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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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2
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Lu J, Chen S, Bai X, Liao M, Qiu Y, Zheng LL, Yu H. Targeting cholesterol metabolism in Cancer: From molecular mechanisms to therapeutic implications. Biochem Pharmacol 2023; 218:115907. [PMID: 37931664 DOI: 10.1016/j.bcp.2023.115907] [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: 07/18/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Cholesterol is an essential component of cell membranes and helps to maintain their structure and function. Abnormal cholesterol metabolism has been linked to the development and progression of tumors. Changes in cholesterol metabolism triggered by internal or external stimuli can promote tumor growth. During metastasis, tumor cells require large amounts of cholesterol to support their growth and colonization of new organs. Recent research has shown that cholesterol metabolism is reprogrammed during tumor development, and this can also affect the anti-tumor activity of immune cells in the surrounding environment. However, identifying the specific targets in cholesterol metabolism that regulate cancer progression and the tumor microenvironment is still a challenge. Additionally, exploring the potential of combining statin drugs with other therapies for different types of cancer could be a worthwhile avenue for future drug development. In this review, we focus on the molecular mechanisms of cholesterol and its derivatives in cell metabolism and the tumor microenvironment, and discuss specific targets and relevant therapeutic agents that inhibit aspects of cholesterol homeostasis.
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Affiliation(s)
- Jia Lu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Siwei Chen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Xuejiao Bai
- Department of Anesthesiology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Minru Liao
- Department of Anesthesiology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuling Qiu
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
| | - Ling-Li Zheng
- Department of Pharmacy, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, China.
| | - Haiyang Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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3
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Sacher S, Mukherjee A, Ray A. Deciphering structural aspects of reverse cholesterol transport: mapping the knowns and unknowns. Biol Rev Camb Philos Soc 2023; 98:1160-1183. [PMID: 36880422 DOI: 10.1111/brv.12948] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 02/03/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023]
Abstract
Atherosclerosis is a major contributor to the onset and progression of cardiovascular disease (CVD). Cholesterol-loaded foam cells play a pivotal role in forming atherosclerotic plaques. Induction of cholesterol efflux from these cells may be a promising approach in treating CVD. The reverse cholesterol transport (RCT) pathway delivers cholesteryl ester (CE) packaged in high-density lipoproteins (HDL) from non-hepatic cells to the liver, thereby minimising cholesterol load of peripheral cells. RCT takes place via a well-organised interplay amongst apolipoprotein A1 (ApoA1), lecithin cholesterol acyltransferase (LCAT), ATP binding cassette transporter A1 (ABCA1), scavenger receptor-B1 (SR-B1), and the amount of free cholesterol. Unfortunately, modulation of RCT for treating atherosclerosis has failed in clinical trials owing to our lack of understanding of the relationship between HDL function and RCT. The fate of non-hepatic CEs in HDL is dependent on their access to proteins involved in remodelling and can be regulated at the structural level. An inadequate understanding of this inhibits the design of rational strategies for therapeutic interventions. Herein we extensively review the structure-function relationships that are essential for RCT. We also focus on genetic mutations that disturb the structural stability of proteins involved in RCT, rendering them partially or completely non-functional. Further studies are necessary for understanding the structural aspects of RCT pathway completely, and this review highlights alternative theories and unanswered questions.
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Affiliation(s)
- Sukriti Sacher
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase III, New Delhi, 110019, India
| | - Abhishek Mukherjee
- Dhiti Life Sciences Pvt Ltd, B-107, Okhla Phase I, New Delhi, 110020, India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase III, New Delhi, 110019, India
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4
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Ferru-Clément R, Boucher G, Forest A, Bouchard B, Bitton A, Lesage S, Schumm P, Lazarev M, Brant S, Duerr RH, McGovern DPB, Silverberg M, Cho JH, Ananthakrishnan A, Xavier RJ, Rioux JD, Des Rosiers C. Serum Lipidomic Screen Identifies Key Metabolites, Pathways, and Disease Classifiers in Crohn's Disease. Inflamm Bowel Dis 2023; 29:1024-1037. [PMID: 36662167 PMCID: PMC10320374 DOI: 10.1093/ibd/izac281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND There is an unmet medical need for biomarkers that capture host and environmental contributions in inflammatory bowel diseases (IBDs). This study aimed at testing the potential of circulating lipids as disease classifiers given their major roles in inflammation. METHODS We applied a previously validated comprehensive high-resolution liquid chromatography-mass spectrometry-based untargeted lipidomic workflow covering 25 lipid subclasses to serum samples from 100 Crohn's disease (CD) patients and 100 matched control subjects. Findings were replicated and expanded in another 200 CD patients and 200 control subjects. Key metabolites were tested for associations with disease behavior and location, and classification models were built and validated. Their association with disease activity was tested using an independent cohort of 42 CD patients. RESULTS We identified >70 metabolites with strong association (P < 1 × 10-4, q < 5 × 10-4) to CD. Highly performing classification models (area under the curve > 0.84-0.97) could be built with as few as 5 to 9 different metabolites, representing 6 major correlated lipid clusters. These classifiers included a phosphatidylethanolamine ether (O-16:0/20:4), a sphingomyelin (d18:1/21:0) and a cholesterol ester (14:1), a very long-chain dicarboxylic acid [28:1(OH)] and sitosterol sulfate. These classifiers and correlated lipids indicate a dysregulated metabolism in host cells, notably in peroxisomes, as well as dysbiosis, oxidative stress, compromised inflammation resolution, or intestinal membrane integrity. A subset of these were associated with disease behavior or location. CONCLUSIONS Untargeted lipidomic analyses uncovered perturbations in the circulating human CD lipidome, likely resulting from multiple pathogenic mechanisms. Models using as few as 5 biomarkers had strong disease classifier characteristics, supporting their potential use in diagnosis or prognosis.
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Affiliation(s)
- Romain Ferru-Clément
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Laboratoire Histocompatibilité et Immunogénétique, Établissement français du sang–Nouvelle-Aquitaine, site de Poitiers, Poitiers, France
| | | | - Anik Forest
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
| | | | - Alain Bitton
- Division of Gastroenterology, McGill University Health Centre, Montreal, QC, Canada
| | - Sylvie Lesage
- Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Phil Schumm
- Department of Public Health Sciences, University of Chicago, IL, USA
| | - Mark Lazarev
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steve Brant
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Richard H Duerr
- Department of Medicine, University of Pittsburgh, Pennsylvania, PA, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Silverberg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Judy H Cho
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ashwin Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ramnik J Xavier
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Département de Médicine, Université de Montréal, Montreal, QC, Canada
| | - Christine Des Rosiers
- Research Center, Montreal Heart Institute, Montreal, QC, Canada
- Département de Nutrition, Université de Montréal, Montreal, QC, Canada
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Bhale AS, Venkataraman K. Delineating the impact of pathogenic mutations on the conformational dynamics of HDL's vital protein ApoA1: a combined computational and molecular dynamic simulation approach. J Biomol Struct Dyn 2023; 41:15661-15681. [PMID: 36943736 DOI: 10.1080/07391102.2023.2191131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/09/2023] [Indexed: 03/23/2023]
Abstract
Apolipoprotein A1 (ApoA1), is the important component of high-density lipoproteins (HDL), that has key role in HDL biogenesis, cholesterol trafficking, and reverse cholesterol transport (RCT). Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in ApoA1 have been linked to cardiovascular diseases and amyloidosis as they alter the protein's native structure and function. Therefore in this study, we attempted to understand the molecular pathogenicity profile of nsSNPs of ApoA1 using various computational approaches. We used state-of-the-art computational methods to thoroughly investigate the 295 ApoA1 nsSNPs at sequence and structural levels. Seven nsSNPs (L13R, L84R, L84P, L99P, R173P, L187P, and L238P) out of 295 were classified as the most deleterious and destabilizing. In order to estimate the effect of such destabilizing mutations on the protein conformation, all-atom molecular dynamics simulations (MDS) of ApoA1 wild-type (WT), L99P and R173P for 100 ns, was carried out using GROMACS 5.0.1 package. The MD simulation investigation revealed significant structural alterations in L99P and R173P. In addition, they had changed principal component analysis and electrostatic surface potential, decreased structural compactness, and intramolecular hydrogen bonds, which supported the rationale underpinning ApoA1 dysfunction with such mutations. This work sheds light on ApoA1 dysfunction due to single amino acid alterations, and offers new insight into the molecular basis of ApoA1-related diseases progression.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aishwarya Sudam Bhale
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Krishnan Venkataraman
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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6
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Mitusińska K, Bzówka M, Magdziarz T, Góra A. Geometry-Based versus Small-Molecule Tracking Method for Tunnel Identification: Benefits and Pitfalls. J Chem Inf Model 2022; 62:6803-6811. [PMID: 36374085 PMCID: PMC9795556 DOI: 10.1021/acs.jcim.2c00985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Different methods for tunnel identification, geometry-based and small-molecule tracking approaches, were compared to provide their benefits and pitfalls. Results obtained for both crystal structures and molecular dynamics (MD) simulations were analyzed to investigate if a more computationally demanding method would be beneficial. Careful examination of the results is essential for the low-diameter tunnel description, and assessment of the tunnel functionality based only on their geometrical parameters is challenging. We showed that the small-molecule tracking approach can provide a detailed description of the system; however, it can also be the most computationally demanding.
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7
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Giorgi L, Niemelä A, Kumpula EP, Natri O, Parkkila P, Huiskonen JT, Koivuniemi A. Mechanistic Insights into the Activation of Lecithin–Cholesterol Acyltransferase in Therapeutic Nanodiscs Composed of Apolipoprotein A-I Mimetic Peptides and Phospholipids. Mol Pharm 2022; 19:4135-4148. [DOI: 10.1021/acs.molpharmaceut.2c00540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Giorgi
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Akseli Niemelä
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Esa-Pekka Kumpula
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Ossi Natri
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Petteri Parkkila
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
- Division of Nano and Biophysics, Department of Physics, Chalmers University of Technology, Goteborg 412 96, Sweden
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Artturi Koivuniemi
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
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8
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Zhang W, Liu Z, Zhou Y, Lai C, Sun B, He M, Zhai Z, Wang J, Wang Q, Wang X, Wang F, Pan Y. Elucidating the molecular mechanisms of perfluorooctanoic acid-serum protein interactions by structural mass spectrometry. CHEMOSPHERE 2022; 291:132945. [PMID: 34798108 DOI: 10.1016/j.chemosphere.2021.132945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/08/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Perfluorooctanoic acid (PFOA) is a persistent environmental pollutant and will continually accumulate in blood due to its chemical inertness and strong interaction with serum proteins, especially serum albumin (SA), inducing highly adverse health risks. However, the molecular mechanisms of dynamic interactions between PFOA with serum proteins remain unclear, limiting the development of potential therapeutic strategies. Herein, we developed an integrated structural strategy to systematically profile the molecular details of dynamic interactions among PFOA, SA, and β-cyclodextrin (β-CD) by combing native mass spectrometry (nMS), lysine reactivity profiling (LRP), and molecular docking (MD) simulation. The SA site 1, site 2 pockets, and cleft nearby are observed as the primary interaction regions of PFOA. Further, β-CD can disrupt the PFOA combinations with bovine SA regions around sites Lys20, Lys280, Lys350, and Lys431-Lys439, with an overall reversing efficiency of about 26% at an identical concentration to PFOA. The interactome of PFOA with complex human serum proteins is globally profiled with molecular interaction details, including human serum albumin, apolipoprotein A-I, alpha-2-macroglobulin, and complement C3. Our results reveal molecular insights into the detail of the interaction between PFOA and serum proteins, beneficial to understanding PFOA toxicology.
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Affiliation(s)
- Wenxiang Zhang
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China; CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ye Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min He
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziyang Zhai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jian Wang
- The Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Qi Wang
- The Second Hospital of Dalian Medical University, Dalian, 116023, China
| | - Xian Wang
- Key Laboratory of Analytical Chemistry of State Ethnic Affairs Commission, College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, 430074, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China.
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9
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Wang Y, Wang G, Jing R, Hu T, Likhodii S, Sun G, Randell E, Jia G, Yu T, Zhang W. Metabolomics analysis of human plasma metabolites reveals the age- and sex-specific associations. J LIQ CHROMATOGR R T 2019. [DOI: 10.1080/10826076.2019.1701016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Yixiao Wang
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Guangshu Wang
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Ru’nan Jing
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Ting Hu
- Department of Computer Science, Memorial University, St John’s, Canada
| | - Sergei Likhodii
- Provincial Toxicology Centre, Provincial Health Services Authority, Vancouver, Canada
| | - Guang Sun
- Faculty of Medicine, Discipline of Medicine, Memorial University, St. John’s, Canada
| | - Edward Randell
- Faculty of Medicine, Department of Laboratory Medicine, Memorial University, St. John’s, Canada
| | - Guihua Jia
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Tianmiao Yu
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin, P. R. China
| | - Weidong Zhang
- School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin, P. R. China
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10
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Kokkonen P, Bednar D, Pinto G, Prokop Z, Damborsky J. Engineering enzyme access tunnels. Biotechnol Adv 2019; 37:107386. [PMID: 31026496 DOI: 10.1016/j.biotechadv.2019.04.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022]
Abstract
Enzymes are efficient and specific catalysts for many essential reactions in biotechnological and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic efficiency, stability or specificity required for these industrial processes. The current enzyme engineering methods offer solutions to this problem, but they mainly target the buried active site where the chemical reaction takes place. Despite being many times ignored, the tunnels and channels connecting the environment with the active site are equally important for the catalytic properties of enzymes. Changes in the enzymatic tunnels and channels affect enzyme activity, specificity, promiscuity, enantioselectivity and stability. This review provides an overview of the emerging field of enzyme access tunnel engineering with case studies describing design of all the aforementioned properties. The software tools for the analysis of geometry and function of the enzymatic tunnels and channels and for the rational design of tunnel modifications will also be discussed. The combination of new software tools and enzyme engineering strategies will provide enzymes with access tunnels and channels specifically tailored for individual industrial processes.
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Affiliation(s)
- Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar Pinto
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
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11
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Wilson CJ, Das M, Jayaraman S, Gursky O, Engen JR. Effects of Disease-Causing Mutations on the Conformation of Human Apolipoprotein A-I in Model Lipoproteins. Biochemistry 2018; 57:4583-4596. [PMID: 30004693 DOI: 10.1021/acs.biochem.8b00538] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plasma high-density lipoproteins (HDLs) are protein-lipid nanoparticles that transport lipids and protect against atherosclerosis. Human apolipoprotein A-I (apoA-I) is the principal HDL protein whose mutations can cause either aberrant lipid metabolism or amyloid disease. Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) was used to study the apoA-I conformation in model discoidal lipoproteins similar in size to large plasma HDL. We examined how point mutations associated with hereditary amyloidosis (F71Y and L170P) or atherosclerosis (L159R) influence the local apoA-I conformation in model lipoproteins. Unlike other apoA-I forms, the large particles showed minimal conformational heterogeneity, suggesting a fully extended protein conformation. Mutation-induced structural perturbations in lipid-bound protein were attenuated compared to the free protein and indicated close coupling between the two belt-forming apoA-I molecules. These perturbations propagated to distant lipoprotein sites, either increasing or decreasing their protection. This HDX MS study of large model HDL, compared with previous studies of smaller particles, ascertained that apoA-I's central region helps accommodate the protein conformation to lipoproteins of various sizes. This study also reveals that the effects of mutations on lipoprotein conformational dynamics are much weaker than those in a lipid-free protein. Interestingly, the mutation-induced perturbations propagate to distant sites nearly 10 nm away and alter their protection in ways that cannot be predicted from the lipoprotein structure and stability. We propose that long-range mutational effects are mediated by both protein and lipid and can influence lipoprotein functionality.
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Affiliation(s)
- Christopher J Wilson
- Department of Chemistry and Chemical Biology , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
| | - Madhurima Das
- Department of Physiology & Biophysics , Boston University School of Medicine , 700 Albany Street , Boston , Massachusetts 02118 , United States
| | - Shobini Jayaraman
- Department of Physiology & Biophysics , Boston University School of Medicine , 700 Albany Street , Boston , Massachusetts 02118 , United States
| | - Olga Gursky
- Department of Physiology & Biophysics , Boston University School of Medicine , 700 Albany Street , Boston , Massachusetts 02118 , United States.,Amyloidosis Research Center , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - John R Engen
- Department of Chemistry and Chemical Biology , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
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