ensemble to be analysed. Therefore, performance estimates for consensus methods based on large meta-datasets (e.g. CASP) might overrate their applicability in more realistic modelling situations with smaller sets of models based on individual methods.
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Affiliation(s)
- Pascal Benkert
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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21
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Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T. Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc 2009; 4:1-13. [PMID: 19131951 DOI: 10.1038/nprot.2008.197] [Citation(s) in RCA: 930] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Homology modeling aims to build three-dimensional protein structure models using experimentally determined structures of related family members as templates. SWISS-MODEL workspace is an integrated Web-based modeling expert system. For a given target protein, a library of experimental protein structures is searched to identify suitable templates. On the basis of a sequence alignment between the target protein and the template structure, a three-dimensional model for the target protein is generated. Model quality assessment tools are used to estimate the reliability of the resulting models. Homology modeling is currently the most accurate computational method to generate reliable structural models and is routinely used in many biological applications. Typically, the computational effort for a modeling project is less than 2 h. However, this does not include the time required for visualization and interpretation of the model, which may vary depending on personal experience working with protein structures.
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Affiliation(s)
- Lorenza Bordoli
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH 4056 Basel, Switzerland
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Zhu J, Fan H, Periole X, Honig B, Mark AE. Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins 2009; 72:1171-88. [PMID: 18338384 DOI: 10.1002/prot.22005] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A protocol is presented for the global refinement of homology models of proteins. It combines the advantages of temperature-based replica-exchange molecular dynamics (REMD) for conformational sampling and the use of statistical potentials for model selection. The protocol was tested using 21 models. Of these 14 were models of 10 small proteins for which high-resolution crystal structures were available, the remainder were targets of the recent CASPR exercise. It was found that REMD in combination with currently available force fields could sample near-native conformational states starting from high-quality homology models. Conformations in which the backbone RMSD of secondary structure elements (SSE-RMSD) was lower than the starting value by 0.5-1.0 A were found for 15 out of the 21 cases (average 0.82 A). Furthermore, when a simple scoring function consisting of two statistical potentials was used to rank the structures, one or more structures with SSE-RMSD of at least 0.2 A lower than the starting value was found among the five best ranked structures in 11 out of the 21 cases. The average improvement in SSE-RMSD for the best models was 0.42 A. However, none of the scoring functions tested identified the structures with the lowest SSE-RMSD as the best models although all identified the native conformation as the one with lowest energy. This suggests that while the proposed protocol proved effective for the refinement of high-quality models of small proteins scoring functions remain one of the major limiting factors in structure refinement. This and other aspects by which the methodology could be further improved are discussed.
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Affiliation(s)
- Jiang Zhu
- Howard Hughes Medical Institute and Columbia University, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, USA
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Kryshtafovych A, Fidelis K. Protein structure prediction and model quality assessment. Drug Discov Today 2009; 14:386-93. [PMID: 19100336 DOI: 10.1016/j.drudis.2008.11.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 11/05/2008] [Accepted: 11/18/2008] [Indexed: 01/02/2023]
Abstract
Protein structures have proven to be a crucial piece of information for biomedical research. Of the millions of currently sequenced proteins only a small fraction is experimentally solved for structure and the only feasible way to bridge the gap between sequence and structure data is computational modeling. Half a century has passed since it was shown that the amino acid sequence of a protein determines its shape, but a method to translate the sequence code reliably into the 3D structure still remains to be developed. This review summarizes modern protein structure prediction techniques with the emphasis on comparative modeling, and describes the recent advances in methods for theoretical model quality assessment.
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Affiliation(s)
- Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome Center, University of California Davis, Davis, CA 95616, USA.
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Tan CW, Jones DT. Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. BMC Bioinformatics 2008; 9:94. [PMID: 18267018 PMCID: PMC2267779 DOI: 10.1186/1471-2105-9-94] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Accepted: 02/11/2008] [Indexed: 11/13/2022] Open
Abstract
Background We present a novel method of protein fold decoy discrimination using machine learning, more specifically using neural networks. Here, decoy discrimination is represented as a machine learning problem, where neural networks are used to learn the native-like features of protein structures using a set of positive and negative training examples. A set of native protein structures provides the positive training examples, while negative training examples are simulated decoy structures obtained by reversing the sequences of native structures. Various features are extracted from the training dataset of positive and negative examples and used as inputs to the neural networks. Results Results have shown that the best performing neural network is the one that uses input information comprising of PSI-BLAST [1] profiles of residue pairs, pairwise distance and the relative solvent accessibilities of the residues. This neural network is the best among all methods tested in discriminating the native structure from a set of decoys for all decoy datasets tested. Conclusion This method is demonstrated to be viable, and furthermore evolutionary information is successfully used in the neural networks to improve decoy discrimination.
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Affiliation(s)
- Ching-Wai Tan
- Department of Computer Science, University College London, London, UK.
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