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Roterman I, Stapor K, Dułak D, Konieczny L. External Force Field for Protein Folding in Chaperonins-Potential Application in In Silico Protein Folding. ACS OMEGA 2024; 9:18412-18428. [PMID: 38680295 PMCID: PMC11044213 DOI: 10.1021/acsomega.4c00409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
The present study discusses the influence of the TRiC chaperonin involved in the folding of the component of reovirus mu1/σ3. The TRiC chaperone is treated as a provider of a specific external force field in the fuzzy oil drop model during the structural formation of a target folded protein. The model also determines the status of the final product, which represents the structure directed by an external force field in the form of a chaperonin. This can be used for in silico folding as the process is environment-dependent. The application of the model enables the quantitative assessment of the folding dependence of an external force field, which appears to have universal application.
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Affiliation(s)
- Irena Roterman
- Department
of Bioinformatics and Telemedicine, Jagiellonian
University—Medical College, Medyczna 7, Kraków 30-688, Poland
| | - Katarzyna Stapor
- Faculty
of Automatic, Electronics and Computer Science, Department of Applied
Informatics, Silesian University of Technology, Akademicka 16, Gliwice 44-100, Poland
| | - Dawid Dułak
- ABB
Business Services Sp. z o.o, ul Żegańska 1, Warszawa 04-713, Poland
| | - Leszek Konieczny
- Chair
of Medical Biochemistry—Jagiellonian University—Medical
College, Kopernika 7, Kraków 31-034, Poland
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2
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Roterman I, Stapor K, Konieczny L. Structural Specificity of Polymorphic Forms of α-Synuclein Amyloid. Biomedicines 2023; 11:biomedicines11051324. [PMID: 37238996 DOI: 10.3390/biomedicines11051324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/16/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The structural transformation producing amyloids is a phenomenon that sheds new light on the protein folding problem. The analysis of the polymorphic structures of the α-synuclein amyloid available in the PDB database allows analysis of the amyloid-oriented structural transformation itself, but also the protein folding process as such. The polymorphic amyloid structures of α-synuclein analyzed employing the hydrophobicity distribution (fuzzy oil drop model) reveal a differentiation with a dominant distribution consistent with the micelle-like system (hydrophobic core with polar shell). This type of ordering of the hydrophobicity distribution covers the entire spectrum from the example with all three structural units (single chain, proto-fibril, super-fibril) exhibiting micelle-like form, through gradually emerging examples of local disorder, to structures with an extremely different structuring pattern. The water environment directing protein structures towards the generation of ribbon micelle-like structures (concentration of hydrophobic residues in the center of the molecule forming a hydrophobic core with the exposure of polar residues on the surface) also plays a role in the amyloid forms of α-synuclein. The polymorphic forms of α-synuclein reveal local structural differentiation with a common tendency to accept the micelle-like structuralization in certain common fragments of the polypeptide chain of this protein.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Medyczna 7, 30-688 Krakow, Poland
| | - Katarzyna Stapor
- Department of Applied Informatics, Silesian University of Technology, Akademicka 2A, 44-100 Gliwice, Poland
| | - Leszek Konieczny
- Medical Biochemistry, Jagiellonian University-Medical College, Kopernika 7, 31-034 Krakow, Poland
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3
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Molecular Design and In-Silico Analysis of Trisubstituted Benzimidazole Derivatives as Ftsz Inhibitor. J CHEM-NY 2023. [DOI: 10.1155/2023/9307613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Tuberculosis (TB) is the fastest spreading infectious disease and one of the top ten diseases that kill millions of people annually. The rapid spread of a multidrug-resistant strain of Mycobacterium tuberculosis leads to multidrug-resistance tuberculosis (MDR-TB), which is very difficult to treat. Filament temperature-sensitive protein ring-Z (Ftsz) protein could be the best target to inhibit bacterial cytokinesis. This research is conducted to predict the antitubercular activity of trisubstituted benzimidazole derivatives targeting FtsZ protein by an in-silico approach (molecular docking, pharmacokinetic parameter, drug likeliness, toxicity prediction, and biological activity prediction). Amine and aldehyde substitutions are used as primary scaffolds to design 20 trisubstituted benzimidazole derivatives for molecular docking. AutoDock vina v.1.2.0 software was used to predict the binding interaction between ligand and receptor (FtsZ, PDB ID : 1RQ7). The drug-likeliness properties and toxicity of ligands were predicted from SwissADMET and ToxiM web servers, respectively. Compound A15 (2,3,5,6-tetrafluoro-N1-{6-fluoro-5-[4-(1H-imidazole-1-yl) phenoxy]-1H-1,3-benzodiazol-2-yl} benzene-1,4-diamine) showed the best binding energy (ΔG = −10.2 kcal/mol/) along with four hydrogen bond interactions (GLY107, PHE180, ASP 184). Similarly, compounds A19 and A20 have the best binding score of −9.8 kcal/mol, with excellent pharmacokinetic parameters. It is found that the binding energy of all ligands (ΔG = −8.0 to −10.2 kcal/mol) is better than the reference compound Moxifloxacin (ΔG = −7.7 kcal/mol). None of the ligands violate Lipinski’s rule, but all ligands’ toxicity is slightly high (>0.8 score). It is reported that the amine-substituted benzimidazole derivatives have better binding energy than the aldehyde substitution. Therefore, it is concluded that compounds A19 and A20 can be the best candidate as Ftsz protein inhibitors but an in-vitro animal study and toxicity study are necessary to validate these data.
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Abstract
There is an opinion in professional literature that edge-strands in β-sheet are critical to the processes of amyloid transformation. Propagation of fibrillar forms mainly takes place on the basis of β-sheet type interactions. In many proteins, the edge strands represent only a partially matched form to the β-sheet. Therefore, the edge-strand takes slightly distorted forms. The assessment of the level of arrangement can be carried out based on studying the secondary structure as well as the structure of the hydrophobic core. For this purpose, a fuzzy oil drop model was used to determine the contribution of each fragment with a specific secondary structure to the construction of the system being the effect of a certain synergy, which results in the construction of a hydrophobic core. Studying the participation of β-sheets edge fragments in the hydrophobic core construction is the subject of the current analysis. Statuses of these edge fragments in β-sheets in ferredoxin-like folds are treated as factors that disturb the symmetry of the system.
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5
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Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity. Symmetry (Basel) 2019. [DOI: 10.3390/sym11101215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The solenoid is a highly ordered structure observed in proteins, characterized by a set of symmetries. A group of enzymes—lyases containing solenoid fragments—was subjected to analysis with focus on their distribution of hydrophobicity/hydrophilicity, applying the fuzzy oil drop model. The model differentiates between a monocentric distribution hydrophobic core (spherical symmetry—mathematically modeled by a 3D Gaussian) and linear propagation of hydrophobicity (symmetry based on translation of structural units, i.e., chains—evident in amyloids). The linearly ordered solenoid carries information that affects the structure of the aqueous solvent in its neighborhood. Progressive disruption of its symmetry (via incorporation of asymmetrical fragments of varying size) appears to facilitate selective interaction with the intended substrate during enzymatic catalysis.
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Gadzała M, Dułak D, Kalinowska B, Baster Z, Bryliński M, Konieczny L, Banach M, Roterman I. The aqueous environment as an active participant in the protein folding process. J Mol Graph Model 2018; 87:227-239. [PMID: 30580160 DOI: 10.1016/j.jmgm.2018.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/05/2018] [Accepted: 12/12/2018] [Indexed: 01/27/2023]
Abstract
Existing computational models applied in the protein structure prediction process do not sufficiently account for the presence of the aqueous solvent. The solvent is usually represented by a predetermined number of H2O molecules in the bounding box which contains the target chain. The fuzzy oil drop (FOD) model, presented in this paper, follows an alternative approach, with the solvent assuming the form of a continuous external hydrophobic force field, with a Gaussian distribution. The effect of this force field is to guide hydrophobic residues towards the center of the protein body, while promoting exposure of hydrophilic residues on its surface. This work focuses on the following sample proteins: Engrailed homeodomain (RCSB: 1enh), Chicken villin subdomain hp-35, n68h (RCSB: 1yrf), Chicken villin subdomain hp-35, k65(nle), n68h, k70(nle) (RCSB: 2f4k), Thermostable subdomain from chicken villin headpiece (RCSB: 1vii), de novo designed single chain three-helix bundle (a3d) (RCSB: 2a3d), albumin-binding domain (RCSB: 1prb) and lambda repressor-operator complex (RCSB: 1lmb).
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Affiliation(s)
| | - Dawid Dułak
- ABB Business Services Sp. z o.o. ul. Żegańska 1, 04-713, Warszawa, Poland.
| | - Barbara Kalinowska
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 11 Łojasiewicza Street, Kraków, Poland; Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Łazarza 16, 31-530, Kraków, Poland
| | - Zbigniew Baster
- Department of Molecular and Interfacial Biophysics, Faculty of Physics, Astronomy, Applied Computer Science Jagiellonian University, 11 Łojasiewicza Street, Kraków, Poland; Markey Cancer Center, University of Kentucky, 789 South Limestone Street, Lexington, KY, USA
| | - Michał Bryliński
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA; Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University - Medical College, Kopernika 7E, 31-034, Kraków, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Łazarza 16, 31-530, Kraków, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Łazarza 16, 31-530, Kraków, Poland.
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Kalinowska B, Banach M, Wiśniowski Z, Konieczny L, Roterman I. Is the hydrophobic core a universal structural element in proteins? J Mol Model 2017. [PMID: 28623601 PMCID: PMC5487895 DOI: 10.1007/s00894-017-3367-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The hydrophobic core, when subjected to analysis based on the fuzzy oil drop model, appears to be a universal structural component of proteins irrespective of their secondary, supersecondary, and tertiary conformations. A study has been performed on a set of nonhomologous proteins representing a variety of CATH categories. The presence of a well-ordered hydrophobic core has been confirmed in each case, regardless of the protein’s biological function, chain length or source organism. In light of fuzzy oil drop (FOD) analysis, various supersecondary forms seem to share a common structural factor in the form of a hydrophobic core, emerging either as part of the whole protein or a specific domain. The variable status of individual folds with respect to the FOD model reflects their propensity for conformational changes, frequently associated with biological function. Such flexibility is expressed as variable stability of the hydrophobic core, along with specific encoding of potential conformational changes which depend on the properties of helices and β-folds.
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Affiliation(s)
- Barbara Kalinowska
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530, Krakow, Poland.,Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348, Krakow, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530, Krakow, Poland.,Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348, Krakow, Poland
| | - Zdzisław Wiśniowski
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530, Krakow, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University - Medical College, Kopernika 7, 31-034, Krakow, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Lazarza 16, 31-530, Krakow, Poland.
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Banach M, Konieczny L, Wiśniowski Z, Roterman I. Structure of hydrophobic core in plant carboxylesterase. BIO-ALGORITHMS AND MED-SYSTEMS 2017. [DOI: 10.1515/bams-2017-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe fuzzy oil drop model was applied to characterize the hydrophobic core structure in plant carboxylesterase. The characteristics revealed the status of β-sheets in the central part of the molecule as discordant as opposed to the expected hydrophobicity distribution. Particularly, the β-strands and helices in close proximity to the enzymatic residues recognized as discordant with respect to the ideal hydrophobicity distribution of hydrophobic core are of high importance. It is assumed that this local irregularity is the form of coding the specificity of enzymes. The protein under consideration appears to be the next example proving this assumption.
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Dygut J, Kalinowska B, Banach M, Piwowar M, Konieczny L, Roterman I. Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes. Int J Mol Sci 2016; 17:ijms17101741. [PMID: 27763556 PMCID: PMC5085769 DOI: 10.3390/ijms17101741] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/30/2016] [Accepted: 10/11/2016] [Indexed: 12/20/2022] Open
Abstract
The presented analysis concerns the inter-domain and inter-protein interface in protein complexes. We propose extending the traditional understanding of the protein domain as a function of local compactness with an additional criterion which refers to the presence of a well-defined hydrophobic core. Interface areas in selected homodimers vary with respect to their contribution to share as well as individual (domain-specific) hydrophobic cores. The basic definition of a protein domain, i.e., a structural unit characterized by tighter packing than its immediate environment, is extended in order to acknowledge the role of a structured hydrophobic core, which includes the interface area. The hydrophobic properties of interfaces vary depending on the status of interacting domains—In this context we can distinguish: (1) Shared hydrophobic cores (spanning the whole dimer); (2) Individual hydrophobic cores present in each monomer irrespective of whether the dimer contains a shared core. Analysis of interfaces in dystrophin and utrophin indicates the presence of an additional quasi-domain with a prominent hydrophobic core, consisting of fragments contributed by both monomers. In addition, we have also attempted to determine the relationship between the type of interface (as categorized above) and the biological function of each complex. This analysis is entirely based on the fuzzy oil drop model.
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Affiliation(s)
- Jacek Dygut
- Department of Rehabilitation, Hospital in Przemyśl, Monte Cassino 18, 37-700 Przemyśl, Poland.
| | - Barbara Kalinowska
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland.
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Łazarza 16, 31-530 Krakow, Poland.
| | - Monika Piwowar
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Łazarza 16, 31-530 Krakow, Poland.
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University-Medical College, Kopernika 7, 31-034 Krakow, Poland.
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Łazarza 16, 31-530 Krakow, Poland.
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10
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Influence of the Aqueous Environment on Protein Structure—A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis. ENTROPY 2016. [DOI: 10.3390/e18100351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins. ENTROPY 2015. [DOI: 10.3390/e17031477] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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12
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Varol O, Yuret D, Erman B, Kabakçıoğlu A. Mode coupling points to functionally important residues in myosin II. Proteins 2014; 82:1777-86. [PMID: 24677138 DOI: 10.1002/prot.24531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/07/2014] [Accepted: 01/28/2014] [Indexed: 11/08/2022]
Abstract
Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near-native dynamics of myosin II, which allows us to explore the impact of the interaction between possibly non-Gaussian vibrational modes on fluctutational dynamics. We show that an information-theoretic measure based on mode coupling alone yields a ranking of residues with a statistically significant bias favoring the functionally critical locations identified by experiments on myosin II.
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Affiliation(s)
- Onur Varol
- Colleges of Engineering and Sciences, Koç University, Sarıyer, 34450, İstanbul, Turkey; School of Informatics and Computing, Indiana University, Bloomington, Indiana
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13
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Kalinowska B, Banach M, Konieczny L, Marchewka D, Roterman I. Intrinsically disordered proteins--relation to general model expressing the active role of the water environment. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:315-46. [PMID: 24629190 DOI: 10.1016/b978-0-12-800168-4.00008-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This work discusses the role of unstructured polypeptide chain fragments in shaping the protein's hydrophobic core. Based on the "fuzzy oil drop" model, which assumes an idealized distribution of hydrophobicity density described by the 3D Gaussian, we can determine which fragments make up the core and pinpoint residues whose location conflicts with theoretical predictions. We show that the structural influence of the water environment determines the positions of disordered fragments, leading to the formation of a hydrophobic core overlaid by a hydrophilic mantle. This phenomenon is further described by studying selected proteins which are known to be unstable and contain intrinsically disordered fragments. Their properties are established quantitatively, explaining the causative relation between the protein's structure and function and facilitating further comparative analyses of various structural models.
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Affiliation(s)
- Barbara Kalinowska
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Medical College, Jagiellonian University, Krakow, Poland
| | - Damian Marchewka
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland; Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Krakow, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Krakow, Poland.
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14
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Piwowar M, Banach M, Konieczny L, Roterman I. Structural role of exon-coded fragment of polypeptide chains in selected enzymes. J Theor Biol 2013; 337:15-23. [PMID: 23896319 DOI: 10.1016/j.jtbi.2013.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/12/2013] [Accepted: 07/17/2013] [Indexed: 11/27/2022]
Abstract
This paper discusses the structural role of fragments encoded by individual exons in proteins. Selected enzymes (hydrolases, transferases, ligases) reveal the presence of at least one exon fragment whose contribution to the protein's hydrophobic core is in line with theoretical expectations. This phenomenon is confirmed by quantitative analysis of the hydrophobicity density distribution in protein molecules. Results are compared with a 3D Gaussian function, treated as an "idealized" distribution of hydrophobicity density, with the highest values observed near the center of the molecule and near-zero values on its surface. At least one accordant exon fragment has been identified in each of the proteins subjected to analysis. On the basis of these results the authors propose that accordant exons are responsible for tertiary structural stabilization of proteins by ensuring the generation of a stable hydrophobic core.
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Affiliation(s)
- Monika Piwowar
- Department of Bioinformatics and Telemedicine, Medical College-Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Medical College-Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Medical College-Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College-Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland.
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15
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Banach M, Roterman I, Prudhomme N, Chomilier J. Hydrophobic core in domains of immunoglobulin-like fold. J Biomol Struct Dyn 2013; 32:1583-600. [PMID: 23998258 DOI: 10.1080/07391102.2013.829756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This work analyzes proteins which contain an immunoglobulin fold, focusing on their hydrophobic core structure. The "fuzzy oil drop" model was used to measure the regularity of hydrophobicity distribution in globular domains belonging to proteins which exhibit the above-mentioned fold. Light-chain IgG domains are found to frequently contain regular hydrophobic cores, unlike the corresponding heavy-chain domains. Enzymes and DNA binding proteins present in the data-set are found to exhibit poor accordance with the hydrophobic core model.
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Affiliation(s)
- M Banach
- a Department of Bioinformatics and Telemedicine , Collegium Medicum, Jagiellonian University , Krakow , Poland
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16
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Piwowar M, Banach M, Konieczny L, Roterman I. Structural role of exon-coded fragments in proteins. BIO-ALGORITHMS AND MED-SYSTEMS 2013. [DOI: 10.1515/bams-2013-0020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Comparison of different ranking methods in protein-ligand binding site prediction. Int J Mol Sci 2012; 13:8752-8761. [PMID: 22942732 PMCID: PMC3430263 DOI: 10.3390/ijms13078752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 06/19/2012] [Accepted: 07/02/2012] [Indexed: 11/17/2022] Open
Abstract
In recent years, although many ligand-binding site prediction methods have been developed, there has still been a great demand to improve the prediction accuracy and compare different prediction algorithms to evaluate their performances. In this work, in order to improve the performance of the protein-ligand binding site prediction method presented in our former study, a comparison of different binding site ranking lists was studied. Four kinds of properties, i.e., pocket size, distance from the protein centroid, sequence conservation and the number of hydrophobic residues, have been chosen as the corresponding ranking criterion respectively. Our studies show that the sequence conservation information helps to rank the real pockets with the most successful accuracy compared to others. At the same time, the pocket size and the distance of binding site from the protein centroid are also found to be helpful. In addition, a multi-view ranking aggregation method, which combines the information among those four properties, was further applied in our study. The results show that a better performance can be achieved by the aggregation of the complementary properties in the prediction of ligand-binding sites.
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18
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Sanders MPA, McGuire R, Roumen L, de Esch IJP, de Vlieg J, Klomp JPG, de Graaf C. From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00210d] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein structure-based pharmacophore (SBP) models derive the molecular features a ligand must contain to be biologically active by conversion of protein properties to reciprocal ligand space. SBPs improve molecular understanding of ligand–protein interactions and can be used as valuable tools for hit and lead optimization, compound library design, and target hopping.
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Affiliation(s)
- Marijn P. A. Sanders
- Computational Drug Discovery Group
- CMBI
- Radboud University Nijmegen
- Nijmegen
- The Netherlands
| | | | - Luc Roumen
- Division of Medicinal Chemistry
- LACDR
- VU University Amsterdam
- Amsterdam
- The Netherlands
| | - Iwan J. P. de Esch
- Division of Medicinal Chemistry
- LACDR
- VU University Amsterdam
- Amsterdam
- The Netherlands
| | - Jacob de Vlieg
- Computational Drug Discovery Group
- CMBI
- Radboud University Nijmegen
- Nijmegen
- The Netherlands
| | | | - Chris de Graaf
- Division of Medicinal Chemistry
- LACDR
- VU University Amsterdam
- Amsterdam
- The Netherlands
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Dai T, Liu Q, Gao J, Cao Z, Zhu R. A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information. BMC Bioinformatics 2011; 12 Suppl 14:S9. [PMID: 22373099 PMCID: PMC3287474 DOI: 10.1186/1471-2105-12-s14-s9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Prediction of protein-ligand binding sites is an important issue for protein function annotation and structure-based drug design. Nowadays, although many computational methods for ligand-binding prediction have been developed, there is still a demanding to improve the prediction accuracy and efficiency. In addition, most of these methods are purely geometry-based, if the prediction methods improvement could be succeeded by integrating physicochemical or sequence properties of protein-ligand binding, it may also be more helpful to address the biological question in such studies. Results In our study, in order to investigate the contribution of sequence conservation in binding sites prediction and to make up the insufficiencies in purely geometry based methods, a simple yet efficient protein-binding sites prediction algorithm is presented, based on the geometry-based cavity identification integrated with sequence conservation information. Our method was compared with the other three classical tools: PocketPicker, SURFNET, and PASS, and evaluated on an existing comprehensive dataset of 210 non-redundant protein-ligand complexes. The results demonstrate that our approach correctly predicted the binding sites in 59% and 75% of cases among the TOP1 candidates and TOP3 candidates in the ranking list, respectively, which performs better than those of SURFNET and PASS, and achieves generally a slight better performance with PocketPicker. Conclusions Our work has successfully indicated the importance of the sequence conservation information in binding sites prediction as well as provided a more accurate way for binding sites identification.
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Affiliation(s)
- Tianli Dai
- College of Life Science and Biotechnology, Tongji University, 200092, Shanghai, China
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Roterman I, Konieczny L, Banach M, Jurkowski W. Intermediates in the protein folding process: a computational model. Int J Mol Sci 2011; 12:4850-60. [PMID: 21954329 PMCID: PMC3179136 DOI: 10.3390/ijms11084850] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 06/07/2011] [Accepted: 07/25/2011] [Indexed: 11/25/2022] Open
Abstract
The paper presents a model for simulating the protein folding process in silico. The two-step model (which consists of the early stage—ES and the late stage—LS) is verified using two proteins, one of which is treated (according to experimental observations) as the early stage and the second as an example of the LS step. The early stage is based solely on backbone structural preferences, while the LS model takes into account the water environment, treated as an external hydrophobic force field and represented by a 3D Gauss function. The characteristics of 1ZTR (the ES intermediate, as compared with 1ENH, which is the LS intermediate) confirm the link between the gradual disappearance of ES characteristics in LS structural forms and the simultaneous emergence of LS properties in the 1ENH protein. Positive verification of ES and LS characteristics in these two proteins (1ZTR and 1ENH respectively) suggest potential applicability of the presented model to in silico protein folding simulations.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +48-12-619-96-94; Fax: +48-12-619-96-93
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland; E-Mail:
| | - Mateusz Banach
- Faculty of Physics, Astronomy, Applied Computer Science, Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland; E-Mail:
| | - Wiktor Jurkowski
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland; E-Mail:
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Marchewka D, Banach M, Roterman I. Internal force field in proteins seen by divergence entropy. Bioinformation 2011; 6:300-2. [PMID: 21769190 PMCID: PMC3134777 DOI: 10.6026/97320630006300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 06/27/2011] [Indexed: 11/29/2022] Open
Abstract
The characteristic distribution of non-binding interactions in a protein is described. It establishes that hydrophobic interactions can be characterized by suitable 3D Gauss functions while electrostatic interactions generally follow a random distribution. The implementation of this observation suggests differentiated optimization procedure for these two types of interactions. The electrostatic interaction may follow traditional energy optimization while the criteria for convergence shall measure the accordance with 3-D Gauss function.
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Affiliation(s)
- Damian Marchewka
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College Krakow, Poland
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Krakow, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College Krakow, Poland
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Krakow, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College Krakow, Poland
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