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Zhang Z, Zhao Y, An T, Yu H, Bi X, Liu H, Xu Y, Yang Z, Chen Y, Wen J. Maize and Common Bean Seed Exudates Mediate Part of Nonhost Resistance to Phytophthora sojae Prior to Infection. PHYTOPATHOLOGY 2022; 112:335-344. [PMID: 34311549 DOI: 10.1094/phyto-05-21-0213-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Phytophthora sojae does not infect nonhost maize (Zea mays) but infects nonhost common bean (Phaseolus vulgaris) under inoculation. Soybean seed exudates participate in mediating host resistance to P. sojae before infection. This study aims to elucidate the role of seed exudates in mediating the nonhost resistance of maize and common bean to P. sojae before infection. The behaviors of P. sojae zoospores in response to the seed exudates were determined using an assay chamber and a concave slide. The proteomes of P. sojae zoospores in response to the seed exudates were analyzed with the tandem mass tag method. The key proteins were quantitatively verified by parallel reaction monitoring. Maize seed exudates exerted a repellent effect on zoospores of P. sojae. This result explains why zoospores sense repelling signaling molecules in maize seed exudates that weaken and strongly inhibit chemotaxis signals in the phosphatidylinositol signaling pathway and arachidonic acid metabolism pathway. Common bean seed exudates did not exhibit any attraction to the zoospores because the guanine nucleotide-binding protein signaling pathway, which is responsible for transmitting chemotactic signals, had no significant change. The proteins protecting the cell membrane structure were significantly downregulated, and the early apoptosis signal glutathione was enhanced in zoospores responding to common bean seed exudates, which resulted in dissolution of the cysts. Maize and common bean seed exudates mediate part of the nonhost resistance to P. sojae via different mechanisms before infection. The immunity of maize to P. sojae is caused by the repellent effect of maize seed exudates on zoospores. Common bean seed exudates participate in mediating nonhost resistance by dissolving the cysts.
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Affiliation(s)
- Zhuoqun Zhang
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yifan Zhao
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Tai An
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Han Yu
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xiangqi Bi
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Haixu Liu
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Ying Xu
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Zhiyue Yang
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yufei Chen
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jingzhi Wen
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin 150030, People's Republic of China
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2
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Kudryavtseva OA, Safina KR, Vakhrusheva OA, Logacheva MD, Penin AA, Neretina TV, Moskalenko VN, Glagoleva ES, Bazykin GA, Kondrashov AS. Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged Cultivation. Genome Biol Evol 2019; 11:2807-2817. [PMID: 31529025 PMCID: PMC6786475 DOI: 10.1093/gbe/evz194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2019] [Indexed: 12/02/2022] Open
Abstract
Podospora anserina is a model ascomycetous fungus which shows pronounced phenotypic senescence when grown on solid medium but possesses unlimited lifespan under submerged cultivation. In order to study the genetic aspects of adaptation of P. anserina to submerged cultivation, we initiated a long-term evolution experiment. In the course of the first 4 years of the experiment, 125 single-nucleotide substitutions and 23 short indels were fixed in eight independently evolving populations. Six proteins that affect fungal growth and development evolved in more than one population; in particular, in the G-protein alpha subunit FadA, new alleles fixed in seven out of eight experimental populations, and these fixations affected just four amino acid sites, which is an unprecedented level of parallelism in experimental evolution. Parallel evolution at the level of genes and pathways, an excess of nonsense and missense substitutions, and an elevated conservation of proteins and their sites where the changes occurred suggest that many of the observed fixations were adaptive and driven by positive selection.
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Affiliation(s)
- Olga A Kudryavtseva
- Department of Mycology and Phycology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ksenia R Safina
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Olga A Vakhrusheva
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Neretina
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- White Sea Biological Station, Lomonosov Moscow State University, Republic of Karelia, Russia
| | | | - Elena S Glagoleva
- Department of Plant Physiology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kondrashov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor
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Sprang SR. Invited review: Activation of G proteins by GTP and the mechanism of Gα-catalyzed GTP hydrolysis. Biopolymers 2016; 105:449-62. [PMID: 26996924 PMCID: PMC5319639 DOI: 10.1002/bip.22836] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/11/2016] [Accepted: 03/17/2016] [Indexed: 02/02/2023]
Abstract
This review addresses the regulatory consequences of the binding of GTP to the alpha subunits (Gα) of heterotrimeric G proteins, the reaction mechanism of GTP hydrolysis catalyzed by Gα and the means by which GTPase activating proteins (GAPs) stimulate the GTPase activity of Gα. The high energy of GTP binding is used to restrain and stabilize the conformation of the Gα switch segments, particularly switch II, to afford stable complementary to the surfaces of Gα effectors, while excluding interaction with Gβγ, the regulatory binding partner of GDP-bound Gα. Upon GTP hydrolysis, the energy of these conformational restraints is dissipated and the two switch segments, particularly switch II, become flexible and are able to adopt a conformation suitable for tight binding to Gβγ. Catalytic site pre-organization presents a significant activation energy barrier to Gα GTPase activity. The glutamine residue near the N-terminus of switch II (Glncat ) must adopt a conformation in which it orients and stabilizes the γ phosphate and the water nucleophile for an in-line attack. The transition state is probably loose with dissociative character; phosphoryl transfer may be concerted. The catalytic arginine in switch I (Argcat ), together with amide hydrogen bonds from the phosphate binding loop, stabilize charge at the β-γ bridge oxygen of the leaving group. GAPs that harbor "regulator of protein signaling" (RGS) domains, or structurally unrelated domains within G protein effectors that function as GAPs, accelerate catalysis by stabilizing the pre-transition state for Gα-catalyzed GTP hydrolysis, primarily by restraining Argcat and Glncat to their catalytic conformations. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 449-462, 2016.
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Affiliation(s)
- Stephen R. Sprang
- Center for Biomolecular Structure and Dynamics, Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, Telephone: (406) 243-6028, Fax: (406) 243-6024,
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4
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Abstract
Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.
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Dror RO, Mildorf TJ, Hilger D, Manglik A, Borhani DW, Arlow DH, Philippsen A, Villanueva N, Yang Z, Lerch MT, Hubbell WL, Kobilka BK, Sunahara RK, Shaw DE. SIGNAL TRANSDUCTION. Structural basis for nucleotide exchange in heterotrimeric G proteins. Science 2015; 348:1361-5. [PMID: 26089515 DOI: 10.1126/science.aaa5264] [Citation(s) in RCA: 208] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
G protein-coupled receptors (GPCRs) relay diverse extracellular signals into cells by catalyzing nucleotide release from heterotrimeric G proteins, but the mechanism underlying this quintessential molecular signaling event has remained unclear. Here we use atomic-level simulations to elucidate the nucleotide-release mechanism. We find that the G protein α subunit Ras and helical domains-previously observed to separate widely upon receptor binding to expose the nucleotide-binding site-separate spontaneously and frequently even in the absence of a receptor. Domain separation is necessary but not sufficient for rapid nucleotide release. Rather, receptors catalyze nucleotide release by favoring an internal structural rearrangement of the Ras domain that weakens its nucleotide affinity. We use double electron-electron resonance spectroscopy and protein engineering to confirm predictions of our computationally determined mechanism.
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Affiliation(s)
- Ron O Dror
- D. E. Shaw Research, New York, NY 10036, USA.
| | | | - Daniel Hilger
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | - Nicolas Villanueva
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Michael T Lerch
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger K Sunahara
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David E Shaw
- D. E. Shaw Research, New York, NY 10036, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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6
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Ren J, Li XR, Liu PC, Cai MJ, Liu W, Wang JX, Zhao XF. G-protein αq participates in the steroid hormone 20-hydroxyecdysone nongenomic signal transduction. J Steroid Biochem Mol Biol 2014; 144 Pt B:313-23. [PMID: 25125388 DOI: 10.1016/j.jsbmb.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 08/02/2014] [Accepted: 08/08/2014] [Indexed: 11/22/2022]
Abstract
The nuclear receptor-mediated genomic pathways of the animal steroid hormones are well known. However, the cell membrane receptor-mediated nongenomic pathways of the animal steroid hormones are little understood. In this study, we report the participation of a G-protein alpha q (Gαq)(1) subunit in the 20E nongenomic pathway in the cell membrane and regulating gene expression during molting and metamorphosis in a lepidopteran insect, Helicoverpa armigera. 20E-induced phosphorylation of Gαq was detected using two-dimensional electrophoresis techniques. Knockdown of Gαq by injecting double-stranded RNA suppressed the development of larvae, delayed metamorphosis, and inhibited 20E-induced gene expression. Gαq was distributed throughout the cell, and migrated toward the plasma membrane upon 20E induction. Gαq was necessary in the 20E-induced intracellular Ca(2+) release and extracellular Ca(2+) influx. The protein kinase C (PKC) inhibitor could repress 20E-induced phosphorylation of cyclin-dependent kinase 10 (CDK10) and transcription factor ultraspiracle (USP1). PKC inhibitor could repress the Gαq phosphorylation and membrane trafficking. These results suggest that Gαq participates in 20E signaling in the cell membrane at the pre-genomic stage by modulating the increase of the intracellular Ca(2+) and phosphorylation of CDK10 and USP1 in 20E transcription complex to regulate gene transcription.
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Affiliation(s)
- Jing Ren
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Xiang-Ru Li
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Peng-Cheng Liu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Mei-Juan Cai
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Wen Liu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jin-Xing Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
| | - Xiao-Fan Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China.
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7
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Yao XQ, Grant BJ. Domain-opening and dynamic coupling in the α-subunit of heterotrimeric G proteins. Biophys J 2014; 105:L08-10. [PMID: 23870276 DOI: 10.1016/j.bpj.2013.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 06/03/2013] [Accepted: 06/05/2013] [Indexed: 11/30/2022] Open
Abstract
Heterotrimeric G proteins are conformational switches that turn on intracellular signaling cascades in response to the activation of G-protein-coupled receptors. Receptor activation by extracellular stimuli promotes a cycle of GTP binding and hydrolysis on the G protein α-subunit (Gα). Important conformational transitions occurring during this cycle have been characterized from extensive crystallographic studies of Gα. However, the link between the observed conformations and the mechanisms involved in G-protein activation and effector interaction remain unclear. Here we describe a comprehensive principal component analysis of available Gα crystallographic structures supplemented with extensive unbiased conventional and accelerated molecular dynamics simulations that together characterize the response of Gα to GTP binding and hydrolysis. Our studies reveal details of activating conformational changes as well as the intrinsic flexibility of the α-helical domain that includes a large-scale 60° domain opening under nucleotide-free conditions. This result is consistent with the recently reported open crystal structure of Gs, the stimulatory G protein for adenylyl cyclase, in complex with the α2 adrenergic receptor. Sets of unique interactions potentially important for the conformational transition are also identified. Moreover simulations reveal nucleotide-dependent dynamical couplings of distal regions and residues potentially important for the allosteric link between functional sites.
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Affiliation(s)
- Xin-Qiu Yao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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8
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Musiani F, Ippoliti E, Micheletti C, Carloni P, Ciurli S. Conformational fluctuations of UreG, an intrinsically disordered enzyme. Biochemistry 2013; 52:2949-54. [PMID: 23560717 DOI: 10.1021/bi4001744] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
UreG proteins are small GTP binding (G) proteins that catalyze the hydrolysis of GTP necessary for the maturation of urease, a virulence factor in bacterial pathogenesis. UreG proteins are the first documented cases of intrinsically disordered enzymes. The comprehension of the dynamics of folding-unfolding events occurring in this protein could shed light on the enzymatic mechanism of UreG. Here, we used the recently developed replica exchange with solute tempering (REST2) computational methodology to explore the conformational space of UreG from Helicobacter pylori (HpUreG) and to identify its structural fluctuations. The same simulation and analysis protocol has been applied to HypB from Methanocaldococcus jannaschii (MjHypB), which is closely related to UreG in both sequence and function, even though it is not intrinsically disordered. A comparison of the two systems reveals that both HpUreG and MjHypB feature a substantial rigidity of the protein regions involved in catalysis, justifying its residual catalytic activity. On the other hand, HpUreG tends to unfold more than MjHypB in portions involved in protein-protein interactions with metallochaperones necessary for the formation of multiprotein complexes known to be involved in urease activation.
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Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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9
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Slater D, Kunnathil S, McBride J, Koppala R. Pharmacology of nonsteroidal antiinflammatory drugs and opioids. Semin Intervent Radiol 2012; 27:400-11. [PMID: 22550382 DOI: 10.1055/s-0030-1267855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chronic pain affects up to 50 million Americans every day. Traditional treatment has included acetaminophen, nonsteroidal antiinflammatory drugs (NSAIDs), or opioids. The combination of NSAIDs and opioids can provide effective treatment for up to 90% of patients with chronic pain, but the NSAIDs have the potential for significant, even life-threatening side effects. Additionally, the nonselective cyclooxygenase inhibitors with 16,000 deaths per year in the United States might not be any safer. The opioids are great for short-term pain, but may need to be adjusted or changed frequently due to the development of tolerance. Understanding of the mechanism of opioids and NSAIDs has improved greatly over the past decade, but is still incomplete.
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Affiliation(s)
- Dick Slater
- Department of Radiology, University of Nebraska Medical Center, Omaha, Nebraska
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10
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Schmittel M, De S, Pramanik S. Reversible ON/OFF Nanoswitch for Organocatalysis: Mimicking the Locking and Unlocking Operation of CaMKII. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108089] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Schmittel M, De S, Pramanik S. Reversible ON/OFF Nanoswitch for Organocatalysis: Mimicking the Locking and Unlocking Operation of CaMKII. Angew Chem Int Ed Engl 2012; 51:3832-6. [DOI: 10.1002/anie.201108089] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/13/2012] [Indexed: 11/11/2022]
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Abstract
With the emerging new crystal structures of G-protein coupled receptors (GPCRs), the number of reported in silico receptor models vastly increases every year. The use of these models in lead optimization (LO) is investigated here. Although there are many studies where GPCR models are used to identify new chemotypes by virtual screening, the classical application in LO is rarely reported. The reason for this may be that the quality of a model, which is appropriate for atomistic modeling, must be very high, and the biology of GPCR ligand-dependent signaling is still not fully understood. However, the few reported studies show that GPCR models can be used efficiently in LO for various problems, such as affinity optimization or tuning of physicochemical parameters.
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13
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Louet M, Perahia D, Martinez J, Floquet N. A concerted mechanism for opening the GDP binding pocket and release of the nucleotide in hetero-trimeric G-proteins. J Mol Biol 2011; 411:298-312. [PMID: 21663745 DOI: 10.1016/j.jmb.2011.05.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 05/14/2011] [Accepted: 05/20/2011] [Indexed: 11/26/2022]
Abstract
G-protein hetero-trimers play a fundamental role in cell function. Their dynamic behavior at the atomic level remains to be understood. We have studied the Gi hetero-trimer through a combination of molecular dynamics simulations and normal mode analyses. We showed that these big proteins could undergo large-amplitude conformational changes, without any energy penalty and with an intrinsic dynamics centered on their GDP binding pocket. Among the computed collective motions, one of the modes (mode 17) was particularly able to significantly open both the base and the phosphate sides of the GDP binding pocket. This mode describing mainly a motion between the Ras-like and the helical domains of G(α) was in close agreement with some available X-ray data and with many other biochemical/biophysical observations including the kink of helix α5. The use of a new protocol, which allows extraction of the GDP ligand along the computed normal modes, supported that the exit of GDP was largely coupled to an opening motion along mode 17. We propose for the first time a "concerted mechanism" model in which the opening of the GDP pocket and the kink of the α5 helix occur concomitantly and favor GDP release from G(αβγ) complexes. This model is discussed in the context of the G-protein-coupled receptor/G-protein interaction close to the cell membrane.
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Affiliation(s)
- Maxime Louet
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université Montpellier 1-Université Montpellier 2, Faculté de Pharmacie, 15 Avenue Charles Flahault, BP 14491, 34093 Montpellier Cedex 05, France
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14
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Park MS, Smrcka AV, Stern HA. Conformational flexibility and binding interactions of the G protein βγ heterodimer. Proteins 2011; 79:518-27. [PMID: 21064128 DOI: 10.1002/prot.22899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Previous NMR experiments on unbound G protein βγ heterodimer suggested that particular residues in the binding interface are mobile on the nanosecond timescale. In this work we performed nanosecond-timescale molecular dynamics simulations to investigate conformational changes and dynamics of Gβγ in the presence of several binding partners: a high-affinity peptide (SIGK), phosducin, and the GDP-bound α subunit. In these simulations, the high mobility of GβW99 was reduced by SIGK, and it appeared that a tyrosine might stabilize GβW99 by hydrophobic or aromatic stacking interactions in addition to hydrogen bonds. Simulations of the phosducin-Gβγ complex showed that the mobility of GβW99 was restricted, consistent with inferences from NMR. However, large-scale conformational changes of Gβγ due to binding, which were hypothesized in the NMR study, were not observed in the simulations, most likely due to their short (nanosecond) duration. A pocket consisting of hydrophobic amino acids on Gα appears to restrict GβW99 mobility in the crystal structure of the Gαβγ? heterotrimer. The simulation trajectories are consistent with this idea. However, local conformational changes of residues GβW63, GβW211, GβW297, GβW332, and GβW339 were detected during the MD simulations. As expected, the magnitude of atomic fluctuations observed in simulations was greater for α than for the βγ subunits, suggesting that α has greater flexibility. These observations support the notion that to maintain the high mobility of GβW99 observed by solution NMR requires that the Gβ-α interface must open up on time scale longer than can be observed in nanosecond scale simulations.
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Affiliation(s)
- Min-Sun Park
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
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15
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Massarsky A, Trudeau VL, Moon TW. β-blockers as endocrine disruptors: the potential effects of human β-blockers on aquatic organisms. ACTA ACUST UNITED AC 2011; 315:251-65. [DOI: 10.1002/jez.672] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 12/15/2010] [Accepted: 02/01/2011] [Indexed: 12/12/2022]
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16
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Prado-Prado F, García-Mera X, Abeijón P, Alonso N, Caamaño O, Yáñez M, Gárate T, Mezo M, González-Warleta M, Muiño L, Ubeira FM, González-Díaz H. Using entropy of drug and protein graphs to predict FDA drug-target network: theoretic-experimental study of MAO inhibitors and hemoglobin peptides from Fasciola hepatica. Eur J Med Chem 2011; 46:1074-94. [PMID: 21315497 DOI: 10.1016/j.ejmech.2011.01.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 01/10/2011] [Accepted: 01/13/2011] [Indexed: 12/11/2022]
Abstract
There are many drugs described with very different affinity to a large number of receptors. In this work, we selected Drug-Target pairs (DTPs/nDTPs) of drugs with high affinity/non-affinity for different targets like proteins. Quantitative Structure-Activity Relationships (QSAR) models become a very useful tool in this context to substantially reduce time and resources consuming experiments. Unfortunately, most QSAR models predict activity against only one protein. To solve this problem, we developed here a multi-target QSAR (mt-QSAR) classifier using the MARCH-INSIDE technique to calculate structural parameters of drug and target plus one Artificial Neuronal Network (ANN) to seek the model. The best ANN model found is a Multi-Layer Perceptron (MLP) with profile MLP 32:32-15-1:1. This MLP classifies correctly 623 out of 678 DTPs (Sensitivity = 91.89%) and 2995 out of 3234 nDTPs (Specificity = 92.61%), corresponding to training Accuracy = 92.48%. The validation of the model was carried out by means of external predicting series. The model classifies correctly 313 out of 338 DTPs (Sensitivity = 92.60%) and 1411 out of 1534 nDTP (Specificity = 91.98%) in validation series, corresponding to total Accuracy = 92.09% for validation series (Predictability). This model favorably compares with other LDA and ANN models developed in this work and Machine Learning classifiers published before to address the same problem in different aspects. These mt-QSARs offer also a good opportunity to construct drug-protein Complex Networks (CNs) that can be used to explore large and complex drug-protein receptors databases. Finally, we illustrated two practical uses of this model with two different experiments. In experiment 1, we report prediction, synthesis, characterization, and MAO-A and MAO-B pharmacological assay of 10 rasagiline derivatives promising for anti-Parkinson drug design. In experiment 2, we report sampling, parasite culture, SEC and 1DE sample preparation, MALDI-TOF MS and MS/MS analysis, MASCOT search, MM/MD 3D structure modeling, and QSAR prediction for different peptides of hemoglobin found in the proteome of the human parasite Fasciola hepatica; which is promising for anti-parasite drug targets discovery.
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Khafizov K. GoLoco motif proteins binding to Galpha(i1): insights from molecular simulations. J Mol Model 2009; 15:1491-9. [PMID: 19437048 PMCID: PMC2847169 DOI: 10.1007/s00894-009-0516-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 04/01/2009] [Indexed: 11/30/2022]
Abstract
Molecular dynamics simulations, computational alanine scanning and sequence analysis were used to investigate the structural properties of the Gαi1/GoLoco peptide complex. Using these methodologies, binding of the GoLoco motif peptide to the Gαi1 subunit was found to restrict the relative movement of the helical and catalytic domains in the Gαi1 subunit, which is in agreement with a proposed mechanism of GDP dissociation inhibition by GoLoco motif proteins. In addition, the results provide further insights into the role of the “Switch IV” region located within the helical domain of Gα, the conformation of which might be important for interactions with various Gα partners.
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Affiliation(s)
- Kamil Khafizov
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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