1
|
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.
Collapse
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
| |
Collapse
|
2
|
Roterman I, Stapor K, Konieczny L. New insights on the catalytic center of proteins from peptidylprolyl isomerase group based on the FOD-M model. J Cell Biochem 2023. [PMID: 37139783 DOI: 10.1002/jcb.30407] [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: 02/06/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Generating the structure of the hydrophobic core is based on the orientation of hydrophobic residues towards the central part of the protein molecule with the simultaneous exposure of polar residues. Such a course of the protein folding process takes place with the active participation of the polar water environment. While the self-assembly process leading to the formation of micelles concerns freely moving bi-polar molecules, bipolar amino acids in polypeptide chain have limited mobility due to the covalent bonds. Therefore, proteins form a more or less perfect micelle-like structure. The criterion is the hydrophobicity distribution, which to a greater or lesser extent reproduces the distribution expressed by the 3D Gaussian function on the protein body. The vast majority of proteins must ensure solubility, so a certain part of it-as it is expected-should reproduce the structuring of micelles. The biological activity of proteins is encoded in the part that does not reproduce the micelle-like system. The location and quantitative assessment of the contribution of orderliness to disorder is of critical importance for the determination of biological activity. The form of maladjustment to the 3D Gauss function may be varied-hence the obtained high diversity of specific interactions with strictly defined molecules: ligands or substrates. The correctness of this interpretation was verified on the basis of the group of enzymes Peptidylprolyl isomerase-E.C.5.2.1.8. In proteins representing this class of enzymes, zones responsible for solubility-micelle-like hydrophobicity system-the location and specificity of the incompatible part in which the specific activity of the enzyme is located and coded were identified. The present study showed that the enzymes of the discussed group show two different schemes of the structure of catalytic center (taking into account the status as defined by the fuzzy oil drop model).
Collapse
Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Kraków, Poland
| | - Katarzyna Stapor
- Department of Applied Informatics, Faculty of Automatic, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University-Medical College, Kraków, Poland
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Yang F, Jiang W, Chen X, Chen X, Wu J, Huang J, Cai X, Wang S. Identification of Novel Antifreeze Peptides from Takifugu obscurus Skin and Molecular Mechanism in Inhibiting Ice Crystal Growth. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14148-14156. [PMID: 36314886 DOI: 10.1021/acs.jafc.2c04393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Foodborne hydrolyzed antifreeze peptides have been widely used in the food industry and the biomedical field. However, the components of hydrolyzed peptides are complex and the molecular mechanism remains unclear. This study focused on identification and mechanism analysis of novel antifreeze peptides from Takifugu obscurus skin by traditional methods and computer-assisted techniques. Results showed that three peptides (EGPRAGGAPG, GDAGPSGPAGPTG, and GEAGPAGPAG) possessed cryoprotection via reducing the freezing point and inhibiting ice crystal growth. Molecular docking confirmed that the cryoprotective property was related to peptide structure, especially α-helix, and hydrogen bond sites. Moreover, the antifreeze peptides were double-faces, which controlled ice crystals while affecting the arrangement of surrounding water molecules, thus exhibiting a strong antifreeze activity. This investigation deepens the comprehension of the mechanism of antifreeze peptides at molecular scale, and the novel efficient antifreeze peptides can be developed in antifreeze materials design and applied in food industry.
Collapse
Affiliation(s)
- Fujia Yang
- College of Chemical Engineering, Fuzhou University, Fuzhou350108, P.R. China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Wenting Jiang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Xu Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Xuan Chen
- College of Chemical Engineering, Fuzhou University, Fuzhou350108, P.R. China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Jinhong Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai200240, P.R. China
| | - Jianlian Huang
- Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing of Ministry of Agriculture and Rural Affairs, Xiamen361022, P.R. China
- Fujian Anjoy Foods Co. Ltd., Xiamen361022, P.R. China
| | - Xixi Cai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou350108, P.R. China
| |
Collapse
|
5
|
Meireles MR, Stelmach LH, Bandinelli E, Vieira GF. Unveiling the influence of factor VIII physicochemical properties on hemophilia A phenotype through an in silico methodology. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 219:106768. [PMID: 35367915 DOI: 10.1016/j.cmpb.2022.106768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 01/24/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND OBJECTIVES Hemophilia A (HA) is an X-linked blood disorder. It is caused by pathogenic F8 gene variants, among which missense mutations are the most prevalent. The resulting amino acid substitutions may have different impacts on physicochemical properties and, consequently, on protein functionality. Regular prediction tools do not include structural elements and their physiological significance, which hampers our ability to functionally link variants to disease phenotype, opening an ample field for investigation. The present study aims to elucidate how physicochemical changes generated by substitutions in different protein domains relate to HA, and which of these features are more consequential to protein function and its impact on HA phenotype. METHODS An in silico evaluation of 71 F8 variants found in patients with different HA phenotypes (mild, moderate, severe) was performed to understand protein modifications and functional impact. Homology modeling was used for the structural analysis of physicochemical changes including electrostatic potential, hydrophobicity, solvent-accessible/excluded surface areas, disulfide disruptions, and substitutions indexes. These variants and properties were analyzed by hierarchical clustering analysis (HCA) and principal component analysis (PCA), independently and in combination, to investigate their relative contribution. RESULTS About 69% of variants show electrostatic changes, and almost all show hydrophobicity and surface area modifications. HCA combining all physicochemical properties analyzed was better in reflecting the impact of different variants in disease severity, more so than the single feature analysis. On the other hand, PCA led to the identification of prominent properties involved in the clustering results for variants of different domains. CONCLUSIONS The methodology developed here enables the assessment of structural features not available in other prediction tools (e.g., surface distribution of electrostatic potential), evaluating what kind of physicochemical changes are involved in FVIII functional disruption. HCA results allow distinguishing substitutions according to their properties, and yielded clusters which were more homogeneous in phenotype. All evaluated properties are involved in determining disease severity. The nature, as well as the position of the variants in the protein, were shown to be relevant for physicochemical changes, demonstrating that all these aspects must be collectively considered to fine-tune an approach to predict HA severity.
Collapse
Affiliation(s)
- Mariana R Meireles
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, Porto Alegre 91501-970, RS, Brasil
| | - Lara H Stelmach
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, Porto Alegre 91501-970, RS, Brasil
| | - Eliane Bandinelli
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, Porto Alegre 91501-970, RS, Brasil
| | - Gustavo F Vieira
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, Porto Alegre 91501-970, RS, Brasil; Universidade La Salle, Canoas, RS, Brasil.
| |
Collapse
|
6
|
The Functional Significance of Hydrophobic Residue Distribution in Bacterial Beta-Barrel Transmembrane Proteins. MEMBRANES 2021; 11:membranes11080580. [PMID: 34436343 PMCID: PMC8399255 DOI: 10.3390/membranes11080580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022]
Abstract
β-barrel membrane proteins have several important biological functions, including transporting water and solutes across the membrane. They are active in the highly hydrophobic environment of the lipid membrane, as opposed to soluble proteins, which function in a more polar, aqueous environment. Globular soluble proteins typically have a hydrophobic core and a polar surface that interacts favorably with water. In the fuzzy oil drop (FOD) model, this distribution is represented by the 3D Gauss function (3DG). In contrast, membrane proteins expose hydrophobic residues on the surface, and, in the case of ion channels, the polar residues face inwards towards a central pore. The distribution of hydrophobic residues in membrane proteins can be characterized by means of 1–3DG, a complementary 3D Gauss function. Such an analysis was carried out on the transmembrane proteins of bacteria, which, despite the considerable similarities of their super-secondary structure (β-barrel), have highly differentiated properties in terms of stabilization based on hydrophobic interactions. The biological activity and substrate specificity of these proteins are determined by the distribution of the polar and nonpolar amino acids. The present analysis allowed us to compare the ways in which the different proteins interact with antibiotics and helped us understand their relative importance in the development of the resistance mechanism. We showed that beta barrel membrane proteins with a hydrophobic core interact less strongly with the molecules they transport.
Collapse
|
7
|
Ptak-Kaczor M, Banach M, Stapor K, Fabian P, Konieczny L, Roterman I. Solubility and Aggregation of Selected Proteins Interpreted on the Basis of Hydrophobicity Distribution. Int J Mol Sci 2021; 22:ijms22095002. [PMID: 34066830 PMCID: PMC8125953 DOI: 10.3390/ijms22095002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 11/30/2022] Open
Abstract
Protein solubility is based on the compatibility of the specific protein surface with the polar aquatic environment. The exposure of polar residues to the protein surface promotes the protein’s solubility in the polar environment. The aquatic environment also influences the folding process by favoring the centralization of hydrophobic residues with the simultaneous exposure to polar residues. The degree of compatibility of the residue distribution, with the model of the concentration of hydrophobic residues in the center of the molecule, with the simultaneous exposure of polar residues is determined by the sequence of amino acids in the chain. The fuzzy oil drop model enables the quantification of the degree of compatibility of the hydrophobicity distribution observed in the protein to a form fully consistent with the Gaussian 3D function, which expresses an idealized distribution that meets the preferences of the polar water environment. The varied degrees of compatibility of the distribution observed with the idealized one allow the prediction of preferences to interactions with molecules of different polarity, including water molecules in particular. This paper analyzes a set of proteins with different levels of hydrophobicity distribution in the context of the solubility of a given protein and the possibility of complex formation.
Collapse
Affiliation(s)
- Magdalena Ptak-Kaczor
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland; (M.P.-K.); (M.B.)
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland; (M.P.-K.); (M.B.)
| | - Katarzyna Stapor
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Piotr Fabian
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Leszek Konieczny
- Chair of Medical Biochemistry—Jagiellonian University—Medical College, Kopernika 7, 31-034 Kraków, Poland;
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland; (M.P.-K.); (M.B.)
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
- Correspondence:
| |
Collapse
|
8
|
Downhill, Ultrafast and Fast Folding Proteins Revised. Int J Mol Sci 2020; 21:ijms21207632. [PMID: 33076540 PMCID: PMC7589632 DOI: 10.3390/ijms21207632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/06/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023] Open
Abstract
Research on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded in sequence dogma seems to be clearly justified, especially in the case of proteins referred to as fast-folding, ultra-fast-folding or downhill. In the present work, an attempt to determine the characteristics of this group of proteins using fuzzy oil drop model is undertaken. According to the fuzzy oil drop model, a protein is a specific micelle composed of bi-polar molecules such as amino acids. Protein folding is regarded as a spherical micelle formation process. The presence of covalent peptide bonds between amino acids eliminates the possibility of free mutual arrangement of neighbors. An example would be the construction of co-micelles composed of more than one type of bipolar molecules. In the case of fast folding proteins, the amino acid sequence represents the optimal bipolarity system to generate a spherical micelle. In order to achieve the native form, it is enough to have an external force field provided by the water environment which directs the folding process towards the generation of a centric hydrophobic core. The influence of the external field can be expressed using the 3D Gaussian function which is a mathematical model of the folding process orientation towards the concentration of hydrophobic residues in the center with polar residues exposed on the surface. The set of proteins under study reveals a hydrophobicity distribution compatible with a 3D Gaussian distribution, taken as representing an idealized micelle-like distribution. The structure of the present hydrophobic core is also discussed in relation to the distribution of hydrophobic residues in a partially unfolded form.
Collapse
|
9
|
Protein folding vs. COVID-19 and the Mediterranean diet. BIO-ALGORITHMS AND MED-SYSTEMS 2020. [DOI: 10.1515/bams-2020-0029] [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
Abstract
The experience of the ongoing pandemic gives rise to a variety of questions, touching – among others – upon its biological aspects. Among the most often raised issues is why the situation has deteriorated to such a degree in the Mediterranean basin and the American eastern seaboard. This work identifies possible links between the protein folding process and the aforementioned epidemic. Given the circumstances, it should be regarded as a popular science article.
Collapse
|
10
|
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.
Collapse
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;
| |
Collapse
|
11
|
The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins. Molecules 2019; 24:molecules24234395. [PMID: 31816829 PMCID: PMC6930452 DOI: 10.3390/molecules24234395] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 01/18/2023] Open
Abstract
Selected amyloid structures available in the Protein Data Bank have been subjected to a comparative analysis. Classification is based on the distribution of hydrophobicity in amyloids that differ with respect to sequence, chain length, the distribution of beta folds, protofibril structure, and the arrangement of protofibrils in each superfibril. The study set includes the following amyloids: Aβ (1-42), which is listed as Aβ (15-40) and carries the D23N mutation, and Aβ (11-42) and Aβ (1-40), both of which carry the E22Δ mutation, tau amyloid, and α-synuclein. Based on the fuzzy oil drop model (FOD), we determined that, despite their conformational diversity, all presented amyloids adopt a similar structural pattern that can be described as a ribbon-like micelle. The same model, when applied to globular proteins, results in structures referred to as "globular micelles," emerging as a result of interactions between the proteins' constituent residues and the aqueous solvent. Due to their composition, amyloids are unable to attain entropically favorable globular forms and instead attempt to limit contact between hydrophobic residues and water by producing elongated structures. Such structures typically contain quasi hydrophobic cores that stretch along the fibril's long axis. Similar properties are commonly found in ribbon-like micelles, with alternating bands of high and low hydrophobicity emerging as the fibrils increase in length. Thus, while globular proteins are generally consistent with a 3D Gaussian distribution of hydrophobicity, the distribution instead conforms to a 2D Gaussian distribution in amyloid fibrils.
Collapse
|
12
|
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.
Collapse
|
13
|
Vance TDR, Bayer-Giraldi M, Davies PL, Mangiagalli M. Ice-binding proteins and the 'domain of unknown function' 3494 family. FEBS J 2019; 286:855-873. [PMID: 30680879 DOI: 10.1111/febs.14764] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/03/2019] [Accepted: 01/22/2019] [Indexed: 02/03/2023]
Abstract
Ice-binding proteins (IBPs) control the growth and shape of ice crystals to cope with subzero temperatures in psychrophilic and freeze-tolerant organisms. Recently, numerous proteins containing the domain of unknown function (DUF) 3494 were found to bind ice crystals and, hence, are classified as IBPs. DUF3494 IBPs constitute today the most widespread of the known IBP families. They can be found in different organisms including bacteria, yeasts and microalgae, supporting the hypothesis of horizontal transfer of its gene. Although the 3D structure is always a discontinuous β-solenoid with a triangular cross-section and an adjacent alpha-helix, DUF3494 IBPs present very diverse activities in terms of the magnitude of their thermal hysteresis and inhibition of ice recrystallization. The proteins are secreted into the environments around the host cells or are anchored on their cell membranes. This review covers several aspects of this new class of IBPs, which promise to leave their mark on several research fields including structural biology, protein biochemistry and cryobiology.
Collapse
Affiliation(s)
- Tyler D R Vance
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Maddalena Bayer-Giraldi
- Department of Glaciology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Italy
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Hexapeptide Tandem Repeats Dictate the Formation of Silkmoth Chorion, a Natural Protective Amyloid. J Mol Biol 2018; 430:3774-3783. [PMID: 29964045 DOI: 10.1016/j.jmb.2018.06.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 12/29/2022]
Abstract
Silkmoth chorion is a fibrous structure composed mainly of two major protein classes, families A and B. Both families of silkmoth chorion proteins present a highly conserved, in sequence and in length, central domain, consisting of Gly-rich tandem hexapeptide repetitive segments, flanked by two more variable N-terminal and C-terminal arms. Primary studies identified silkmoth chorion as a functional protective amyloid by unveiling the amyloidogenic properties of the central domain of both protein families. In this work, we attempt to detect the principal source of amyloidogenicity of the central domain by focusing on the role of the tandem hexapeptide sequence repeats. Concurrently, we discuss a possible mechanism for the self-assembly of class A protofilaments, suggesting that the aggregation-prone hexapeptide building blocks may fold into a triangle-shaped β-helical structure.
Collapse
|
16
|
Roterman I, Banach M, Konieczny L. Antifreeze proteins. Bioinformation 2017; 13:400-401. [PMID: 29379256 PMCID: PMC5767914 DOI: 10.6026/97320630013400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/09/2017] [Accepted: 12/09/2017] [Indexed: 12/25/2022] Open
Abstract
The antifreeze protein (AFP) activity is explained using two models. The first model is using ice binding and the second is using antiice structuralization of water molecules. The description of AFP function using anti-ice structuralization of water molecules is less explored. Therefore, it is of interest to explain AFP function using this model. Protein folding is often described using models where hydrophobic residues move away from water getting buried and hydrophilic residues are exposed to the surface. Thus, the 3D Gauss function stretched on the protein molecule describes the hydrophobicity distribution in a protein molecule. Small antifreeze proteins (less than 150 residues) are often represented by structures with hydrophobic core. Large antifreeze proteins (above 200 residues) contain solenoid (modular repeats). The hydrophobic field of solenoid show different distribution with linear propagation of the bands of different hydrophobicity level having high and low hydrophobicity that is propagated parallel to the long axis of solenoid. This specific ordering of hydrophobicity implies water molecules ordering different from ice. We illustrate this phenomenon using two antifreeze proteins to describe the hypothesis.
Collapse
Affiliation(s)
- Irena Roterman
- 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, Lojasiewicza 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, Lojasiewicza 11, 30-348 Krakow, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University - Medical College, Kopernika 7, 31-034 Krakow, Poland
| |
Collapse
|
17
|
Dułak D, Banach M, Wiśniowski Z, Konieczny L, Roterman I. Mechanism of ligand binding – PDZ domain taken as example. BIO-ALGORITHMS AND MED-SYSTEMS 2017. [DOI: 10.1515/bams-2017-0022] [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 mechanism of specific ligand binding by proteins is discussed using the PDZ domain complexing the pentapeptide. This process is critical for clustering the membrane ion channel. The traditional model based on the Beta-sheet extension by complexed pentapeptide is interpreted as a hydrophobic core extension supported by additional Beta-strand generated by complexed pentapeptide. The explanation is based on the fuzzy oil drop model applied to the crystal structure of PDZ-pentapeptide.
Collapse
|