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Banach M, Fabian P, Stapor K, Konieczny L, Roterman I. Structure of the Hydrophobic Core Determines the 3D Protein Structure-Verification by Single Mutation Proteins. Biomolecules 2020; 10:E767. [PMID: 32423068 PMCID: PMC7281683 DOI: 10.3390/biom10050767] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023] Open
Abstract
Four de novo proteins differing in single mutation positions, with a chain length of 56 amino acids, represent diverse 3D structures: monomeric 3α and 4β + α folds. The reason for this diversity is seen in the different structure of the hydrophobic core as a result of synergy leading to the generation of a system in which the polypeptide chain as a whole participates. On the basis of the fuzzy oil drop model, where the structure of the hydrophobic core is expressed by means of the hydrophobic distribution function in the form of a 3D Gaussian distribution, it has been shown that the composition of the hydrophobic core in these two structural forms is different. In addition, the use of a model to determine the structure of the early intermediate in the folding process allows to indicate differences in the polypeptide chain geometry, which, combined with the construction of a common hydrophobic nucleus as an effect of specific synergy, may indicate the reason for the diversity of the folding process of the polypeptide chain. The results indicate the need to take into account the presence of an external force field originating from the water environment and that its active impact on the formation of a hydrophobic core whose participation in the stabilization of the tertiary structure is fundamental.
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Affiliation(s)
- Mateusz Banach
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-533 Krakow, Poland;
| | - Piotr Fabian
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (P.F.); (K.S.)
| | - Katarzyna Stapor
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (P.F.); (K.S.)
| | - 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, 31-533 Krakow, Poland;
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Abstract
Proteins with a high degree of sequence similarity representing different structures provide a key to understand how protein sequence codes for 3D structure. An analysis using the fuzzy oil drop model was carried out on two pairs of proteins with different secondary structures and with high sequence identities. It has been shown that distributions of hydrophobicity for these proteins are approximated well using single 3D Gaussian function. In other words, the similar sequences fold into different 3D structures, however, alternative structures also have symmetric and monocentric hydrophobic cores. It should be noted that a significant change in the helical to beta-structured form in the N-terminal section takes places in the fragment much preceding the location of the mutated regions. It can be concluded that the final structure is the result of a complicated synergy effect in which the whole chain participates simultaneously.
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Smolarczyk T, Stapor K, Roterman-Konieczna I. Backbone dihedral angles prediction servers for protein early-stage structure prediction. BIO-ALGORITHMS AND MED-SYSTEMS 2019. [DOI: 10.1515/bams-2019-0034] [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
AbstractThree-dimensional protein structure prediction is an important task in science at the intersection of biology, chemistry, and informatics, and it is crucial for determining the protein function. In the two-stage protein folding model, based on an early- and late-stage intermediates, we propose to use state-of-the-art secondary structure prediction servers for backbone dihedral angles prediction and devise an early-stage structure. Early-stage structures are used as a starting point for protein folding simulations, and any errors in this stage affect the final predictions. We have shown that modern secondary structure prediction servers could increase the accuracy of early-stage predictions compared to previously reported models.
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Affiliation(s)
- Tomasz Smolarczyk
- Institute of Informatics, Silesian University of Technology, Akademicka 16, Gliwice, Poland
| | - Katarzyna Stapor
- Institute of Informatics, Silesian University of Technology, Akademicka 16, Gliwice, Poland
| | - Irena Roterman-Konieczna
- Department of Bioinformatics and Telemedicine, Jagiellonian University Medical College, Kraków, Poland
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Fabian P, Stapor K, Banach M, Ptak-Kaczor M, Konieczny L, Roterman I. Different Synergy in Amyloids and Biologically Active Forms of Proteins. Int J Mol Sci 2019; 20:E4436. [PMID: 31505841 PMCID: PMC6769701 DOI: 10.3390/ijms20184436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 08/31/2019] [Accepted: 09/04/2019] [Indexed: 11/16/2022] Open
Abstract
Protein structure is the result of the high synergy of all amino acids present in the protein. This synergy is the result of an overall strategy for adapting a specific protein structure. It is a compromise between two trends: The optimization of non-binding interactions and the directing of the folding process by an external force field, whose source is the water environment. The geometric parameters of the structural form of the polypeptide chain in the form of a local radius of curvature that is dependent on the orientation of adjacent peptide bond planes (result of the respective Phi and Psi rotation) allow for a comparative analysis of protein structures. Certain levels of their geometry are the criteria for comparison. In particular, they can be used to assess the differences between the structural form of biologically active proteins and their amyloid forms. On the other hand, the application of the fuzzy oil drop model allows the assessment of the role of amino acids in the construction of tertiary structure through their participation in the construction of a hydrophobic core. The combination of these two models-the geometric structure of the backbone and the determining of the participation in the construction of the tertiary structure that is applied for the comparative analysis of biologically active and amyloid forms-is presented.
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Affiliation(s)
- Piotr Fabian
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Katarzyna Stapor
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Łazarza 16, 31-530 Kraków, Poland
| | - Magdalena Ptak-Kaczor
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Łazarza 16, 31-530 Kraków, Poland
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University-Medical College, 31-034 Krakow, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Łazarza 16, 31-530 Kraków, Poland.
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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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Dułak D, Gadzała M, Banach M, Ptak M, Wiśniowski Z, Konieczny L, Roterman I. Filamentous Aggregates of Tau Proteins Fulfil Standard Amyloid Criteria Provided by the Fuzzy Oil Drop (FOD) Model. Int J Mol Sci 2018; 19:E2910. [PMID: 30257460 PMCID: PMC6213535 DOI: 10.3390/ijms19102910] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/12/2018] [Accepted: 09/20/2018] [Indexed: 01/02/2023] Open
Abstract
Abnormal filamentous aggregates that are formed by tangled tau protein turn out to be classic amyloid fibrils, meeting all the criteria defined under the fuzzy oil drop model in the context of amyloid characterization. The model recognizes amyloids as linear structures where local hydrophobicity minima and maxima propagate in an alternating manner along the fibril's long axis. This distribution of hydrophobicity differs greatly from the classic monocentric hydrophobic core observed in globular proteins. Rather than becoming a globule, the amyloid instead forms a ribbonlike (or cylindrical) structure.
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Affiliation(s)
- Dawid Dułak
- ABB Business Services Sp. z o.o. ul. Żegańska 1, 04-713 Warszawa, Poland.
| | | | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Łazarza 16, 31-530 Kraków, Poland.
| | - Magdalena Ptak
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Łazarza 16, 31-530 Kraków, Poland.
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland.
| | - Zdzisław Wiśniowski
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Łazarza 16, 31-530 Kraków, Poland.
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Kraków, Poland.
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Łazarza 16, 31-530 Kraków, Poland.
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