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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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Dai J, Zhang G, Alkhofash RA, Mekonnen B, Saravanan S, Xue B, Fan ZC, Betleja E, Cole DG, Liu P, Lechtreck K. Loss of ARL13 impedes BBSome-dependent cargo export from Chlamydomonas cilia. J Cell Biol 2022; 221:213429. [PMID: 36040375 PMCID: PMC9436004 DOI: 10.1083/jcb.202201050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/12/2022] [Accepted: 07/11/2022] [Indexed: 12/25/2022] Open
Abstract
The GTPase Arl13b participates in ciliary protein transport, but its contribution to intraflagellar transport (IFT), the main motor-based protein shuttle of cilia, remains largely unknown. Chlamydomonas arl13 mutant cilia were characterized by both abnormal reduction and accumulation of select membrane-associated proteins. With respect to the latter, a similar set of proteins including phospholipase D (PLD) also accumulated in BBSome-deficient cilia. IFT and BBSome traffic were apparently normal in arl13. However, transport of PLD, which in control cells moves by BBSome-dependent IFT, was impaired in arl13, causing PLD to accumulate in cilia. ARL13 only rarely and transiently traveled by IFT, indicating that it is not a co-migrating adapter securing PLD to IFT trains. In conclusion, the loss of Chlamydomonas ARL13 impedes BBSome-dependent protein transport, resulting in overlapping biochemical defects in arl13 and bbs mutant cilia.
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Affiliation(s)
- Jin Dai
- Cellular Biology, University of Georgia, Athens, GA
| | - Gui Zhang
- Cellular Biology, University of Georgia, Athens, GA
| | | | | | | | - Bin Xue
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhen-Chuan Fan
- State Key Laboratory of Food Nutrition and Safety, Institute of Health Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | | | | | - Peiwei Liu
- College of Life Science, Shandong Normal University, Jinan, Shandong, China
| | - Karl Lechtreck
- Cellular Biology, University of Georgia, Athens, GA,Correspondence to Karl F. Lechtreck:
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Ahmad S, Strunk CH, Schott-Verdugo SN, Jaeger KE, Kovacic F, Gohlke H. Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity. J Chem Inf Model 2021; 61:5626-5643. [PMID: 34748335 DOI: 10.1021/acs.jcim.1c00973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PlaF is a cytoplasmic membrane-bound phospholipase A1 from Pseudomonas aeruginosa that alters the membrane glycerophospholipid (GPL) composition and fosters the virulence of this human pathogen. PlaF activity is regulated by a dimer-to-monomer transition followed by tilting of the monomer in the membrane. However, how substrates reach the active site and how the characteristics of the active site tunnels determine the activity, specificity, and regioselectivity of PlaF for natural GPL substrates have remained elusive. Here, we combined unbiased and biased all-atom molecular dynamics (MD) simulations and configurational free-energy computations to identify access pathways of GPL substrates to the catalytic center of PlaF. Our results map out a distinct tunnel through which substrates access the catalytic center. PlaF variants with bulky tryptophan residues in this tunnel revealed decreased catalysis rates due to tunnel blockage. The MD simulations suggest that GPLs preferably enter the active site with the sn-1 acyl chain first, which agrees with the experimentally demonstrated PLA1 activity of PlaF. We propose that the acyl chain-length specificity of PlaF is determined by the structural features of the access tunnel, which results in favorable free energy of binding of medium-chain GPLs. The suggested egress route conveys fatty acid (FA) products to the dimerization interface and, thus, contributes to understanding the product feedback regulation of PlaF by FA-triggered dimerization. These findings open up opportunities for developing potential PlaF inhibitors, which may act as antibiotics against P. aeruginosa.
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Affiliation(s)
- Sabahuddin Ahmad
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christoph Heinrich Strunk
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan N Schott-Verdugo
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,Centro de Bioinformática y Simulación Molecular (CBSM), Faculty of Engineering, University of Talca, 3460000 Talca, Chile.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute of Bio- and Geosciences (IBG-1: Biotechnology), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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Wu Q, Gao K, Zheng S, Zhu X, Liang Y, Pan J. Calmodulin regulates a TRP channel (ADF1) and phospholipase C (PLC) to mediate elevation of cytosolic calcium during acidic stress that induces deflagellation in
Chlamydomonas. FASEB J 2018; 32:3689-3699. [DOI: 10.1096/fj.201701396rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qiong Wu
- Ministry of Education (MOE) Key Laboratory of Protein SciencesTsinghua‐Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijingChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Kang Gao
- Hebei Key Laboratory of Molecular and Cellular BiologyCollege of Life ScienceHebei Normal UniversityShijiazhuangChina
| | - Shuzhi Zheng
- Hebei Key Laboratory of Molecular and Cellular BiologyCollege of Life ScienceHebei Normal UniversityShijiazhuangChina
| | - Xin Zhu
- Ministry of Education (MOE) Key Laboratory of Protein SciencesTsinghua‐Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijingChina
| | - Yinwen Liang
- Ministry of Education (MOE) Key Laboratory of Protein SciencesTsinghua‐Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijingChina
| | - Junmin Pan
- Ministry of Education (MOE) Key Laboratory of Protein SciencesTsinghua‐Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijingChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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Ranjan P, Kateriya S. Localization and dimer stability of a newly identified microbial rhodopsin from a polar, non-motile green algae. BMC Res Notes 2018; 11:65. [PMID: 29361974 PMCID: PMC5781313 DOI: 10.1186/s13104-018-3181-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/16/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The eukaryotic plasma membrane localized light-gated proton-pumping rhodopsins possesses great optogenetic applications for repolarization (silencing) of the neuronal activity simply by light illumination. Very few plasma membrane localized proton-pumping rhodopsins of a eukaryotic origin are known that have optogenetic potential. Our objective was to identify and characterize microbial rhodopsin of an eukaryotic origin that expresses on plasma membrane. The plasma membrane localized light-gated proton pump of an eukaryotic origin hold great promise to be used as an optogenetic tools for the neurobiology. RESULTS Here, we had characterized the cellular expression and membrane localization of a new rhodopsin in Antarctican algae Coccomyxa subellipsoidea. It is the first algal ion pumping rhodopsin that localizes to the plasma membrane of the eukaryotic cells. Coccomyxa subellipsoidea rhodopsin exists in the monomeric and dimeric state both the in vivo and in vitro. The dimeric form of the Coccomyxa subellipsoidea rhodopsin is resistant to heat and detergent denaturants.
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Affiliation(s)
- Peeyush Ranjan
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Suneel Kateriya
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India. .,School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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Ranjan P, Kashyap RS, Goel M, Veetil SK, Kateriya S. Cellular organelles facilitate dimerization of a newly identified Arf from Chlamydomonas reinhardtii. JOURNAL OF PHYCOLOGY 2014; 50:1137-1145. [PMID: 26988793 DOI: 10.1111/jpy.12245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 08/22/2014] [Indexed: 06/05/2023]
Abstract
GTPases of the Ras superfamily regulate a wide variety of cellular processes including vesicular transport and various secretory pathways of the cell. ADP - ribosylation factor (ARF) belongs to one of the five major families of the Ras superfamily and serves as an important component of vesicle formation and transport machinery of the cells. The binding of GTP to these Arfs and its subsequent hydrolysis, induces conformational changes in these proteins leading to their enzymatic activities. The dimeric form of Arf is associated with membrane pinch-off during vesicle formation. In this report, we have identified an arf gene from the unicellular green alga Chlamydomonas reinhardtii, CrArf, and showed that the oligomeric state of the protein in C. renhardtii is modulated by the cellular membrane environment of the organism. Protein cross-linking experiments showed that the purified recombinant CrArf has the ability to form a dimer. Both the 20-kDa monomeric and 40-kDa dimeric forms of CrArf were recognized from Chlamydomonas total cell lysate (CrTLC) and purified recombinant CrArf by the CrArf specific antibody. The membranous environment of the cell appeared to facilitate dimerization of the CrArf, as dimeric form was found exclusively associated with the membrane bound organelles. The subcellular localization studies in Chlamydomonas suggested that CrArf mainly localized in the cytosol and was mislocalized in vesicle transport machinery inhibitor treated cells. This research sheds light on the importance of the cellular membrane environment for regulating the oligomeric state of CrArf protein in this organism and associated functional role.
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Affiliation(s)
- Peeyush Ranjan
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Rudra Shankar Kashyap
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Manisha Goel
- Department of Biophysics, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Sindhu Kandoth Veetil
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Suneel Kateriya
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021, India
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Mikami K. Structural divergence and loss of phosphoinositide-specific phospholipase C signaling components during the evolution of the green plant lineage: implications from structural characteristics of algal components. FRONTIERS IN PLANT SCIENCE 2014; 5:380. [PMID: 25140171 PMCID: PMC4122161 DOI: 10.3389/fpls.2014.00380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/17/2014] [Indexed: 05/03/2023]
Affiliation(s)
- Koji Mikami
- Division of Marine Life Science, Genetics and Genomics, Faculty of Fisheries Sciences, Hokkaido UniversityHakodate, Japan
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Evolutionarily conserved residues at an oligomerization interface of the influenza A virus neuraminidase are essential for viral survival. Virology 2013; 447:32-44. [DOI: 10.1016/j.virol.2013.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 07/22/2013] [Accepted: 08/13/2013] [Indexed: 11/23/2022]
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Pokotylo I, Kolesnikov Y, Kravets V, Zachowski A, Ruelland E. Plant phosphoinositide-dependent phospholipases C: variations around a canonical theme. Biochimie 2013; 96:144-57. [PMID: 23856562 DOI: 10.1016/j.biochi.2013.07.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/04/2013] [Indexed: 01/01/2023]
Abstract
Phosphoinositide-specific phospholipase C (PI-PLC) cleaves, in a Ca(2+)-dependent manner, phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2) into diacylglycerol (DAG) and inositol triphosphate (IP3). PI-PLCs are multidomain proteins that are structurally related to the PI-PLCζs, the simplest animal PI-PLCs. Like these animal counterparts, they are only composed of EF-hand, X/Y and C2 domains. However, plant PI-PLCs do not have a conventional EF-hand domain since they are often truncated, while some PI-PLCs have no EF-hand domain at all. Despite this simple structure, plant PI-PLCs are involved in many essential plant processes, either associated with development or in response to environmental stresses. The action of PI-PLCs relies on the mediators they produce. In plants, IP3 does not seem to be the sole active soluble molecule. Inositol pentakisphosphate (IP5) and inositol hexakisphosphate (IP6) also transmit signals, thus highlighting the importance of coupling PI-PLC action with inositol-phosphate kinases and phosphatases. PI-PLCs also produce a lipid molecule, but plant PI-PLC pathways show a peculiarity in that the active lipid does not appear to be DAG but its phosphorylated form, phosphatidic acid (PA). Besides, PI-PLCs can also act by altering their substrate levels. Taken together, plant PI-PLCs show functional differences when compared to their animal counterparts. However, they act on similar general signalling pathways including calcium homeostasis and cell phosphoproteome. Several important questions remain unanswered. The cross-talk between the soluble and lipid mediators generated by plant PI-PLCs is not understood and how the coupling between PI-PLCs and inositol-kinases or DAG-kinases is carried out remains to be established.
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Affiliation(s)
- Igor Pokotylo
- Institute of Bioorganic Chemistry and Petrochemistry, NAS of Ukraine, Kiev, Ukraine.
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