1
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Zheng X, Zou B, Cai W, Xu X, Du M, Na X, Zhu B, Wu C. Heat-induced agglomeration of water-soluble cod proteins toward gelled structures. Int J Biol Macromol 2024; 260:129418. [PMID: 38232880 DOI: 10.1016/j.ijbiomac.2024.129418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/19/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
Cod proteins (CPs) have potential applications in designing desirable gel-based products, and this study aimed to unravel their heat-induced aggregation pattern and further probe the roles in protein gels. SDS-PAGE analysis indicated that high-precipitation-coefficient aggregates (HPCAs) of CPs aggregates were composed of considerable polymers of myosin heavy chains and actin, and their low-precipitation-coefficient aggregates (LPCAs) contained myosin light chains and tropomyosin. Studies from correlation analysis between the structure and aggregation kinetics revealed that the generation of β-sheet and SS bonds were responsible for their spontaneous thermal aggregation induced by heating temperature and protein concentration, respectively. Additionally, as protein denaturation ratio increased, more and larger HPCAs were formed, which was evidenced driving the network formation of protein gels and resulting in higher storage modulus (G') values. These novel findings may be applicable to other animal proteins for better tailoring the manufacturing of muscle gel-based products.
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Affiliation(s)
- Xiaohan Zheng
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood, China; State Key Laboratory of Marine Food Processing and Safety Control, China; Liaoning Key Laboratory of Food Nutrition and Health, China
| | - Bowen Zou
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood, China; State Key Laboratory of Marine Food Processing and Safety Control, China; Liaoning Key Laboratory of Food Nutrition and Health, China
| | - Wenqiang Cai
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood, China; State Key Laboratory of Marine Food Processing and Safety Control, China; Liaoning Key Laboratory of Food Nutrition and Health, China
| | - Xianbing Xu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood, China; State Key Laboratory of Marine Food Processing and Safety Control, China; Liaoning Key Laboratory of Food Nutrition and Health, China
| | - Ming Du
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood, China; State Key Laboratory of Marine Food Processing and Safety Control, China; Liaoning Key Laboratory of Food Nutrition and Health, China
| | - Xiaokang Na
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood, China; State Key Laboratory of Marine Food Processing and Safety Control, China; Liaoning Key Laboratory of Food Nutrition and Health, China.
| | - Beiwei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood, China; State Key Laboratory of Marine Food Processing and Safety Control, China; Liaoning Key Laboratory of Food Nutrition and Health, China
| | - Chao Wu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood, China; State Key Laboratory of Marine Food Processing and Safety Control, China; Liaoning Key Laboratory of Food Nutrition and Health, China.
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2
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Colberg M, Schofield J. Diffusive dynamics of a model protein chain in solution. J Chem Phys 2024; 160:075101. [PMID: 38375905 DOI: 10.1063/5.0182607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the transition rates among states that appear in the Markov model when the monomer dynamics is diffusive can be determined by computing the relative entropy of states and their mean first passage times, quantities that are unchanged by the specification of the energies of the relevant states. In this paper, we verify the folding dynamics described by a diffusive linear chain model of the crambin protein in three distinct solvent systems, each differing in complexity: a hard-sphere solvent, a solvent undergoing multi-particle collision dynamics, and an implicit solvent model. The predicted transition rates among configurations agree quantitatively with those observed in explicit molecular dynamics simulations for all three solvent models. These results suggest that the local monomer-monomer interactions provide sufficient friction for the monomer dynamics to be diffusive on timescales relevant to changes in conformation. Factors such as structural ordering and dynamic hydrodynamic effects appear to have minimal influence on transition rates within the studied solvent densities.
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Affiliation(s)
- Margarita Colberg
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jeremy Schofield
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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3
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Zou B, Zheng X, Na X, Cheng S, Qie Z, Xu X, Du M, Wu C. Constructing a strongly interacting Pea-Cod binary protein system by introducing metal cations toward enhanced gelling properties. Food Res Int 2024; 178:113955. [PMID: 38309874 DOI: 10.1016/j.foodres.2024.113955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
Abstract
Developing prospective plant-animal binary protein systems with desirable nutritional and rheological properties stands as a significant and challenging pursuit within the food industry. Our understanding of the effect of adding salt on the aggregation behavior of food proteins is currently based on single model protein systems, however, this knowledge is rather limited following binary protein systems. Herein, various ionic strength settings are used to mitigate the repulsive forces between pea-cod mixed proteins during the thermal process, which further benefits the construction of a strengthened gel network. Transmission electron microscopy (TEM) and dynamic light scattering (DLS) collectively demonstrated that larger heat-induced protein aggregates were formed, which increased in size with higher ionic strength. In the presence of 2.5 mM CaCl2 and 50 mM NaCl, the disulfide bonds significantly increased from 19.3 to 27.53 and 30.5 μM/g, respectively. Notably, similar aggregation behavior could be found when introducing 2.5 mM CaCl2 or 25 mM NaCl, due to the enhanced aggregation tendency by specific binding of Ca2+ to proteins. With relevance to the strengthened cross-links between protein molecules, salt endowed composite gels with preferable gelling properties, evidenced by increased storage modulus. Additionally, the gelling temperature of mixed proteins decreased below 50 °C at elevated ionic strength. Simultaneously, the proportion of network proteins in composite gels increased remarkably from 82.05 % to 93.61 % and 92.31 % upon adding 5.0 mM CaCl2 and 100 mM NaCl, respectively. The findings provide a valuable foundation for designing economically viable and health-oriented plant-animal binary protein systems.
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Affiliation(s)
- Bowen Zou
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing & Safety Control, Dalian Polytechnic University, Dalian 116034, China; Liaoning Key Laboratory of Food Nutrition and Health, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood
| | - Xiaohan Zheng
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing & Safety Control, Dalian Polytechnic University, Dalian 116034, China; Liaoning Key Laboratory of Food Nutrition and Health, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood
| | - Xiaokang Na
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing & Safety Control, Dalian Polytechnic University, Dalian 116034, China; Liaoning Key Laboratory of Food Nutrition and Health, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood.
| | - Shuzhen Cheng
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing & Safety Control, Dalian Polytechnic University, Dalian 116034, China; Liaoning Key Laboratory of Food Nutrition and Health, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood
| | - Zihan Qie
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing & Safety Control, Dalian Polytechnic University, Dalian 116034, China; Liaoning Key Laboratory of Food Nutrition and Health, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood
| | - Xianbing Xu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing & Safety Control, Dalian Polytechnic University, Dalian 116034, China; Liaoning Key Laboratory of Food Nutrition and Health, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood
| | - Ming Du
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing & Safety Control, Dalian Polytechnic University, Dalian 116034, China; Liaoning Key Laboratory of Food Nutrition and Health, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood
| | - Chao Wu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; State Key Laboratory of Marine Food Processing & Safety Control, Dalian Polytechnic University, Dalian 116034, China; Liaoning Key Laboratory of Food Nutrition and Health, Dalian Polytechnic University, Dalian 116034, China; National Engineering Research Center of Seafood.
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4
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Zhang J, Zou Y, Yan B, Zhang N, Zhao J, Zhang H, Chen W, Fan D. Microwave treatment on structure and digestibility characteristics of Spirulina platensis protein. Curr Res Food Sci 2023; 7:100581. [PMID: 37691697 PMCID: PMC10484979 DOI: 10.1016/j.crfs.2023.100581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/14/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023] Open
Abstract
As a novel protein resource, the low digestibility of Spirulina platensis protein (SPP) limits its large-scale application. From the perspective of food processing methods, different heating treatments were explored to improve the structure and digestibility of SPP. In this study, SPP was heated by water bath and microwave at the same heating rate and heating temperature. Microwave accelerated protein denaturation and structure unfolded as the heating intensity increases, causing more exposed hydrophobic residues and enhancing surface hydrophobicity. The data of free sulfhydryl group, particle size, and gel electrophoresis, showed that microwave treatment promoted the formation of protein aggregates. The structural changes can potentially improve the accessibility of digestive enzymes, promote the in vitro digestibility rate, and further accelerate the production of small molecular peptides and the release of free amino acids. This study provided an innovative approach to improve the digestibility and therefore the utilization efficiency of SPP.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Yingying Zou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Bowen Yan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Nana Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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5
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Zheng X, Zou B, Ren C, Xu X, Du M, Wu C. Mechanisms of heat-mediated aggregation behavior of water-soluble cod protein. Food Chem 2023; 419:135973. [PMID: 37011572 DOI: 10.1016/j.foodchem.2023.135973] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/20/2023] [Accepted: 03/15/2023] [Indexed: 04/05/2023]
Abstract
Cod proteins (CPs) are considered potential functional ingredients for developing gel-based foods, but present studies on the aggregation behavior of CPs upon heating remain limited. With this respect, the heat-induced aggregation kinetics of CPs at a subunit level was investigated. Based on different centrifugal forces, CPs aggregates were divided into three fractions: large-sized, intermediary-sized, and small-sized aggregates. SDS-PAGE and diagonal SDS-PAGE indicated that myosin heavy chains exhibited a higher affinity with actin to form intermediary-sized and large-sized aggregates; tropomyosin and myosin light chains were hardly engaged in the thermal aggregation and formed small-sized aggregates. The highly-polymerized aggregates adopted considerable transitions of helix-to-sheet in protein structures, whereas the structure of small-sized aggregates featured substantial helix-coil transitions. Furthermore, molecular interactions at different heating stages were revealed. These novel insights might advance our knowledge on the heat-induced aggregation behavior of CPs and provide fundamental information for the application of CPs in gel-based foods.
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Affiliation(s)
- Xiaohan Zheng
- National Engineering Research Center of Seafood, China; School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Collaborative Innovation Center of Provincial and Ministerial Co-construction for Seafood Deep Processing, China
| | - Bowen Zou
- National Engineering Research Center of Seafood, China; School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Collaborative Innovation Center of Provincial and Ministerial Co-construction for Seafood Deep Processing, China
| | - Chao Ren
- National Engineering Research Center of Seafood, China; School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Collaborative Innovation Center of Provincial and Ministerial Co-construction for Seafood Deep Processing, China
| | - Xianbing Xu
- National Engineering Research Center of Seafood, China; School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Collaborative Innovation Center of Provincial and Ministerial Co-construction for Seafood Deep Processing, China
| | - Ming Du
- National Engineering Research Center of Seafood, China; School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Collaborative Innovation Center of Provincial and Ministerial Co-construction for Seafood Deep Processing, China
| | - Chao Wu
- National Engineering Research Center of Seafood, China; School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Collaborative Innovation Center of Provincial and Ministerial Co-construction for Seafood Deep Processing, China.
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6
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Huang K, Shi J, Li M, Sun R, Guan W, Cao H, Guan X, Zhang Y. Intervention of microwave irradiation on structure and quality characteristics of quinoa protein aggregates. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107677] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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7
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Sakaguchi M, Mukaeda H, Kume A, Toyoda Y, Sakoh T, Kawakita M. Evaluation of the roles of hydrophobic residues in the N-terminal region of archaeal trehalase in its folding. Appl Microbiol Biotechnol 2021; 105:3181-3194. [PMID: 33791835 DOI: 10.1007/s00253-021-11237-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/01/2021] [Accepted: 03/14/2021] [Indexed: 11/30/2022]
Abstract
Thermoplasma trehalase Tvn1315 is predicted to be composed of a β-sandwich domain (BD) and a catalytic domain (CD) based on the structure of the bacterial GH15 family glucoamylase (GA). Tvn1315 as well as Tvn1315 (Δ5), in which the 5 N-terminal amino acids are deleted, could be expressed in Escherichia coli as active enzymes, but deletion of 10 residues (Δ10) led to inclusion body formation. To further investigate the role of the N-terminal region of BD, we constructed five mutants of Δ5, in which each of the 5th to 10th residues of the N-terminus of Tvn1315 was mutated to Ala. Every mutant protein could be recovered in soluble form, but only a small fraction of the Y9A mutant was recovered in the soluble fraction. The Y9A mutant recovered in soluble form had similar specific activity to the other proteins. Subsequent mutation analysis at the 9th position of Tvn1315 in Δ5 revealed that aromatic as well as bulky hydrophobic residues could function properly, but residues with hydroxy groups impaired the solubility. Similar results were obtained with mutants based on untruncated Tvn1315. When the predicted BD, Δ5BD, Δ10BD, and BD mutants were expressed, the Δ10BD protein formed inclusion bodies, and the BD mutants behaved similarly to the Δ5 and full-length enzyme mutants. These results suggest that the hydrophobic region is involved in the solubilization of BD during the folding process. Taken together, these results indicate that the solubility of CD depends on BD folding. KEY POINTS: • N-terminal hydrophobic region of the BD is involved in the protein folding. • The N-terminal hydrophobic region of the BD is also involved in the BD folding. • BD is able to weakly interact with the insoluble β-glucan.
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Affiliation(s)
- Masayoshi Sakaguchi
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan.
| | - Hinako Mukaeda
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Anna Kume
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Yukiko Toyoda
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Takumi Sakoh
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
| | - Masao Kawakita
- Department of Chemistry and Life Science, Kogakuin University, 2,665-1 Nakano-cho, Hachioji, Tokyo, 192-0015, Japan
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8
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Hattori LT, Gutoski M, Vargas Benítez CM, Nunes LF, Lopes HS. A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model. Comput Biol Chem 2020; 84:107192. [PMID: 31918170 DOI: 10.1016/j.compbiolchem.2019.107192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/04/2023]
Abstract
The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world, the more the impact of results and their applicability. This work presents 17 real protein sequences extracted from the Protein Data Bank for a benchmark to the PSP problem using the tri-dimensional Hydrophobic-Polar with Side-Chains model (3D-HP-SC). The native structure of these proteins was found by maximizing the number of hydrophobic contacts between the side-chains of amino acids. The problem was treated as an optimization problem and solved by means of an Integer Programming approach. Although the method optimally solves the problem, the processing time has an exponential trend. Therefore, due to computational limitations, the method is a proof-of-concept and it is not applicable to large sequences. For unknown sequences, an upper bound of the number of hydrophobic contacts (using this model) can be found, due to a linear relationship with the number of hydrophobic residues. The comparison between the predicted and the biological structures showed that the highest similarity between them was found with distance thresholds around 5.2-8.2 Å. Both the dataset and the programs developed will be freely available to foster further research in the area.
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Affiliation(s)
- Leandro Takeshi Hattori
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil.
| | - Matheus Gutoski
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil
| | - César Manuel Vargas Benítez
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil
| | - Luiz Fernando Nunes
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil.
| | - Heitor Silvério Lopes
- Bioinformatics and Computational Intelligence Laboratory, Federal University of Technology Paraná (UTFPR), Av. 7 de Setembro, 3165, 80230-901 Curitiba (PR), Brazil.
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9
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Brylinski M. eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 2014; 10:e1003829. [PMID: 25232727 PMCID: PMC4168975 DOI: 10.1371/journal.pcbi.1003829] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/24/2014] [Indexed: 01/26/2023] Open
Abstract
Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4–9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.
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Affiliation(s)
- Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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10
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Melnik TN, Majorina MA, Larina DS, Kashparov IA, Samatova EN, Glukhov AS, Melnik BS. Independent of their localization in protein the hydrophobic amino acid residues have no effect on the molten globule state of apomyoglobin and the disulfide bond on the surface of apomyoglobin stabilizes this intermediate state. PLoS One 2014; 9:e98645. [PMID: 24892675 PMCID: PMC4043776 DOI: 10.1371/journal.pone.0098645] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 05/06/2014] [Indexed: 01/07/2023] Open
Abstract
At present it is unclear which interactions in proteins reveal the presence of intermediate states, their stability and formation rate. In this study, we have investigated the effect of substitutions of hydrophobic amino acid residues in the hydrophobic core of protein and on its surface on a molten globule type intermediate state of apomyoglobin. It has been found that independent of their localization in protein, substitutions of hydrophobic amino acid residues do not affect the stability of the molten globule state of apomyoglobin. It has been shown also that introduction of a disulfide bond on the protein surface can stabilize the molten globule state. However in the case of apomyoglobin, stabilization of the intermediate state leads to relative destabilization of the native state of apomyoglobin. The result obtained allows us not only to conclude which mutations can have an effect on the intermediate state of the molten globule type, but also explains why the introduction of a disulfide bond (which seems to “strengthen” the protein) can result in destabilization of the protein native state of apomyoglobin.
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Affiliation(s)
- Tatiana N. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Maria A. Majorina
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Daria S. Larina
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Ivan A. Kashparov
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
| | - Ekaterina N. Samatova
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | | | - Bogdan S. Melnik
- Institute of Protein Research, RAS, Pushchino, Moscow Region, Russia
- * E-mail:
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11
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Piwowar M, Banach M, Konieczny L, Chomilier J, Roterman I. Structural role of exons in hemoglobin. BIO-ALGORITHMS AND MED-SYSTEMS 2013. [DOI: 10.1515/bams-2013-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Wu X, Yang G, Zu Y, Fu Y, Zhou L, Yuan X. The Trp-cage miniprotein with single-site mutations: Studies of stability and dynamics using molecular dynamics. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.06.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Abstract
Hydrophobicity underpins self-assembly in many natural and synthetic molecular and nanoscale systems. A signature of hydrophobicity is its temperature dependence. The first experimental evaluation of the temperature and size dependence of hydration free energy in a single hydrophobic polymer is reported, which tests key assumptions in models of hydrophobic interactions in protein folding. Herein, the hydration free energy required to extend three hydrophobic polymers with differently sized aromatic side chains was directly measured by single molecule force spectroscopy. The results are threefold. First, the hydration free energy per monomer is found to be strongly dependent on temperature and does not follow interfacial thermodynamics. Second, the temperature dependence profiles are distinct among the three hydrophobic polymers as a result of a hydrophobic size effect at the subnanometer scale. Third, the hydration free energy of a monomer on a macromolecule is different from a free monomer; corrections for the reduced hydration free energy due to hydrophobic interaction from neighboring units are required.
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14
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Jani V, Sonavane UB, Joshi R. Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape. J Biomol Struct Dyn 2011; 28:845-60. [PMID: 21469746 DOI: 10.1080/07391102.2011.10508612] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Reaching the experimental time scale of millisecond is a grand challenge for protein folding simulations. The development of advanced Molecular Dynamics techniques like Replica Exchange Molecular Dynamics (REMD) makes it possible to reach these experimental timescales. In this study, an attempt has been made to reach the multi microsecond simulation time scale by carrying out folding simulations on a three helix bundle protein, Villin, by combining REMD and Amber United Atom model. Twenty replicas having different temperatures ranging from 295 K to 390 K were simulated for 1.5 µs each. The lowest Root Mean Square Deviation (RMSD) structure of 2.5 Å was obtained with respect to native structure (PDB code 1VII), with all the helices formed. The folding population landscapes were built using segment-wise RMSD and Principal Components as reaction coordinates. These analyses suggest the two-stage folding for Villin. The combination of REMD and Amber United Atom model may be useful to understand the folding mechanism of various fast folding proteins.
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Affiliation(s)
- Vinod Jani
- Bioinformatics Team, Scientific and Engineering Computing Group, Centre for Development of Advanced Computing, Pune University Campus, Ganeshkhind, Pune - 411007, Maharashtra, India
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15
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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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16
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Hamacher K. Free energy of contact formation in proteins: efficient computation in the elastic network approximation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:016703. [PMID: 21867339 DOI: 10.1103/physreve.84.016703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Indexed: 05/31/2023]
Abstract
Biomolecular simulations have become a major tool in understanding biomolecules and their complexes. However, one can typically only investigate a few mutants or scenarios due to the severe computational demands of such simulations, leading to a great interest in method development to overcome this restriction. One way to achieve this is to reduce the complexity of the systems by an approximation of the forces acting upon the constituents of the molecule. The harmonic approximation used in elastic network models simplifies the physical complexity to the most reduced dynamics of these molecular systems. The reduced polymer modeled this way is typically comprised of mass points representing coarse-grained versions of, e.g., amino acids. In this work, we show how the computation of free energy contributions of contacts between two residues within the molecule can be reduced to a simple lookup operation in a precomputable matrix. Being able to compute such contributions is of great importance: protein design or molecular evolution changes introduce perturbations to these pair interactions, so we need to understand their impact. Perturbation to the interactions occurs due to randomized and fixated changes (in molecular evolution) or designed modifications of the protein structures (in bioengineering). These perturbations are modifications in the topology and the strength of the interactions modeled by the elastic network models. We apply the new algorithm to (1) the bovine trypsin inhibitor, a well-known enzyme in biomedicine, and show the connection to folding properties and the hydrophobic collapse hypothesis and (2) the serine proteinase inhibitor CI-2 and show the correlation to Φ values to characterize folding importance. Furthermore, we discuss the computational complexity and show empirical results for the average case, sampled over a library of 77 structurally diverse proteins. We found a relative speedup of up to 10 000-fold for large proteins with respect to repeated application of the initial model.
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Affiliation(s)
- Kay Hamacher
- TU Darmstadt, Departments of Biology, Physics, and Computer Science, Darmstadt, Germany.
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17
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Roterman I, Konieczny L, Jurkowski W, Prymula K, Banach M. Two-intermediate model to characterize the structure of fast-folding proteins. J Theor Biol 2011; 283:60-70. [PMID: 21635900 DOI: 10.1016/j.jtbi.2011.05.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 05/17/2011] [Accepted: 05/18/2011] [Indexed: 01/15/2023]
Abstract
This paper introduces a new model that enables researchers to conduct protein folding simulations. A two-step in silico process is used in the course of structural analysis of a set of fast-folding proteins. The model assumes an early stage (ES) that depends solely on the backbone conformation, as described by its geometrical properties--specifically, by the V-angle between two sequential peptide bond planes (which determines the radius of curvature, also called R-radius, according to a second-degree polynomial form). The agreement between the structure under consideration and the assumed model is measured in terms of the magnitude of dispersion of both parameters with respect to idealized values. The second step, called late-stage folding (LS), is based on the "fuzzy oil drop" model, which involves an external hydrophobic force field described by a three-dimensional Gauss function. The degree of conformance between the structure under consideration and its idealized model is expressed quantitatively by means of the Kullback-Leibler entropy, which is a measure of disparity between the observed and expected hydrophobicity distributions. A set of proteins, representative of the fast-folding group - specifically, cold shock proteins - is shown to agree with the proposed model.
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Affiliation(s)
- I Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Lazarza 16, 31-530 Krakow, Poland.
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18
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Ji XL, Liu SQ. Is stoichiometry-driven protein folding getting out of thermodynamic control? J Biomol Struct Dyn 2011; 28:621-3; discussion 669-674. [PMID: 21142237 DOI: 10.1080/07391102.2011.10508598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Xing-Lai Ji
- Laboratory for Conservation and Utilization of Bio-Resources, Ministry of Education, Yunnan University, Kunming 650091, PR China
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19
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Li ITS, Walker GC. Interfacial Free Energy Governs Single Polystyrene Chain Collapse in Water and Aqueous Solutions. J Am Chem Soc 2010; 132:6530-40. [DOI: 10.1021/ja101155h] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Isaac T. S. Li
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
| | - Gilbert C. Walker
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6
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20
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Prymula K, Sałapa K, Roterman I. "Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids. J Mol Model 2010; 16:1269-82. [PMID: 20084418 DOI: 10.1007/s00894-009-0639-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 12/07/2009] [Indexed: 12/25/2022]
Abstract
The proteins composed of short polypeptides (about 70 amino acid residues) representing the following functional groups (according to PDB notation): growth hormones, serine protease inhibitors, antifreeze proteins, chaperones and proteins of unknown function, were selected for structural and functional analysis. Classification based on the distribution of hydrophobicity in terms of deficiency/excess as the measure of structural and functional specificity is presented. The experimentally observed distribution of hydrophobicity in the protein body is compared to the idealized one expressed by a three-dimensional Gauss function. The differences between these two distributions reveal the specificity of structural/functional characteristics of the protein. The residues of hydrophobicity deficiency versus the idealized distribution are assumed to indicate cavities with the potential to bind ligands, while the residues of hydrophobicity excess are interpreted as potentially participating in protein-protein complexation. The distribution of hydrophobicity irregularity seems to be specific for particular structures and functions of proteins. A comparative analysis of such profiles is carried out to identify the potential biological activity of proteins of unknown function.
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Affiliation(s)
- Katarzyna Prymula
- Department of Bioinformatics, Telemedicine Jagiellonian University - Collegium Medicum, Lazarza 16, 31-530, Krakow, Poland
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21
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Prymula K, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Evangelista G, Minervini G, Polticelli F, WisÌniowski Z, SaÅapa K, MatczynÌska E, Roterman I. In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature. Chem Biodivers 2009; 6:2311-36. [DOI: 10.1002/cbdv.200800338] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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Zobnina V, Roterman I. Application of the fuzzy-oil-drop model to membrane protein simulation. Proteins 2009; 77:378-94. [PMID: 19455711 DOI: 10.1002/prot.22443] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The analysis of structural properties and biological activity of membrane proteins requires long lasting simulation of molecular dynamics. The large number of atoms present in protein molecule, membrane (phospholipids), and water environment makes the simulation of large scale. The implementation of simplified model representing the natural environment for membrane proteins is presented and compared with the vacuum simulation and simulation in the presence of water molecules and membrane phospholipids presented explicite. The comparative structural analysis and computational times for these three models makes the simplified model promising.
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Affiliation(s)
- Veronica Zobnina
- Department of Bioinformatics and Telemedicine, Collegium Medicum-Jagiellonian University, Krakow, Poland
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23
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Galat A. On transversal hydrophobicity of some proteins and their modules. J Chem Inf Model 2009; 49:1821-30. [PMID: 19569645 DOI: 10.1021/ci9001316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hydrophobicity of proteins encoded in the genomes of diverse organisms was quantified using two novel concepts: (A) amino acid (AA) bulkiness-dependent hydrophobicity profiles and (B) spatial context of hydrophobicity distribution in AA triads. Both concepts were introduced into an algorithm that was used for extracting protein clusters from diverse genomic databases whose sequence attributes were similar to those in the multiple sequence alignment (MSA) of a given family of proteins. The sequences of the G protein-coupled receptors (GPCRs) encoded in different genomes were used as templates for testing the above concepts. The following sequence attributes were used for protein clustering: (A) sequence similarity scores (IDs); (B) amino acid composition (AAC); (C) hydrophobicity; (D) AA-bulkiness; and (E) alpha-helical propensity potentials. Diverse GPCRs display variable distributions of AA bulkiness-dependent buildups and declines in the hydrophobicity profiles that may be related to their function-dependent way of packing and allostery in the membrane. It is shown that intramolecular transversal nonbonded interactions between the TM segments in diverse GPCRs involve about 50% of hydrophobic atoms. Similar interaction networks exist between alpha-helices of tetratricopeptide (TPR) motifs-containing immunophilins and other proteins containing alpha-helical bundles.
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Affiliation(s)
- Andrzej Galat
- Institute de Biologie et de Technologies de Saclay, IBiTec/DSV/CEA, CE-Saclay, F-91191 Gif-sur-Yvette Cedex, France.
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24
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Banach M, Stąpor K, Roterman I. Chaperonin structure: the large multi-subunit protein complex. Int J Mol Sci 2009; 10:844-861. [PMID: 19399224 PMCID: PMC2672005 DOI: 10.3390/ijms10030844] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 02/23/2009] [Accepted: 02/26/2009] [Indexed: 11/16/2022] Open
Abstract
The multi sub-unit protein structure representing the chaperonins group is analyzed with respect to its hydrophobicity distribution. The proteins of this group assist protein folding supported by ATP. The specific axial symmetry GroEL structure (two rings of seven units stacked back to back - 524 aa each) and the GroES (single ring of seven units - 97 aa each) polypeptide chains are analyzed using the hydrophobicity distribution expressed as excess/deficiency all over the molecule to search for structure-to-function relationships. The empirically observed distribution of hydrophobic residues is confronted with the theoretical one representing the idealized hydrophobic core with hydrophilic residues exposure on the surface. The observed discrepancy between these two distributions seems to be aim-oriented, determining the structure-to-function relation. The hydrophobic force field structure generated by the chaperonin capsule is presented. Its possible influence on substrate folding is suggested.
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Affiliation(s)
- Mateusz Banach
- Department of Bioinformatics and Telemedicine – Jagiellonian University, Collegium Medicum, Lazarza 16, 31-531 Krakow, Poland; E-Mail:
- Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland; E-Mail:
| | - Katarzyna Stąpor
- Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland; E-Mail:
- Silesian Technical University, Institute of Computer Science, Akademicka 16 44-100 Gliwice, Poland; E-Mail:
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine – Jagiellonian University, Collegium Medicum, Lazarza 16, 31-531 Krakow, Poland; E-Mail:
- Faculty of Physics, Astronomy and Applied Computer Science - Jagiellonian University, Reymonta 4, 30-059 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
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25
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Minervini G, Evangelista G, Polticelli F, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Wiśniowski Z, Matczyńska E, Prymula K, Roterman I. Never born proteins as a test case for ab initio protein structures prediction. Bioinformation 2009; 3:177-9. [PMID: 19238243 PMCID: PMC2637968 DOI: 10.6026/97320630003177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Accepted: 11/23/2008] [Indexed: 12/03/2022] Open
Abstract
The number of natural proteins although large is significantly smaller than the theoretical number of proteins that can be
obtained combining the 20 natural amino acids, the so-called “never born proteins” (NBPs). The study of the structure and
properties of these proteins allows to investigate the sources of the natural proteins being of unique characteristics or
special properties. However the structural study of NPBs can also been intended as an ideal test for evaluating the
efficiency of software packages for the ab initio protein structure prediction. In this research, 10.000 three-dimensional
structures of proteins of completely random sequence generated according to ROSETTA and FOD model were compared. The
results show the limits of these software packages, but at the same time indicate that in many cases there is a significant
agreement between the prediction obtained.
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Affiliation(s)
- Giovanni Minervini
- Department of Biology, University Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy
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26
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Stochastic protein folding simulation in the three-dimensional HP-model. Comput Biol Chem 2008; 32:248-55. [PMID: 18485827 DOI: 10.1016/j.compbiolchem.2008.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 03/17/2008] [Indexed: 11/23/2022]
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27
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Galat A, Gross G, Drevet P, Sato A, Ménez A. Conserved structural determinants in three-fingered protein domains. FEBS J 2008; 275:3207-25. [DOI: 10.1111/j.1742-4658.2008.06473.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Davis JE, Warren GL, Patel S. Revised charge equilibration potential for liquid alkanes. J Phys Chem B 2008; 112:8298-310. [PMID: 18570394 DOI: 10.1021/jp8003129] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a revised liquid alkane force field based on the charge equilibration formalism for incorporating electrostatic nonadditive effects arising from local polarization. The model is a revision of earlier work by Patel and Brooks, specifically addressing deficiencies in the dihedral potential, electrostatic, and Lennard-Jones (van der Waals) parameters of the force field. We discuss refinement of the alkane backbone torsion potential to match high-level ab initio relative conformational energetics for pentane, hexane, and heptane. We further discuss refinement of the electrostatic and Lennard-Jones (van der Waals) parameters to reproduce the experimental polarizability, liquid density, and vaporization enthalpy of hexane. Finally, we calculate bulk liquid properties including densities, vaporization enthalpies, self-diffusion constants, isothermal compressibilities, constant pressure heat capacities, and NMR T 1 relaxation times for a series of linear alkanes ranging from hexane to pentadecane based on the current revised model. We also compute free energies of hydration for pentane, hexane, and heptane. The revised force field offers a significantly improved overall description of these properties relative to the original parametrization. The current alkane force field represents a platform for ongoing development of a CHARMM (Chemistry at Harvard Molecular Mechanics) polarizable force field for lipids and integral membrane proteins.
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Affiliation(s)
- Joseph E Davis
- Department of Chemistry and Biochemistry, University of Delaware, 238 Brown Laboratory Newark, Delaware 19716, USA
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29
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Bryliński M, Prymula K, Jurkowski W, Kochańczyk M, Stawowczyk E, Konieczny L, Roterman I. Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput Biol 2007; 3:e94. [PMID: 17530916 PMCID: PMC1876487 DOI: 10.1371/journal.pcbi.0030094] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 04/11/2007] [Indexed: 11/19/2022] Open
Abstract
A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localization of active sites in proteins. This paper describes a computational model that can be used to identify potential areas that are able to interact with other molecules (ligands, substrates, inhibitors, etc.). The model for active site recognition is based on the analysis of hydrophobicity distribution in protein molecules. It is shown, based on the analyses of proteins with known biological activity and of proteins of unknown function, that the region of significantly irregular hydrophobicity distribution in proteins appears to be function related.
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Affiliation(s)
- Michał Bryliński
- Department of Bioinformatics and Telemedicine, Jagiellonian University–Collegium Medicum, Kraków, Poland
- Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Katarzyna Prymula
- Department of Bioinformatics and Telemedicine, Jagiellonian University–Collegium Medicum, Kraków, Poland
- Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Wiktor Jurkowski
- Department of Bioinformatics and Telemedicine, Jagiellonian University–Collegium Medicum, Kraków, Poland
| | - Marek Kochańczyk
- Department of Bioinformatics and Telemedicine, Jagiellonian University–Collegium Medicum, Kraków, Poland
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Kraków, Poland
| | - Ewa Stawowczyk
- Department of Bioinformatics and Telemedicine, Jagiellonian University–Collegium Medicum, Kraków, Poland
| | - Leszek Konieczny
- Institute of Medical Biochemistry, Jagiellonian University–Collegium Medicum, Kraków, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University–Collegium Medicum, Kraków, Poland
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Kraków, Poland
- * To whom correspondence should be addressed. E-mail:
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30
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Brylinski M, Kochanczyk M, Broniatowska E, Roterman I. Localization of ligand binding site in proteins identified in silico. J Mol Model 2007; 13:665-75. [PMID: 17394030 DOI: 10.1007/s00894-007-0191-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 02/26/2007] [Indexed: 01/21/2023]
Abstract
Knowledge-based models for protein folding assume that the early-stage structural form of a polypeptide is determined by the backbone conformation, followed by hydrophobic collapse. Side chain-side chain interactions, mostly of hydrophobic character, lead to the formation of the hydrophobic core, which seems to stabilize the structure of the protein in its natural environment. The fuzzy-oil-drop model is employed to represent the idealized hydrophobicity distribution in the protein molecule. Comparing it with the one empirically observed in the protein molecule reveals that they are not in agreement. It is shown in this study that the irregularity of hydrophobic distributions is aim-oriented. The character and strength of these irregularities in the organization of the hydrophobic core point to the specificity of a particular protein's structure/function. When the location of these irregularities is determined versus the idealized fuzzy-oil-drop, function-related areas in the protein molecule can be identified. The presented model can also be used to identify ways in which protein-protein complexes can possibly be created. Active sites can be predicted for any protein structure according to the presented model with the free prediction server at http://www.bioinformatics.cm-uj.krakow.pl/activesite. The implication based on the model presented in this work suggests the necessity of active presence of ligand during the protein folding process simulation.
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Affiliation(s)
- Michal Brylinski
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Collegium Medicum, Łazarza 16, 31-530, Krakow, Poland
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