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GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation. Comput Biol Chem 2023; 104:107835. [PMID: 36893567 DOI: 10.1016/j.compbiolchem.2023.107835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/01/2023] [Accepted: 02/16/2023] [Indexed: 03/05/2023]
Abstract
Functional interaction of Ras signaling proteins with upstream, negative regulatory GTPase activating proteins (GAPs) represents a crucial step in cellular decision making related to growth and survival. Key components of the catalytic transition state for Ras deactivation by GAP-accelerated hydrolysis of Ras-bound guanosine triphosphate (GTP) are thought to include an arginine residue from the GAP (the arginine finger), a glutamine residue from Ras (Q61), and a water molecule that is likely coordinated by Q61 to engage in nucleophilic attack on GTP. Here, we use in-vitro fluorescence experiments to show that 0.1-100 mM concentrations of free arginine, imidazole, and other small nitrogenous molecule fail to accelerate GTP hydrolysis, even in the presence of the catalytic domain of a mutant GAP lacking its arginine finger (R1276A NF1). This result is surprising given that imidazole can chemically rescue enzyme activity in arginine-to-alanine mutant protein tyrosine kinases (PTKs) that share many active site components with Ras/GAP complexes. Complementary all-atom molecular dynamics (MD) simulations reveal that an arginine finger GAP mutant still functions to enhance Ras Q61-GTP interaction, though less extensively than wild-type GAP. This increased Q61-GTP proximity may promote more frequent fluctuations into configurations that enable GTP hydrolysis as a component of the mechanism by which GAPs accelerate Ras deactivation in the face of arginine finger mutations. The failure of small molecule analogs of arginine to chemically rescue catalytic deactivation of Ras is consistent with the idea that the influence of the GAP goes beyond the simple provision of its arginine finger. However, the failure of chemical rescue in the presence of R1276A NF1 suggests that the GAPs arginine finger is either unsusceptible to rescue due to exquisite positioning or that it is involved in complex multivalent interactions. Therefore, in the context of oncogenic Ras proteins with mutations at codons 12 or 13 that inhibit arginine finger penetration toward GTP, drug-based chemical rescue of GTP hydrolysis may have bifunctional chemical/geometric requirements that are more difficult to satisfy than those that result from arginine-to-alanine mutations in other enzymes for which chemical rescue has been demonstrated.
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Kozlova MI, Shalaeva DN, Dibrova DV, Mulkidjanian AY. Common Patterns of Hydrolysis Initiation in P-loop Fold Nucleoside Triphosphatases. Biomolecules 2022; 12:biom12101345. [PMID: 36291554 PMCID: PMC9599529 DOI: 10.3390/biom12101345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/20/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
The P-loop fold nucleoside triphosphate (NTP) hydrolases (also known as Walker NTPases) function as ATPases, GTPases, and ATP synthases, are often of medical importance, and represent one of the largest and evolutionarily oldest families of enzymes. There is still no consensus on their catalytic mechanism. To clarify this, we performed the first comparative structural analysis of more than 3100 structures of P-loop NTPases that contain bound substrate Mg-NTPs or their analogues. We proceeded on the assumption that structural features common to these P-loop NTPases may be essential for catalysis. Our results are presented in two articles. Here, in the first, we consider the structural elements that stimulate hydrolysis. Upon interaction of P-loop NTPases with their cognate activating partners (RNA/DNA/protein domains), specific stimulatory moieties, usually Arg or Lys residues, are inserted into the catalytic site and initiate the cleavage of gamma phosphate. By analyzing a plethora of structures, we found that the only shared feature was the mechanistic interaction of stimulators with the oxygen atoms of gamma-phosphate group, capable of causing its rotation. One of the oxygen atoms of gamma phosphate coordinates the cofactor Mg ion. The rotation must pull this oxygen atom away from the Mg ion. This rearrangement should affect the properties of the other Mg ligands and may initiate hydrolysis according to the mechanism elaborated in the second article.
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Affiliation(s)
- Maria I. Kozlova
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Daria N. Shalaeva
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Daria V. Dibrova
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Armen Y. Mulkidjanian
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
- Center of Cellular Nanoanalytics, Osnabrueck University, D-49069 Osnabrueck, Germany
- Correspondence: ; Tel.: +49-541-969-2698
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The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors. Nat Commun 2021; 12:6274. [PMID: 34725361 PMCID: PMC8560773 DOI: 10.1038/s41467-021-26526-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/23/2021] [Indexed: 12/31/2022] Open
Abstract
Cancer cells bearing distinct KRAS mutations exhibit variable sensitivity to SHP2 inhibitors (SHP2i). Here we show that cells harboring KRAS Q61H are uniquely resistant to SHP2i, and investigate the underlying mechanisms using biophysics, molecular dynamics, and cell-based approaches. Q61H mutation impairs intrinsic and GAP-mediated GTP hydrolysis, and impedes activation by SOS1, but does not alter tyrosyl phosphorylation. Wild-type and Q61H-mutant KRAS are both phosphorylated by Src on Tyr32 and Tyr64 and dephosphorylated by SHP2, however, SHP2i does not reduce ERK phosphorylation in KRAS Q61H cells. Phosphorylation of wild-type and Gly12-mutant KRAS, which are associated with sensitivity to SHP2i, confers resistance to regulation by GAP and GEF activities and impairs binding to RAF, whereas the near-complete GAP/GEF-resistance of KRAS Q61H remains unaltered, and high-affinity RAF interaction is retained. SHP2 can stimulate KRAS signaling by modulating GEF/GAP activities and dephosphorylating KRAS, processes that fail to regulate signaling of the Q61H mutant. SHP2 promotes RAS-driven MAPK signalling, but it is unclear why cancer cells with distinct KRAS mutations exhibit differential sensitivity to SHP2 inhibition. Here the authors show that KRAS Q61H is decoupled from SHP2- mediated upstream regulation, thus Q61H pancreatic cancer cells maintain MAPK signalling and are refractory to SHP2 inhibitors.
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4
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Abstract
As a member of small GTPase family, KRAS protein is a key physiological modulator of various cellular activities including proliferation. However, mutations of KRAS present in numerous cancer types, most frequently in pancreatic (> 60%), colorectal (> 40%), and lung cancers, drive oncogenic processes through overactivation of proliferation. The G12C mutation of KRAS protein is especially abundant in the case of these types of malignancies. Despite its key importance in human disease, KRAS was assumed to be non-druggable for a long time since the protein seemingly lacks potential drug-binding pockets except the nucleotide-binding site, which is difficult to be targeted due to the high affinity of KRAS for both GDP and GTP. Recently, a new approach broke the ice and provided evidence that upon covalent targeting of the G12C mutant KRAS, a highly dynamic pocket was revealed. This novel targeting is especially important since it serves with an inherent solution for drug selectivity. Based on these results, various structure-based drug design projects have been launched to develop selective KRAS mutant inhibitors. In addition to the covalent modification strategy mostly applicable for G12C mutation, different innovative solutions have been suggested for the other frequently occurring oncogenic G12 mutants. Here we summarize the latest advances of this field, provide perspectives for novel approaches, and highlight the special properties of KRAS, which might issue some new challenges.
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Affiliation(s)
- Kinga Nyíri
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, 1111, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary.
| | - Gergely Koppány
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, 1111, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, 1111, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary.
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5
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Kumar SU, Priya Doss CG. Residue interaction networks of K-Ras protein with water molecules identifies the potential role of switch II and P-loop. Comput Biol Med 2021; 135:104597. [PMID: 34237589 DOI: 10.1016/j.compbiomed.2021.104597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/01/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023]
Abstract
The mutant K-Ras with aberrant signaling is the primary cause of several cancers. The proposed study investigated the influence of water molecules in K-Ras crystal structure, where they have a significant function by understanding their residue interaction networks (RINs). We analyzed the RINs of K-Ras with and without water molecules and determined their interaction properties. RINs were developed with the help of StructureViz2 and RINspector; further, the changes in K-Ras backbone flexibility were predicted with the DynaMine. We found that the residues K42, I142, and L159 are the hotspots from water, including the K-Ras-GTP complex with the highest residue centrality analysis (RCA) Z-score. The DynaMine prediction calculated the NMR S2 value for the frequently mutated positions G12, G13, and Q61 showing a minor shift in flexibility, which make up the P-Loop and switch II of the K-Ras protein. This flexibility shift can account for changes in conformational activity and the protein's GTPase activity, making it difficult to recognize by the effectors and exchange factors. Taken together, our study helps in understanding the functional importance of the water molecules in K-Ras protein and the impact of mutation that modulate the conformational state of the protein.
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Affiliation(s)
- S Udhaya Kumar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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6
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Ras Isoforms from Lab Benches to Lives-What Are We Missing and How Far Are We? Int J Mol Sci 2021; 22:ijms22126508. [PMID: 34204435 PMCID: PMC8233758 DOI: 10.3390/ijms22126508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/21/2022] Open
Abstract
The central protein in the oncogenic circuitry is the Ras GTPase that has been under intense scrutiny for the last four decades. From its discovery as a viral oncogene and its non-oncogenic contribution to crucial cellular functioning, an elaborate genetic, structural, and functional map of Ras is being created for its therapeutic targeting. Despite decades of research, there still exist lacunae in our understanding of Ras. The complexity of the Ras functioning is further exemplified by the fact that the three canonical Ras genes encode for four protein isoforms (H-Ras, K-Ras4A, K-Ras4B, and N-Ras). Contrary to the initial assessment that the H-, K-, and N-Ras isoforms are functionally similar, emerging data are uncovering crucial differences between them. These Ras isoforms exhibit not only cell-type and context-dependent functions but also activator and effector specificities on activation by the same receptor. Preferential localization of H-, K-, and N-Ras in different microdomains of the plasma membrane and cellular organelles like Golgi, endoplasmic reticulum, mitochondria, and endosome adds a new dimension to isoform-specific signaling and diverse functions. Herein, we review isoform-specific properties of Ras GTPase and highlight the importance of considering these towards generating effective isoform-specific therapies in the future.
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Wang Y, Ji D, Lei C, Chen Y, Qiu Y, Li X, Li M, Ni D, Pu J, Zhang J, Fu Q, Liu Y, Lu S. Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins. Comput Struct Biotechnol J 2021; 19:1184-1199. [PMID: 33680360 PMCID: PMC7902900 DOI: 10.1016/j.csbj.2021.01.044] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ras undergoes interconversion between the active GTP-bound state and the inactive GDP-bound state. This GTPase cycle, which controls the activities of Ras, is accelerated by Ras GTPase-activating proteins (GAPs) and guanine nucleotide exchange factors (SOS). Oncogenic Ras mutations could affect the GTPase cycle and impair Ras functions. Additionally, Src-induced K-Ras Y32/64 dual phosphorylation has been reported to disrupt GTPase cycle and hinder Ras downstream signaling. However, the underlying mechanisms remain unclear. To address this, we performed molecular dynamics simulations (~30 μs in total) on unphosphorylated and phosphorylated K-Ras4B in GTP- and GDP-bound states, and on their complexes with GTPase cycle regulators (GAP and SOS) and the effector protein Raf. We found that K-Ras4B dual phosphorylation mainly alters the conformation at the nucleotide binding site and creates disorder at the catalytic site, resulting in the enlargement of GDP binding pocket and the retard of Ras-GTP intrinsic hydrolysis. We observed phosphorylation-induced shift in the distribution of Ras-GTP inactive-active sub-states and recognized potential druggable pockets in the phosphorylated Ras-GTP. Moreover, decreased catalytic competence or signal delivery abilities due to reduced binding affinities and/or distorted catalytic conformations of GAP, SOS and Raf were observed. In addition, the allosteric pathway from Ras/Raf interface to the distal Raf L4 loop was compromised by Ras phosphorylation. These results reveal the mechanisms by which phosphorylation influences the intrinsic or GAP/SOS catalyzed transformations between GTP- and GDP-bound states of Ras and its signal transduction to Raf. Our findings project Ras phosphorylation as a target for cancer drug discovery.
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Affiliation(s)
- Yuanhao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Dong Ji
- Department of Anesthesiology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, China
| | - Chaoyu Lei
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yingfei Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yuran Qiu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Xinyi Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Duan Ni
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- The Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Jun Pu
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200120, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Qiang Fu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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8
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Riccardi C, Perrone L, Napolitano F, Sampaolo S, Melone MAB. Understanding the Biological Activities of Vitamin D in Type 1 Neurofibromatosis: New Insights into Disease Pathogenesis and Therapeutic Design. Cancers (Basel) 2020; 12:E2965. [PMID: 33066259 PMCID: PMC7602022 DOI: 10.3390/cancers12102965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/18/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Vitamin D is a fat-soluble steroid hormone playing a pivotal role in calcium and phosphate homeostasis as well as in bone health. Vitamin D levels are not exclusively dependent on food intake. Indeed, the endogenous production-occurring in the skin and dependent on sun exposure-contributes to the majority amount of vitamin D present in the body. Since vitamin D receptors (VDRs) are ubiquitous and drive the expression of hundreds of genes, the interest in vitamin D has tremendously grown and its role in different diseases has been extensively studied. Several investigations indicated that vitamin D action extends far beyond bone health and calcium metabolism, showing broad effects on a variety of critical illnesses, including cancer, infections, cardiovascular and autoimmune diseases. Epidemiological studies indicated that low circulating vitamin D levels inversely correlate with cutaneous manifestations and bone abnormalities, clinical hallmarks of neurofibromatosis type 1 (NF1). NF1 is an autosomal dominant tumour predisposition syndrome causing significant pain and morbidity, for which limited treatment options are available. In this context, vitamin D or its analogues have been used to treat both skin and bone lesions in NF1 patients, alone or combined with other therapeutic agents. Here we provide an overview of vitamin D, its characteristic nutritional properties relevant for health benefits and its role in NF1 disorder. We focus on preclinical and clinical studies that demonstrated the clinical correlation between vitamin D status and NF1 disease, thus providing important insights into disease pathogenesis and new opportunities for targeted therapy.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy;
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
| | - Lorena Perrone
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
| | - Filomena Napolitano
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
| | - Simone Sampaolo
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
| | - Mariarosa Anna Beatrice Melone
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini 5, I-80131 Naples, Italy; (L.P.); (F.N.); (S.S.)
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Temple University, BioLife Building (015-00), 1900 North 12th Street, Philadelphia, PA 19122-6078, USA
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9
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Harrell Stewart DR, Clark GJ. Pumping the brakes on RAS - negative regulators and death effectors of RAS. J Cell Sci 2020; 133:133/3/jcs238865. [PMID: 32041893 DOI: 10.1242/jcs.238865] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mutations that activate the RAS oncoproteins are common in cancer. However, aberrant upregulation of RAS activity often occurs in the absence of activating mutations in the RAS genes due to defects in RAS regulators. It is now clear that loss of function of Ras GTPase-activating proteins (RasGAPs) is common in tumors, and germline mutations in certain RasGAP genes are responsible for some clinical syndromes. Although regulation of RAS is central to their activity, RasGAPs exhibit great diversity in their binding partners and therefore affect signaling by multiple mechanisms that are independent of RAS. The RASSF family of tumor suppressors are essential to RAS-induced apoptosis and senescence, and constitute a barrier to RAS-mediated transformation. Suppression of RASSF protein expression can also promote the development of excessive RAS signaling by uncoupling RAS from growth inhibitory pathways. Here, we will examine how these effectors of RAS contribute to tumor suppression, through both RAS-dependent and RAS-independent mechanisms.
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Affiliation(s)
- Desmond R Harrell Stewart
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY 40222, USA
| | - Geoffrey J Clark
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY 40222, USA
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10
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Miningou N, Blackwell KT. The road to ERK activation: Do neurons take alternate routes? Cell Signal 2020; 68:109541. [PMID: 31945453 DOI: 10.1016/j.cellsig.2020.109541] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 01/11/2020] [Accepted: 01/12/2020] [Indexed: 01/29/2023]
Abstract
The ERK cascade is a central signaling pathway that regulates a wide variety of cellular processes including proliferation, differentiation, learning and memory, development, and synaptic plasticity. A wide range of inputs travel from the membrane through different signaling pathway routes to reach activation of one set of output kinases, ERK1&2. The classical ERK activation pathway beings with growth factor activation of receptor tyrosine kinases. Numerous G-protein coupled receptors and ionotropic receptors also lead to ERK through increases in the second messengers calcium and cAMP. Though both types of pathways are present in diverse cell types, a key difference is that most stimuli to neurons, e.g. synaptic inputs, are transient, on the order of milliseconds to seconds, whereas many stimuli acting on non-neural tissue, e.g. growth factors, are longer duration. The ability to consolidate these inputs to regulate the activation of ERK in response to diverse signals raises the question of which factors influence the difference in ERK activation pathways. This review presents both experimental studies and computational models aimed at understanding the control of ERK activation and whether there are fundamental differences between neurons and other cells. Our main conclusion is that differences between cell types are quite subtle, often related to differences in expression pattern and quantity of some molecules such as Raf isoforms. In addition, the spatial location of ERK is critical, with regulation by scaffolding proteins producing differences due to colocalization of upstream molecules that may differ between neurons and other cells.
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Affiliation(s)
- Nadiatou Miningou
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, VA 22030, United States of America
| | - Kim T Blackwell
- Interdisciplinary Program in Neuroscience and Bioengineering Department, George Mason University, Fairfax, VA 22030, United States of America.
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11
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Calixto AR, Moreira C, Pabis A, Kötting C, Gerwert K, Rudack T, Kamerlin SCL. GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases. J Am Chem Soc 2019; 141:10684-10701. [PMID: 31199130 DOI: 10.1021/jacs.9b03193] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the Gαi subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H2PO4- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.
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Affiliation(s)
- Ana R Calixto
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Cátia Moreira
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Anna Pabis
- Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 , Uppsala , Sweden
| | - Carsten Kötting
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Klaus Gerwert
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Till Rudack
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Shina C L Kamerlin
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
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12
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Guo P, Driver D, Zhao Z, Zheng Z, Chan C, Cheng X. Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality. ACS NANO 2019; 13:6207-6223. [PMID: 31067030 PMCID: PMC6595433 DOI: 10.1021/acsnano.8b08849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nanomotors in nanotechnology are as important as engines in daily life. Many ATPases are nanoscale biomotors classified into three categories based on the motion mechanisms in transporting substrates: linear, rotating, and the recently discovered revolving motion. Most biomotors adopt a multisubunit ring-shaped structure that hydrolyzes ATP to generate force. How these biomotors control the motion direction and regulate the sequential action of their multiple subunits is intriguing. Many ATPases are hexameric with each monomer containing a conserved arginine finger. This review focuses on recent findings on how the arginine finger controls motion direction and coordinates adjacent subunit interactions in both revolving and rotating biomotors. Mechanisms of intersubunit interactions and sequential movements of individual subunits are evidenced by the asymmetrical appearance of one dimer and four monomers in high-resolution structural complexes. The arginine finger is situated at the interface of two subunits and extends into the ATP binding pocket of the downstream subunit. An arginine finger mutation results in deficiency in ATP binding/hydrolysis, substrate binding, and transport, highlighting the importance of the arginine finger in regulating energy transduction and motor function. Additionally, the roles of channel chirality and channel size are discussed as related to controlling one-way trafficking and differentiating the revolving and rotating mechanisms. Finally, the review concludes by discussing the conformational changes and entropy conversion triggered by ATP binding/hydrolysis, offering a view different from the traditional concept of ATP-mediated mechanochemical energy coupling. The elucidation of the motion mechanism and direction control in ATPases could facilitate nanomotor fabrication in nanotechnology.
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Affiliation(s)
- Peixuan Guo
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
- E-mail:
| | - Dana Driver
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhengyi Zhao
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhen Zheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Chun Chan
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Xiaolin Cheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
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13
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Tichauer RH, Favre G, Cabantous S, Brut M. Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21 N-ras and the Resulting GTP Electronic Density. J Phys Chem B 2019; 123:3935-3944. [PMID: 30991803 DOI: 10.1021/acs.jpcb.9b02660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
p21ras protein activity, regulated by GTP hydrolysis, constitutes an active field of research for the development of cancer targeted therapies that would concern ∼30% of human tumors to which specific mutations have been associated. Indeed, the catalyzing mechanisms provided by the protein environment during GTP hydrolysis and how they are impaired by specific mutations remain to be fully elucidated. In this article, we present results from molecular mechanics (MM) molecular dynamics (MD) simulations and density functional theory (DFT) calculations carried out for wild-type p21 N-ras and six Gln 61 mutants. In the first part, we present the water distribution within the active site of the wild-type protein according to MM MD. Significant differences are observed when comparing the results to the previous distribution assessed through quantum mechanics/molecular mechanics (QM/MM) MD. Such method-dependent results highlight the importance of accounting for the electrostatic coupling between the protein complex and the solvent molecules in identifying hydration sites. In the second part, we present the results from DFT calculations performed to determine the electronic distribution of the GTP ligand, considering the wild-type active site arrangement according to both classical and hybrid approaches. Only in the QM/MM-based configuration is the ligand electronic density similar to that of a GDP-like state observed experimentally. For this reason, in the last set of calculations carried out for p21 N-ras Gln 61 mutants, only the active site structural conformations obtained through hybrid MD are considered. Through the analysis of the GTP electronic density, we conclude that the wild-type active site arrangement according to QM/MM MD is closer to a catalytically efficient conformation of the protein than the arrangement according to MM MD. Hence, water distribution according to the hybrid approach must correspond to the optimal placement of solvent in the active site. Within all of the studied Gln 61 substituted proteins, p21ras major catalyzing effect, which consists of stabilizing a more GDP-like state, is lost.
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Affiliation(s)
- Ruth H Tichauer
- LAAS-CNRS , Université de Toulouse , CNRS, UPS, Toulouse , France
| | - Gilles Favre
- Cancer Research Center of Toulouse , INSERM U1037, Université de Toulouse , 31037 Toulouse , France
| | - Stéphanie Cabantous
- Cancer Research Center of Toulouse , INSERM U1037, Université de Toulouse , 31037 Toulouse , France
| | - Marie Brut
- LAAS-CNRS , Université de Toulouse , CNRS, UPS, Toulouse , France
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14
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Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput Biol 2019; 15:e1006658. [PMID: 30921324 PMCID: PMC6438456 DOI: 10.1371/journal.pcbi.1006658] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
At the root of the so-called precision medicine or precision oncology, which is our focus here, is the hypothesis that cancer treatment would be considerably better if therapies were guided by a tumor’s genomic alterations. This hypothesis has sparked major initiatives focusing on whole-genome and/or exome sequencing, creation of large databases, and developing tools for their statistical analyses—all aspiring to identify actionable alterations, and thus molecular targets, in a patient. At the center of the massive amount of collected sequence data is their interpretations that largely rest on statistical analysis and phenotypic observations. Statistics is vital, because it guides identification of cancer-driving alterations. However, statistics of mutations do not identify a change in protein conformation; therefore, it may not define sufficiently accurate actionable mutations, neglecting those that are rare. Among the many thematic overviews of precision oncology, this review innovates by further comprehensively including precision pharmacology, and within this framework, articulating its protein structural landscape and consequences to cellular signaling pathways. It provides the underlying physicochemical basis, thereby also opening the door to a broader community.
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15
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Agrahari AK, Muskan M, George Priya Doss C, Siva R, Zayed H. Computational insights of K1444N substitution in GAP-related domain of NF1 gene associated with neurofibromatosis type 1 disease: a molecular modeling and dynamics approach. Metab Brain Dis 2018; 33:1443-1457. [PMID: 29804243 DOI: 10.1007/s11011-018-0251-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/17/2018] [Indexed: 12/18/2022]
Abstract
The NF1 gene encodes for neurofibromin protein, which is ubiquitously expressed, but most highly in the central nervous system. Non-synonymous SNPs (nsSNPs) in the NF1 gene were found to be associated with Neurofibromatosis Type 1 disease, which is characterized by the growth of tumors along nerves in the skin, brain, and other parts of the body. In this study, we used several in silico predictions tools to analyze 16 nsSNPs in the RAS-GAP domain of neurofibromin, the K1444N (K1423N) mutation was predicted as the most pathogenic. The comparative molecular dynamic simulation (MDS; 50 ns) between the wild type and the K1444N (K1423N) mutant suggested a significant change in the electrostatic potential. In addition, the RMSD, RMSF, Rg, hydrogen bonds, and PCA analysis confirmed the loss of flexibility and increase in compactness of the mutant protein. Further, SASA analysis revealed exchange between hydrophobic and hydrophilic residues from the core of the RAS-GAP domain to the surface of the mutant domain, consistent with the secondary structure analysis that showed significant alteration in the mutant protein conformation. Our data concludes that the K1444N (K1423N) mutant lead to increasing the rigidity and compactness of the protein. This study provides evidence of the benefits of the computational tools in predicting the pathogenicity of genetic mutations and suggests the application of MDS and different in silico prediction tools for variant assessment and classification in genetic clinics.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Meghana Muskan
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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16
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Tichauer RH, Favre G, Cabantous S, Landa G, Hemeryck A, Brut M. Water Distribution within Wild-Type NRas Protein and Q61 Mutants during Unrestrained QM/MM Dynamics. Biophys J 2018; 115:1417-1430. [PMID: 30224050 DOI: 10.1016/j.bpj.2018.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022] Open
Abstract
Point mutations in p21ras are associated with ∼30% of human tumors by disrupting its GTP hydrolysis cycle, which is critical to its molecular switch function in cellular signaling pathways. In this work, we investigate the impact of Gln 61 substitutions in the structure of the p21N-ras active site and particularly focus on water reorganization around GTP, which appears to be crucial to evaluate favorable and unfavorable hydration sites for hydrolysis. The NRas-GTP complex is analyzed using a hybrid quantum mechanics/molecular mechanics approach, treating for the first time to our knowledge transient water molecules at the ab initio level and leading to results that account for the electrostatic coupling between the protein complex and the solvent. We show that for the wild-type protein, water molecules are found around the GTP γ-phosphate group, forming an arch extended from residues 12 to 35. Two density peaks are observed, supporting previous results that suggest the presence of two water molecules in the active site, one in the vicinity of residue 35 and a second one stabilized by hydrogen bonds formed with nitrogen backbone atoms of residues 12 and 60. The structural changes observed in NRas Gln 61 mutants result in the drastic delocalization of water molecules that we discuss. In mutants Q61H and Q61K, for which water distribution is overlocalized next to residue 60, the second density peak supports the hypothesis of a second water molecule. We also conclude that Gly 60 indirectly participates in GTP hydrolysis by correctly positioning transient water molecules in the protein complex and that Gln 61 has an indirect steric effect in stabilizing the preorganized catalytic site.
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Affiliation(s)
- Ruth H Tichauer
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse, INSERM U1037, Toulouse, France; Université de Toulouse, Toulouse, France
| | - Stéphanie Cabantous
- Cancer Research Center of Toulouse, INSERM U1037, Toulouse, France; Université de Toulouse, Toulouse, France
| | - Georges Landa
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anne Hemeryck
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie Brut
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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17
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Mueller MP, Goody RS. Review: Ras GTPases and myosin: Qualitative conservation and quantitative diversification in signal and energy transduction. Biopolymers 2017; 105:422-30. [PMID: 27018658 PMCID: PMC5084828 DOI: 10.1002/bip.22840] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/22/2016] [Accepted: 03/25/2016] [Indexed: 12/03/2022]
Abstract
Most GTPases and many ATPases belong to the P‐loop class of proteins with significant structural and mechanistic similarities. Here we compare and contrast the basic properties of the Ras family GTPases and myosin, and conclude that there are fundamental similarities but also distinct differences related to their specific roles. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 422–430, 2016.
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Affiliation(s)
- Matthias P Mueller
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
| | - Roger S Goody
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany
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18
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Vithani N, Batra S, Prakash B, Nair NN. Elucidating the GTP Hydrolysis Mechanism in FeoB: A Hydrophobic Amino-Acid Substituted GTPase. ACS Catal 2016. [DOI: 10.1021/acscatal.6b03365] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Neha Vithani
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Sahil Batra
- Department
of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Balaji Prakash
- Department
of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, 570020, India
| | - Nisanth N. Nair
- Department
of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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19
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Lu S, Jang H, Nussinov R, Zhang J. The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B. Sci Rep 2016; 6:21949. [PMID: 26902995 PMCID: PMC4763299 DOI: 10.1038/srep21949] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 02/04/2016] [Indexed: 02/08/2023] Open
Abstract
Ras mediates cell proliferation, survival and differentiation. Mutations in K-Ras4B are predominant at residues G12, G13 and Q61. Even though all impair GAP-assisted GTP → GDP hydrolysis, the mutation frequencies of K-Ras4B in human cancers vary. Here we aim to figure out their mechanisms and differential oncogenicity. In total, we performed 6.4 μs molecular dynamics simulations on the wild-type K-Ras4B (K-Ras4BWT-GTP/GDP) catalytic domain, the K-Ras4BWT-GTP–GAP complex, and the mutants (K-Ras4BG12C/G12D/G12V-GTP/GDP, K-Ras4BG13D-GTP/GDP, K-Ras4BQ61H-GTP/GDP) and their complexes with GAP. In addition, we simulated ‘exchanged’ nucleotide states. These comprehensive simulations reveal that in solution K-Ras4BWT-GTP exists in two, active and inactive, conformations. Oncogenic mutations differentially elicit an inactive-to-active conformational transition in K-Ras4B-GTP; in K-Ras4BG12C/G12D-GDP they expose the bound nucleotide which facilitates the GDP-to-GTP exchange. These mechanisms may help elucidate the differential mutational statistics in K-Ras4B-driven cancers. Exchanged nucleotide simulations reveal that the conformational transition is more accessible in the GTP-to-GDP than in the GDP-to-GTP exchange. Importantly, GAP not only donates its R789 arginine finger, but stabilizes the catalytically-competent conformation and pre-organizes catalytic residue Q61; mutations disturb the R789/Q61 organization, impairing GAP-mediated GTP hydrolysis. Together, our simulations help provide a mechanistic explanation of key mutational events in one of the most oncogenic proteins in cancer.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.,Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, USA.,Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.,Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
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20
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Lu S, Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R, Zhang J. Ras Conformational Ensembles, Allostery, and Signaling. Chem Rev 2016; 116:6607-65. [PMID: 26815308 DOI: 10.1021/acs.chemrev.5b00542] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ras proteins are classical members of small GTPases that function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states. Ras activation is regulated by guanine nucleotide exchange factors that catalyze the exchange of GDP by GTP, and inactivation is terminated by GTPase-activating proteins that accelerate the intrinsic GTP hydrolysis rate by orders of magnitude. In this review, we focus on data that have accumulated over the past few years pertaining to the conformational ensembles and the allosteric regulation of Ras proteins and their interpretation from our conformational landscape standpoint. The Ras ensemble embodies all states, including the ligand-bound conformations, the activated (or inactivated) allosteric modulated states, post-translationally modified states, mutational states, transition states, and nonfunctional states serving as a reservoir for emerging functions. The ensemble is shifted by distinct mutational events, cofactors, post-translational modifications, and different membrane compositions. A better understanding of Ras biology can contribute to therapeutic strategies.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine , Shanghai, 200025, China.,Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | | | | | | | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States.,Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Jian Zhang
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine , Shanghai, 200025, China
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21
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Mironov VA, Khrenova MG, Lychko LA, Nemukhin AV. Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras. Proteins 2015; 83:1046-53. [PMID: 25820867 DOI: 10.1002/prot.24802] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 12/25/2022]
Abstract
The free energy profiles for the chemical reaction of the guanosine triphosphate hydrolysis GTP + H2O → GDP + Pi by Ras-GAP for the wild-type and G13V mutated Ras were computed by using molecular dynamics protocols with the QM(ab initio)/MM potentials. The results are consistent with the recent measurements of reaction kinetics in Ras-GAP showing about two-order reduction of the rate constant upon G13V mutation in Ras: the computed activation barrier on the free energy profile is increased by 3 kcal/mol upon the G13V replacement. The major reason for a higher energy barrier is a shift of the "arginine finger" (R789 from GAP) from the favorable position in the active site. The results of simulations provide support for the mechanism of the reference reaction according to which the Q61 side chain directly participates in chemical transformations at the proton transfer stage.
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Affiliation(s)
- Vladimir A Mironov
- Chemistry Department, M.V, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maria G Khrenova
- Chemistry Department, M.V, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Leonora A Lychko
- Chemistry Department, M.V, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexander V Nemukhin
- Chemistry Department, M.V, Lomonosov Moscow State University, Moscow, 119991, Russia.,N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
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22
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Prakash P, Gorfe AA. Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras. MOLECULAR SIMULATION 2014; 40:839-847. [PMID: 26491216 DOI: 10.1080/08927022.2014.895000] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the last 40 years, we have learnt a great deal about the Ras onco-proteins. These intracellular molecular switches are essential for the function of a variety of physiological processes, including signal transduction cascades responsible for cell growth and proliferation. Molecular simulations and free energy calculations have played an essential role in elucidating the conformational dynamics and energetics underlying the GTP hydrolysis reaction catalysed by Ras. Here we present an overview of the main lessons from molecular simulations on the GTPase reaction and conformational dynamics of this important anti-cancer drug target. In the first part, we summarise insights from quantum mechanical and combined quantum mechanical/molecular mechanical simulations as well as other free energy methods and highlight consensus viewpoints as well as remaining controversies. The second part provides a very brief overview of new insights emerging from large-scale molecular dynamics simulations. We conclude with a perspective regarding future studies of Ras where computational approaches will likely play an active role.
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Affiliation(s)
- Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, 6431 Fannin St, Houston, TX 77030, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, 6431 Fannin St, Houston, TX 77030, USA
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23
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Prakash P, Gorfe AA. Lessons from computer simulations of Ras proteins in solution and in membrane. Biochim Biophys Acta Gen Subj 2013; 1830:5211-8. [PMID: 23906604 DOI: 10.1016/j.bbagen.2013.07.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/23/2013] [Accepted: 07/24/2013] [Indexed: 12/22/2022]
Abstract
BACKGROUND A great deal has been learned over the last several decades about the function of Ras proteins in solution and membrane environments. While much of this knowledge has been derived from a plethora of experimental techniques, computer simulations have also played a substantial role. SCOPE OF REVIEW Our goal here is to summarize the contribution of molecular simulations to our current understanding of normal and aberrant Ras function. We focus on lessons from molecular dynamics simulations in aqueous and membrane environments. MAJOR CONCLUSIONS The central message is that a close interaction between theory and simulation on the one hand and cell-biological, spectroscopic and other experimental approaches on the other has played, and will likely continue to play, a vital role in Ras research. GENERAL SIGNIFICANCE Atomistic insights emerging from detailed simulations of Ras in solution and in bilayers may be the key to unlock the secret that to date prevented development of selective anti-Ras inhibitors for cancer therapy.
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Affiliation(s)
- Priyanka Prakash
- University of Texas Health Science Center at Houston, Department of Integrative Biology and Pharmacology, 6431 Fannin St., Houston, TX 77030, USA
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24
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Thomas L, Richards M, Mort M, Dunlop E, Cooper DN, Upadhyaya M. Assessment of the potential pathogenicity of missense mutations identified in the GTPase-activating protein (GAP)-related domain of the neurofibromatosis type-1 (NF1) gene. Hum Mutat 2012; 33:1687-96. [PMID: 22807134 DOI: 10.1002/humu.22162] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 06/28/2012] [Indexed: 11/09/2022]
Abstract
Neurofibromatosis type-1 (NF1) is caused by constitutional mutations of the NF1 tumor-suppressor gene. Although ∼85% of inherited NF1 microlesions constitute truncating mutations, the remaining ∼15% are missense mutations whose pathological relevance is often unclear. The GTPase-activating protein-related domain (GRD) of the NF1-encoded protein, neurofibromin, serves to define its major function as a negative regulator of the Ras-MAPK (mitogen-activated protein kinase) signaling pathway. We have established a functional assay to assess the potential pathogenicity of 15 constitutional nonsynonymous NF1 missense mutations (11 novel and 4 previously reported but not functionally characterized) identified in the NF1-GRD (p.R1204G, p.R1204W, p.R1276Q, p.L1301R, p.I1307V, p.T1324N, p.E1327G, p.Q1336R, p.E1356G, p.R1391G, p.V1398D, p.K1409E, p.P1412R, p.K1436Q, p.S1463F). Individual mutations were introduced into an NF1-GRD expression vector and activated Ras was assayed by an enzyme-linked immunosorbent assay (ELISA). Ten NF1-GRD variants were deemed to be potentially pathogenic by virtue of significantly elevated levels of activated GTP-bound Ras in comparison to wild-type NF1 protein. The remaining five NF1-GRD variants were deemed less likely to be of pathological significance as they exhibited similar levels of activated Ras to the wild-type protein. These conclusions received broad support from both bioinformatic analysis and molecular modeling and serve to improve our understanding of NF1-GRD structure and function.
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Affiliation(s)
- Laura Thomas
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
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25
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Boer JL, Hausinger RP. Klebsiella aerogenes UreF: identification of the UreG binding site and role in enhancing the fidelity of urease activation. Biochemistry 2012; 51:2298-308. [PMID: 22369361 DOI: 10.1021/bi3000897] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Ni-containing active site of Klebsiella aerogenes urease is assembled through the concerted action of the UreD, UreE, UreF, and UreG accessory proteins. UreE functions as a metallochaperone that delivers Ni to a UreD-UreF-UreG complex bound to urease apoprotein, with UreG serving as a GTPase during enzyme activation. This study focuses on the role of UreF, previously proposed to act as a GTPase activating protein (GAP) of UreG. Sixteen conserved UreF surface residues that may play roles in protein-protein interactions were independently changed to Ala. When produced in the context of the entire urease gene cluster, cell-free extracts of nine site-directed mutants had less than 10% of the wild-type urease activity. Enrichment of the variant forms of UreF, as the UreE-F fusion proteins, uniformly resulted in copurification of UreD and urease apoprotein, whereas UreG bound to only a subset of the species. Notably, weakened interaction with UreG correlated with the low-activity mutants. The affected residues in UreF map to a distinct surface on the crystal structure, defining the UreG binding site. In contrast to the hypothesis that UreF is a GAP, the UreD-UreF-UreG-urease apoprotein complex containing K165A UreF exhibited significantly greater levels of GTPase activity than that containing the wild-type protein. Additional studies demonstrated the UreG GTPase activity was largely uncoupled from urease activation for the complex containing this UreF variant. Further experiments with these complexes provided evidence that UreF gates the GTPase activity of UreG to enhance the fidelity of urease metallocenter assembly, especially in the presence of the noncognate metal Zn.
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Affiliation(s)
- Jodi L Boer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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26
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Yang MJ, Zhang X. Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation. Proteins 2011; 79:1774-85. [DOI: 10.1002/prot.23000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/03/2011] [Accepted: 01/17/2011] [Indexed: 11/08/2022]
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27
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Uejima T, Ihara K, Goh T, Ito E, Sunada M, Ueda T, Nakano A, Wakatsuki S. GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5·Vps9 system. J Biol Chem 2010; 285:36689-97. [PMID: 20833725 PMCID: PMC2978598 DOI: 10.1074/jbc.m110.152132] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 08/17/2010] [Indexed: 11/06/2022] Open
Abstract
Many GTPases regulate intracellular transport and signaling in eukaryotes. Guanine nucleotide exchange factors (GEFs) activate GTPases by catalyzing the exchange of their GDP for GTP. Here we present crystallographic and biochemical studies of a GEF reaction with four crystal structures of Arabidopsis thaliana ARA7, a plant homolog of Rab5 GTPase, in complex with its GEF, VPS9a, in the nucleotide-free and GDP-bound forms, as well as a complex with aminophosphonic acid-guanylate ester and ARA7·VPS9a(D185N) with GDP. Upon complex formation with ARA7, VPS9 wedges into the interswitch region of ARA7, inhibiting the coordination of Mg(2+) and decreasing the stability of GDP binding. The aspartate finger of VPS9a recognizes GDP β-phosphate directly and pulls the P-loop lysine of ARA7 away from GDP β-phosphate toward switch II to further destabilize GDP for its release during the transition from the GDP-bound to nucleotide-free intermediates in the nucleotide exchange reaction.
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Affiliation(s)
- Tamami Uejima
- From the Structural Biology Research Center, Institute of Material Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kentaro Ihara
- From the Structural Biology Research Center, Institute of Material Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Tatsuaki Goh
- the Laboratory of Developmental Cell Biology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan, and
| | - Emi Ito
- the Laboratory of Developmental Cell Biology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan, and
| | - Mariko Sunada
- the Laboratory of Developmental Cell Biology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan, and
| | - Takashi Ueda
- the Laboratory of Developmental Cell Biology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan, and
| | - Akihiko Nakano
- the Laboratory of Developmental Cell Biology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan, and
- the Molecular Membrane Biology Laboratory, RIKEN Advanced Science Institute, Saitama 351-0198, Japan
| | - Soichi Wakatsuki
- From the Structural Biology Research Center, Institute of Material Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
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28
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Abstract
Neurofibromin is a cytoplasmic protein that is predominantly expressed in neurons, Schwann cells, oligodendrocytes, astrocytes and leukocytes. It is encoded by the gene NF1, located on chromosome 17, at q11.2, and has different biochemical functions, including association to microtubules and participation in several signaling pathways. Alterations in this protein are responsible for a phacomatosis named neurofibromatosis type 1.
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Affiliation(s)
- A B Trovó-Marqui
- Departamento de Biologia, UNESP-Universidade Estadual Paulista, Brazil
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29
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Grigorenko BL, Nemukhin AV, Topol IA, Cachau RE, Burt SK. QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate. Proteins 2006; 60:495-503. [PMID: 15906320 DOI: 10.1002/prot.20472] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The mechanism of the hydrolysis reaction of guanosine triphosphate (GTP) by the protein complex Ras-GAP (p21(ras) - p120(GAP)) has been modeled by the quantum mechanical-molecular mechanical (QM/MM) and ab initio quantum calculations. Initial geometry configurations have been prompted by atomic coordinates of a structural analog (PDBID:1WQ1). It is shown that the minimum energy reaction path is consistent with an assumption of two-step chemical transformations. At the first stage, a unified motion of Arg789 of GAP, Gln61, Thr35 of Ras, and the lytic water molecule results in a substantial spatial separation of the gamma-phosphate group of GTP from the rest of the molecule (GDP). This phase of hydrolysis process proceeds through the low-barrier transition state TS1. At the second stage, Gln61 abstracts and releases protons within the subsystem including Gln61, the lytic water molecule and the gamma-phosphate group of GTP through the corresponding transition state TS2. Direct quantum calculations show that, in this particular environment, the reaction GTP + H(2)O --> GDP + H(2)PO(4) (-) can proceed with reasonable activation barriers of less than 15 kcal/mol at every stage. This conclusion leads to a better understanding of the anticatalytic effect of cancer-causing mutations of Ras, which has been debated in recent years.
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Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russian Federation
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30
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Becker EW. Relevance of the kinetic equilibrium of forces to the control of the cell cycle by Ras proteins. Biol Chem 2004; 385:41-7. [PMID: 14977045 DOI: 10.1515/bc.2004.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In higher organisms, the replacement of GDP bound to Ras proteins with GTP, under the participation of an exchange factor, is an important step in the initiation of cell division. Ras-GTP activates kinases and other effectors, which pass signals to the cell nucleus and to the cytoskeleton. The active state of Ras is terminated by hydrolysis of the bound GTP with the assistance of an activating protein (GAP). Knowledge of these regulatory events is based on extensive experimental data, but many aspects of their interpretation are still controversial. It is assumed here that a significant part of the free energy released when two partners associate is stored in a 'kinetic equilibrium of forces' (KEF), and used to facilitate the separation from a third partner. The activation of the Raf kinase is explained primarily in terms of an allosteric effect of Ras-GTP on the phosphate transfer in the catalytic region of the kinase. A mechanism is proposed for the modification of GAP by Ras-GTP, which is believed to be a prerequisite for the well-known crosstalk between the Ras- and Rho-dependent signalling pathways. The cell, by meeting the requirements for KEF, manages to reduce activation barriers, thus significantly accelerating the regulatory events and other complex biological reaction sequences.
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Affiliation(s)
- Erwin W Becker
- Institut für Mikrostrukturtechnik, Forschungszentrum Karlsruhe, Universität Karlsruhe, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany.
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31
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Li G, Zhang XC. GTP hydrolysis mechanism of Ras-like GTPases. J Mol Biol 2004; 340:921-32. [PMID: 15236956 DOI: 10.1016/j.jmb.2004.06.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2004] [Revised: 04/30/2004] [Accepted: 06/04/2004] [Indexed: 11/19/2022]
Abstract
The Ras-like GTPases regulate diverse cellular functions via the chemical cycle of binding and hydrolyzing GTP molecules. They alternate between GTP- and GDP-bound conformations. The GTP-bound conformation is biologically active and promotes a cellular function, such as signal transduction, cytoskeleton organization, protein synthesis/translocation, or a membrane budding/fusion event. GTP hydrolysis turns off the GTPase switch by converting it to the inactive GDP-bound conformation. The fundamental GTP hydrolysis mechanism by these GTPases has generated considerable interest over the last two decades but remained to be firmly established. This review provides an update on the catalytic mechanism with discussions on recent developments from kinetic, structural, and model studies in the context of the various GTP hydrolysis models proposed over the years.
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Affiliation(s)
- Guangpu Li
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 940 S.L. Young Blvd, BMSB 853, Oklahoma City, OK 73104, USA.
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32
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Modarressi MH, Cheng M, Tarnasky HA, Lamarche-Vane N, de Rooij DG, Ruan Y, van der Hoorn FA. A novel testicular RhoGAP-domain protein induces apoptosis. Biol Reprod 2004; 71:1980-90. [PMID: 15306557 PMCID: PMC3158803 DOI: 10.1095/biolreprod.104.032805] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The GTPase-activating proteins (GAPs) accelerate the hydrolysis of GTP to GDP by small GTPases. The GTPases play diverse roles in many cellular processes, including proliferation, cell motility, endocytosis, nuclear import/export, and nuclear membrane formation. Little is known about GAP-domain proteins in spermatogenesis. We isolated a novel RhoGAP domain-containing tGAP1 protein from male germ cells that exhibits unusual properties. The tGAP1 is expressed at low levels in early spermatogonia. Robust transcription initiates in midpachytene spermatocytes and continues after meiosis. The 175-kDa tGAP1 protein localizes to the cytoplasm of spermatocytes and to the cytoplasm and nucleus in spermatids. The protein contains four GAP domain-related sequences, in contrast to all other GAP proteins that harbor one such domain. No activity toward RhoA, Rac1, or Cdc42 could be detected. Results of transfection studies in various somatic cells indicated that low-level tGAP1 expression significantly slows down the cell cycle. Expression of higher levels of tGAP1 by infection of somatic cells with recombinant adenoviruses demonstrated that tGAP1 efficiently induces apoptosis, which to our knowledge is the first such demonstration for a RhoGAP protein. Based on its subcellular location in spermatids and its activity, tGAP1 may play a role in nuclear import/export.
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Affiliation(s)
- M. Hossein Modarressi
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Min Cheng
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Heide A. Tarnasky
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Nathalie Lamarche-Vane
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada H3A 2T5
| | - Dirk G. de Rooij
- Departments Endocrinology, Faculty of Biology and of Cell Biology, UMCU, Utrecht University, Utrecht, The Netherlands
| | - Yibing Ruan
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Frans A. van der Hoorn
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1
- Correspondence: Frans A. van der Hoorn, Department of Biochemistry & Molecular Biology, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 4N1. FAX: 403 210 8109;
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33
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Topol IA, Cachau RE, Nemukhin AV, Grigorenko BL, Burt SK. Quantum chemical modeling of the GTP hydrolysis by the RAS-GAP protein complex. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1700:125-36. [PMID: 15210132 DOI: 10.1016/j.bbapap.2004.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2004] [Revised: 03/29/2004] [Accepted: 04/22/2004] [Indexed: 11/22/2022]
Abstract
We present results of the modeling for the hydrolysis reaction of guanosine triphosphate (GTP) in the RAS-GAP protein complex using essentially ab initio quantum chemistry methods. One of the approaches considers a supermolecular cluster composed of 150 atoms at a consistent quantum level. Another is a hybrid QM/MM method based on the effective fragment potential technique, which describes interactions between quantum and molecular mechanical subsystems at the ab initio level of the theory. Our results show that the GTP hydrolysis in the RAS-GAP protein complex can be modeled by a substrate-assisted catalytic mechanism. We can locate a configuration on the top of the barrier corresponding to the transition state of the hydrolysis reaction such that the straightforward descents from this point lead either to reactants GTP+H(2)O or to products guanosine diphosphate (GDP)+H(2)PO(4)(-). However, in all calculations such a single-step process is characterized by an activation barrier that is too high. Another possibility is a two-step reaction consistent with formation of an intermediate. Here the Pgamma-O(Pbeta) bond is already broken, but the lytic water molecule is still in the pre-reactive state. We present arguments favoring the assumption that the first step of the GTP hydrolysis reaction in the RAS-GAP protein complex may be assigned to the breaking of the Pgamma-O(Pbeta) bond prior to the creation of the inorganic phosphate.
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Affiliation(s)
- Igor A Topol
- Advanced Biomedical Computing Center, SAIC Frederick, National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702-1201, USA.
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34
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Abstract
The elucidation of the structure of the RasGAP complex provides what is perhaps the most detailed link between protein structure and cancer causing mutations. In particular, it is known that mutations of Gln 61 destroy the GTPase activity of the complex, locks the cell in its ON state and thus, can cause cancer. It is entirely unclear however, why this specific mutation is so important. The present work uncovers the elusive role of Gln 61 by computer simulation of the GTPase reaction in Ras, RasGAP and of their mutants. Simulations of the effects of mutations of Gln 61 reproduce the corresponding observed changes in activation energies and allow us to analyze the energy contributions to these effects. It is found that Gln 61 does not operate in a direct chemical way nor by a direct electrostatic or steric interaction with the transition state (TS). Instead, oncogenic mutations of Gln 61 lead to the destruction of the exquisitely preorganized catalytic configuration of the active site of the RasGAP complex. This "allosteric" effect causes a major reduction in the electrostatic stabilization of the TS. Our findings have general relevance to other proteins that control signal transduction processes.
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Affiliation(s)
- Avital Shurki
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
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35
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Wang YN, Topol IA, Collins JR, Burt SK. Theoretical studies on the hydrolysis of mono-phosphate and tri-phosphate in gas phase and aqueous solution. J Am Chem Soc 2004; 125:13265-73. [PMID: 14570503 DOI: 10.1021/ja0279794] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphate hydrolysis by GTPases plays an important role as a molecular switch in signal transduction and as an initiator of many other biological processes. Despite the centrality of this ubiquitous reaction, the mechanism is still poorly understood. As a first step to understand the mechanisms of this process, the nonenzymatic hydrolysis of mono-phosphate and tri-phosphate esters were systematically studied in gas phase and aqueous solution using hybrid density functional methods. The dielectric effect of the environment on the energetics of these processes was also explored. Theoretical results show that for mono-phosphate ester, the dissociative pathway is much more favorable than the associative pathway. However, the reaction barriers for the dissociative and associative pathways of tri-phosphate hydrolysis are very close in aqueous solution, though the dissociative pathway is more favorable in the gas phase. High dielectric solvents, such as water, significantly lower the activation barrier of the associative pathway due to the greater solvation energy of the associative transition states than that of the reactant complex. By contrast, the barrier of the dissociative pathway, with respect to the gas phase, is less sensitive to the surrounding dielectric. In the associative hydrolysis pathway of the tri-phosphate ester, negative charge is transferred from the gamma-phosphate to beta-phosphate through the bridging ester oxygen and results in Pgamma-O bond dissociation. No analogous charge transfer was observed in the dissociative pathway, where Pgamma-O bond dissociation resulted from proton transfer from the gamma-phosphate to the bridge oxygen. Finally, the active participation of local water molecules can significantly lower the activation energy of the dissociative pathway for both mono-phosphate and tri-phosphate.
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Affiliation(s)
- Yan-Ni Wang
- Advanced Biomedical Computing Center, National Cancer Institute at Frederick, NCI/NIH, P.O. Box B, Frederick, MD 21702, USA
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36
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Fernández A. Oncogenic mutations and packing defects in protein structure. J Biomol Struct Dyn 2003; 21:9-14. [PMID: 12854955 DOI: 10.1080/07391102.2003.10506901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Oncogenic mutations in expressed proteins are of primary interest to understand tumor formation but their structural consequences bearing on protein function are not clearly understood. In this contribution I report on two illustrative examples, p21ras and p57, revealing that such mutations have an effect on specific structural deficiencies in the packing of the protein structure, i. e., on backbone hydrogen bonds insufficiently shielded from water attack. These structural deficiencies in the wild type are typically "corrected intermolecularly" by protein complexation or protein-ligand association. However, in the oncogenic mutants, these binding signals are partially or completely suppressed: the mutated residues properly wrap or desolvate the hydrogen bonds intramolecularly. Thus, the interactivity of the proteins becomes impaired: their binding affinity decreases sharply, as there is no thermodynamic benefit from removing water surrounding properly desolvated hydrogen bonds. The results, specialized for p21ras and p53, reveal how oncogenic mutations determine a hindrance to GAP-induced hydrolysis (p21) and decrease binding affinity for DNA (p53). Furthermore, the oncogenic potential of mutations in residues not directly engaged in the interface electrostatics is assessed. The results suggest that a high sensitivity of structural defects to genetic accident might be a necessary condition to establish the existence of a proto-oncogene, an angle that merits a systematic study.
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Affiliation(s)
- Ariel Fernández
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.
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37
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Ahmadian MR, Kiel C, Stege P, Scheffzek K. Structural fingerprints of the Ras-GTPase activating proteins neurofibromin and p120GAP. J Mol Biol 2003; 329:699-710. [PMID: 12787671 DOI: 10.1016/s0022-2836(03)00514-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ras specific GTPase activating proteins (GAPs), neurofibromin and p120GAP, bind GTP bound Ras and efficiently complement its active site. Here we present comparative data from mutations and fluorescence-based assays of the catalytic domains of both RasGAPs and interpret them using the crystal structures. Three prominent regions in RasGAPs, the arginine-finger loop, the phenylalanine-leucine-arginine (FLR) region and alpha7/variable loop contain structural fingerprints governing the GAP function. The finger loop is crucial for the stabilization of the transition state of the GTPase reaction. This function is controlled by residues proximal to the catalytic arginine, which are strikingly different between the two RasGAPs. These residues specifically determine the orientation and therefore the positioning of the arginine finger in the Ras active site. The invariant FLR region, a hallmark for RasGAPs, indirectly contributes to GTPase stimulation by forming a scaffold, which stabilizes Ras switch regions. We show that a long hydrophobic side-chain in the FLR region is crucial for this function. The alpha7/variable loop uses several conserved residues including two lysine residues, which are involved in numerous interactions with the switch I region of Ras. This region determines the specificity of the Ras-RasGAP interaction.
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Affiliation(s)
- Mohammad Reza Ahmadian
- Department Structural Biology, Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
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38
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Williams WR. Relative molecular similarity in selected chemical carcinogens and the nucleoside triphosphate chain. PHARMACOLOGY & TOXICOLOGY 2003; 92:57-63. [PMID: 12747574 DOI: 10.1034/j.1600-0773.2003.920202.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Several markers of cell toxicity are useful as screening tests for epigenetic carcinogens. The direct effects of chemicals on ATPase and GTPase function are pertinent to the early stages of carcinogenesis. Interference with triphosphate-diphosphate exchange mechanisms may result from the interaction of carcinogens with the substrate triphosphate chain. To investigate this hypothesis, a computational chemistry programme is used in this study to investigate molecular similarity in ATPase inhibitors, carcinogens and tumour promoters, in relation to the nucleoside triphosphate chain. The results show that atoms in the investigated molecular structures superimpose on sets of oxygen atoms in the triphosphate chain with interatomic distances < 0.3A. Relative molecular similarity to the substrate triphosphate chain is discussed in terms of the established inhibitory properties of carcinogens/tumour promoters on ATPase function, the carcinogen/ tumour promoting properties of ATPase inhibitors and the prediction of carcinogenic activity from chemical structure.
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