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Chen G, Khan IM, He W, Li Y, Jin P, Campanella OH, Zhang H, Huo Y, Chen Y, Yang H, Miao M. Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects. Compr Rev Food Sci Food Saf 2022; 21:2688-2714. [PMID: 35470946 DOI: 10.1111/1541-4337.12965] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
The applications of lipases in esterification, amidation, and transesterification have broadened their potential in the production of fine compounds with high cumulative values. Mostly, the catalytic triad of lipases is covered by either one or two mobile peptides called the "lid" that control the substrate channel to the catalytic center. The lid holds unique conformational allostery via interfacial activation to regulate the dynamics and catalytic functions of lipases, thereby highlighting its importance in redesigning these enzymes for industrial applications. The structural characteristic of lipase, the dynamics of lids, and the roles of lid in lipase catalysis were summarized, providing opportunities for rebuilding lid region by biotechniques (e.g., metagenomic technology and protein engineering) and enzyme immobilization. The review focused on the advantages and disadvantages of strategies rebuilding the lid region. The main shortcomings of biotechnologies on lid rebuilding were discussed such as negative effects on lipase (e.g., a decrease of activity). Additionally, the main shortcomings (e.g., enzyme desorption at high temperatre) in immobilization on hydrophobic supports via interfacial action were presented. Solutions to the mentioned problems were proposed by combinations of computational design with biotechnologies, and improvements of lipase immobilization (e.g., immobilization protocols and support design). Finally, the review provides future perspectives about designing hyperfunctional lipases as biocatalysts in the food industry based on lid conformation and dynamics.
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Affiliation(s)
- Gang Chen
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wensen He
- School of Food Science and Technology, Jiangsu University, Zhenjiang, China
| | - Yongxin Li
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Peng Jin
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Osvaldo H Campanella
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Department of Food Science and Technology, Ohio State University, Columbus, Ohio, USA
| | - Haihua Zhang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yanrong Huo
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yang Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Huqing Yang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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Wang H, Li J, Wang S, Lu X, Zhang G, Zhuang Y, Li L, Wang W, Lin P, Chen C, Wang H, Chen Q, Jiang Y, Qu J, Xu L. Contribution of structural accessibility to the cooperative relationship of TF-lncRNA in myopia. Brief Bioinform 2021; 22:6217725. [PMID: 33834194 DOI: 10.1093/bib/bbab082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 11/12/2022] Open
Abstract
Transcriptional regulation is associated with complicated mechanisms including multiple molecular interactions and collaborative drive. Long noncoding RNAs (lncRNAs) have highly structured characteristics and play vital roles in the regulation of transcription in organisms. However, the specific contributions of conformation feature and underlying molecular mechanisms are still unclear. In the present paper, a hypothesis regarding molecular structure effect is presented, which proposes that lncRNAs fold into a complex spatial architecture and act as a skeleton to recruit transcription factors (TF) targeted binding, and which is involved in cooperative regulation. A candidate set of TF-lncRNA coregulation was constructed, and it was found that structural accessibility affected molecular binding force. In addition, transcription factor binding site (TFBS) regions of myopia-related lncRNA transcripts were disturbed, and it was discovered that base mutations affected the occurrence of significant molecular allosteric changes in important elements and variable splicing regions, mediating the onset and development of myopia. The results originated from structureomics and interactionomics and created conditions for systematic research on the mechanisms of structure-mediated TF-lncRNA coregulation in transcriptional regulation. Finally, these findings will help further the understanding of key regulatory roles of molecular allostery in cell physiological and pathological processes.
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Affiliation(s)
- Hong Wang
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University and cooperates with College of Bioinformatics Science and Technology at Harbin Medical University, Wenzhou 325027, P. R. China
| | - Jing Li
- College of Bioinformatics Science and Technology at Harbin Medical University, Wenzhou 325027, P. R. China
| | - Siyu Wang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Xiaoyan Lu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Guosi Zhang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Youyuan Zhuang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Liansheng Li
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Wencan Wang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Peng Lin
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Chong Chen
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Hao Wang
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Qi Chen
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology at Harbin Medical University, Wenzhou 325027, P. R. China
| | - Jia Qu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
| | - Liangde Xu
- School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering at Wenzhou Medical University, Wenzhou 325027, P. R. China
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Higuchi M, Ishiyama K, Maruoka M, Kanamori R, Takaori-Kondo A, Watanabe N. Paradoxical activation of c-Src as a drug-resistant mechanism. Cell Rep 2021; 34:108876. [PMID: 33761359 DOI: 10.1016/j.celrep.2021.108876] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/29/2020] [Accepted: 02/25/2021] [Indexed: 12/13/2022] Open
Abstract
ATP-competitive inhibitors have been developed as promising anti-cancer agents. However, drug-resistance frequently occurs, and the underlying mechanisms are not fully understood. Here, we show that the activation of c-Src and its downstream phosphorylation cascade can be paradoxically induced by Src-targeted and RTK-targeted kinase inhibitors. We reveal that inhibitor binding induces a conformational change in c-Src, leading to the association of the active form c-Src with focal adhesion kinase (FAK). Reduction of the inhibitor concentration results in the dissociation of inhibitors from the c-Src-FAK complex, which allows c-Src to phosphorylate FAK and initiate FAK-Grb2-mediated Erk signaling. Furthermore, a drug-resistant mutation in c-Src, which reduces the affinity of inhibitors for c-Src, converts Src inhibitors into facilitators of cell proliferation by enhancing the phosphorylation of FAK and Erk in c-Src-mutated cells. Our data thus reveal paradoxical enhancement of cell growth evoked by target-based kinase inhibitors, providing potentially important clues for the future development of effective and safe cancer treatment.
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Affiliation(s)
- Makio Higuchi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenichi Ishiyama
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Hematology and Oncology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiro Maruoka
- Laboratory of Single-Molecule Cell Biology, Tohoku University Graduate School of Life Sciences, Sendai, Japan
| | - Ryosuke Kanamori
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Naoki Watanabe
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan; Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto, Japan.
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Abstract
Bromodomains (BDs) are small protein modules that interact with acetylated marks in histones. These posttranslational modifications are pivotal to regulate gene expression, making BDs promising targets to treat several diseases. While the general structure of BDs is well known, their dynamical features and their interplay with other macromolecules are poorly understood, hampering the rational design of potent and selective inhibitors. Here, we combine extensive molecular dynamics simulations, Markov state modeling, and available structural data to reveal a transiently formed state that is conserved across all BD families. It involves the breaking of two backbone hydrogen bonds that anchor the ZA-loop with the αA helix, opening a cryptic pocket that partially occludes the one associated to histone binding. By analyzing more than 1,900 experimental structures, we unveil just two adopting the hidden state, explaining why it has been previously unnoticed and providing direct structural evidence for its existence. Our results suggest that this state is an allosteric regulatory switch for BDs, potentially related to a recently unveiled BD-DNA-binding mode.
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Affiliation(s)
- Lluís Raich
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Katharina Meier
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 42096 Wuppertal, Germany
| | - Judith Günther
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Clara D Christ
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany;
- Department of Chemistry, Rice University, Houston, TX 77005
| | - Simon Olsson
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany;
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5
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Abstract
While belonging to the nanoscale, protein machines are so complex that tracing even a small fraction of their cycle requires weeks of calculations on supercomputers. Surprisingly, many aspects of their operation can be however already reproduced by using very simple mechanical models of elastic networks. The analysis suggests that, similar to other self-organized complex systems, functional collective dynamics in such proteins is effectively reduced to a low-dimensional attractive manifold.
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Affiliation(s)
- Holger Flechsig
- 1 Nano Life Science Institute (WPI-NanoLSI), Kanazawa University , Kakuma-machi, 920-1192 Kanazawa , Japan
| | - Alexander S Mikhailov
- 1 Nano Life Science Institute (WPI-NanoLSI), Kanazawa University , Kakuma-machi, 920-1192 Kanazawa , Japan.,2 Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin , Germany
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Flügge F, Peters T. Insights into Allosteric Control of Human Blood Group A and B Glycosyltransferases from Dynamic NMR. ChemistryOpen 2019; 8:760-769. [PMID: 31289712 PMCID: PMC6591795 DOI: 10.1002/open.201900116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/03/2019] [Indexed: 12/25/2022] Open
Abstract
Human blood group A and B glycosyltransferases (GTA, GTB) are retaining glycosyltransferases, requiring a catalytic mechanism that conserves the anomeric configuration of the hexopyranose moiety of the donor substrate (UDP-GalNAc, UDP-Gal). Previous studies have shown that GTA and GTB cycle through structurally distinct states during catalysis. Here, we link binding and release of substrates, substrate-analogs, and products to transitions between open, semi-closed, and closed states of the enzymes. Methyl TROSY based titration experiments in combination with zz-exchange experiments uncover dramatic changes of binding kinetics associated with allosteric interactions between donor-type and acceptor-type ligands. Taken together, this highlights how allosteric control of on- and off-rates correlates with conformational changes, driving catalysis to completion.
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Affiliation(s)
- Friedemann Flügge
- Institute of Chemistry and MetabolomicsUniversity of Lübeck23562LübeckGermany
| | - Thomas Peters
- Institute of Chemistry and MetabolomicsUniversity of Lübeck23562LübeckGermany
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Abstract
A key question in immunology is whether antigen recognition and Fc receptor (FcR) binding are allosterically linked. This question is also relevant for therapeutic antibody design. Antibody Fab and Fc domains are connected by flexible unstructured hinge region. Fc chains have conserved glycosylation sites at Asn297, with each conjugated to a core heptasaccharide and forming biantennary Fc glycan. The glycans modulate the Fc conformations and functions. It is well known that the antibody Fab and Fc domains and glycan affect antibody activity, but whether these elements act independently or synergistically is still uncertain. We simulated four antibody complexes: free antibody, antigen-bound antibody, FcR-bound antibody, and an antigen-antibody-FcR complex. We found that, in the antibody's "T/Y" conformation, the glycans, and the Fc domain all respond to antigen binding, with the antibody population shifting to two dominant clusters, both with the Fc-receptor binding site open. The simulations reveal that the Fc-glycan-receptor complexes also segregate into two conformational clusters, one corresponding to the antigen-free antibody-FcR baseline binding, and the other with an antigen-enhanced antibody-FcR interaction. Our study confirmed allosteric communications in antibody-antigen recognition and following FcR activation. Even though we observed allosteric communications through the IgG domains, the most important mechanism that we observed is the communication via population shift, stimulated by antigen binding and propagating to influence FcR recognition.
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Affiliation(s)
- Jun Zhao
- Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, USA
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Jiang XK, Ikejiri Y, Wu C, Rahman S, Georghiou PE, Zeng X, Elsegood MRJ, Redshaw C, Teat SJ, Yamato T. A Hexahomotrioxacalix[3]arene-Based Ditopic Receptor for Alkylammonium Ions Controlled by Ag⁺ Ions. Molecules 2018; 23:E467. [PMID: 29466302 DOI: 10.3390/molecules23020467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/03/2018] [Accepted: 02/05/2018] [Indexed: 11/24/2022] Open
Abstract
A receptor cone-1 based on a hexahomotrioxacalix[3]arene bearing three pyridyl groups was successfully synthesized, which has a C3-symmetric conformation and is capable of binding alkylammonium and metal ions simultaneously in a cooperative fashion. It can bind alkylammonium ions through the π-cavity formed by three aryl rings. This behaviour is consistent with the cone-in/cone-out conformational rearrangement needed to reorganize the cavity for endo-complexation. As a C3-symmetrical pyridyl-substituted calixarene, receptor cone-1 can also bind an Ag+ ion, and the nitrogen atoms are turned towards the inside of the cavity and interact with Ag+. After complexation of tris(2-pyridylamide) derivative receptor cone-1 with Ag+, the original C3-symmetry was retained and higher complexation selectivity for n-BuNH3+ versus t-BuNH3+ was observed. Thus, it is believed that this receptor will have a role to play in the sensing, detection, and recognition of Ag+ and n-BuNH3+ ions.
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9
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Sun X, Laroche G, Wang X, Ågren H, Bowman GR, Giguère PM, Tu Y. Propagation of the Allosteric Modulation Induced by Sodium in the δ-Opioid Receptor. Chemistry 2017; 23:4615-4624. [PMID: 28182309 DOI: 10.1002/chem.201605575] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Indexed: 11/07/2022]
Abstract
Allosteric sodium in the helix bundle of a G protein-coupled receptor (GPCR) can modulate the receptor activation on the intracellular side. This phenomenon has confounded the GPCR community for decades. In this work, we present a theoretical model that reveals the mechanism of the allosteric modulation induced by sodium in the δ-opioid receptor. We found that the allosteric sodium ion exploits a distinct conformation of the key residue Trp2746.48 to propagate the modulation to helices 5 and 6, which further transmits along the helices and regulates their positions on the intracellular side. This mechanism is supported by subsequent functional assays. Remarkably, our results highlight the contrast between the allosteric effects towards two GPCR partners, the G protein and β-arrestin, as indicated by the fact that the allosteric modulation initiated by the sodium ion significantly affects the β-arrestin recruitment, while it alters the G protein signaling only moderately. We believe that the mechanism revealed in this work can be used to explain allosteric effects initiated by sodium in other GPCRs since the allosteric sodium is highly conserved across GPCRs.
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Affiliation(s)
- Xianqiang Sun
- Pharmaceutical Research Center, School of Pharmacy, Guangzhou Medical University, 195 Dongfengxi Rd, Guangzhou, 510182, China
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Genevieve Laroche
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Rd, Ottawa, ON, Canada
| | - Xu Wang
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Patrick M Giguère
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Rd, Ottawa, ON, Canada
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
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10
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Mou L, Cui T, Liu W, Zhang H, Cai Z, Lu S, Gao G. Microsecond molecular dynamics simulations provide insight into the ATP-competitive inhibitor-induced allosteric protection of Akt kinase phosphorylation. Chem Biol Drug Des 2016; 89:723-731. [PMID: 27797456 DOI: 10.1111/cbdd.12895] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/02/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
Abstract
Akt is a serine/threonine protein kinase, a critical mediator of growth factor-induced survival in key cellular pathways. Allosteric signaling between protein intramolecular domains requires long-range communication mediated by hotspot residues, often triggered by ligand binding. Here, based on extensive 3 μs explicit solvent molecular dynamics (MD) simulations of Akt1 kinase domain in the unbound (apo) and ATP-competitive inhibitor, GDC-0068-bound states, we propose a molecular mechanism for allosteric regulation of Akt1 kinase phosphorylation by GDC-0068 binding to the ATP-binding site. MD simulations revealed that the apo Akt1 is flexible with two disengaged N- and C-lobes, equilibrated between the open and closed conformations. GDC-0068 occupancy of the ATP-binding site shifts the conformational equilibrium of Akt1 from the open conformation toward the closed conformation and stabilizes the closed state. This effect enables allosteric signal propagation from the GDC-0068 to the phosphorylated T308 (pT308) in the activation loop and restrains phosphatase access to pT308, thereby protecting the pT308 in the GDC-0068-bound Akt1. Importantly, functional hotspots involved in the allosteric communication from the GDC-0068 to the pT308 are identified. Our analysis of GDC-0068-induced allosteric protection of Akt kinase phosphorylation yields important new insights into the molecular mechanism of allosteric regulation of Akt kinase activity.
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Affiliation(s)
- Linkai Mou
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Tongwei Cui
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Weiguang Liu
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Hong Zhang
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Zhanxiu Cai
- Department of Electrical and Computer Engineering, College of Bioscience and Technology, Weifang Medical University, Weifang, Shandong, China
| | - Shaoyong Lu
- Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guojun Gao
- Department of Urology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
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11
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Denisov IG, Sligar SG. A novel type of allosteric regulation: functional cooperativity in monomeric proteins. Arch Biochem Biophys 2012; 519:91-102. [PMID: 22245335 PMCID: PMC3329180 DOI: 10.1016/j.abb.2011.12.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 10/14/2022]
Abstract
Cooperative functional properties and allosteric regulation in cytochromes P450 play an important role in xenobiotic metabolism and define one of the main mechanisms of drug-drug interactions. Recent experimental results suggest that ability to bind simultaneously two or more small organic molecules can be the essential feature of cytochrome P450 fold, and often results in rich and complex pattern of allosteric behavior. Manifestations of non-Michaelis kinetics include homotropic and heterotropic activation and inhibition effects depending on the stoichiometric ratios of substrate and effector, changes in the regio- and stereospecificity of catalytic transformations, and often give rise to the clinically important drug-drug interactions. In addition, functional response of P450 systems is modulated by the presence of specific and non-specific effector molecules, metal ions, membrane incorporation, formation of homo- and hetero-oligomers, and interactions with the protein redox partners. In this article we briefly overview the main factors contributing to the allosteric effects in cytochromes P450 with the main focus on the sources of cooperative behavior in xenobiotic metabolizing monomeric heme enzymes with their conformational flexibility and extremely broad substrate specificity. The novel mechanism of functional cooperativity in P450 enzymes does not require substantial binding cooperativity, rather it implies the presence of one or more binding sites with higher affinity than the single catalytically active site in the vicinity of the heme iron.
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Affiliation(s)
- Ilia G. Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801
| | - Stephen G. Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801
- Beckman Institute, University of Illinois, Urbana, IL, 61801
- School of Molecular and Cellular Biology, University of Illinois, Urbana, IL, 61801
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12
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Abstract
We introduce a novel approach for elucidating the potential pathways of allosteric communication in biomolecular systems. The methodology, based on Markov propagation of 'information' across the structure, permits us to partition the network of interactions into soft clusters distinguished by their coherent stochastics. Probabilistic participation of residues in these clusters defines the communication patterns inherent to the network architecture. Application to bacterial chaperonin complex GroEL-GroES, an allostery-driven structure, identifies residues engaged in intra- and inter-subunit communication, including those acting as hubs and messengers. A number of residues are distinguished by their high potentials to transmit allosteric signals, including Pro33 and Thr90 at the nucleotide-binding site and Glu461 and Arg197 mediating inter- and intra-ring communication, respectively. We propose two most likely pathways of signal transmission, between nucleotide- and GroES-binding sites across the cis and trans rings, which involve several conserved residues. A striking observation is the opposite direction of information flow within cis and trans rings, consistent with negative inter-ring cooperativity. Comparison with collective modes deduced from normal mode analysis reveals the propensity of global hinge regions to act as messengers in the transmission of allosteric signals.
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Affiliation(s)
- Chakra Chennubhotla
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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