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Hu Z, Martí J. Isomer-sourced structure iteration methods for in silico development of inhibitors: Inducing GTP-bound NRAS-Q61 oncogenic mutations to an "off-like" state. Comput Struct Biotechnol J 2024; 23:2418-2428. [PMID: 38882681 PMCID: PMC11176632 DOI: 10.1016/j.csbj.2024.05.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The NRAS-mutant subset of melanoma represent some of the most aggressive and deadliest types associated with poor overall survival. Unfortunately, for more than 40 years, no therapeutic agent directly targeting NRAS mutations has been clinically approved. In this work, based on microsecond scale molecular dynamics simulations, the effect of Q61 mutations on NRAS conformational characteristics is revealed at the atomic level. The GTP-bound NRAS-Q61R and Q61K mutations show a specific targetable pocket between Switch-II and α-helix 3 whereas the NRAS-Q61L non-polar mutation category shows a different targetable pocket. Moreover, a new isomer-sourced structure iteration method has been developed for the in silico design of potential inhibitor prototypes for oncogenes. We show the possibility of a designed prototype HM-387 to target activated NRAS-Q61R and that it can gradually induce the transition from the activated NRAS-Q61R to an "off-like" state.
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Affiliation(s)
- Zheyao Hu
- Department of Physics, Polytechnic University of Catalonia-Barcelona Tech, B4-B5 Northern Campus UPC, Barcelona, 08034, Catalonia, Spain
| | - Jordi Martí
- Department of Physics, Polytechnic University of Catalonia-Barcelona Tech, B4-B5 Northern Campus UPC, Barcelona, 08034, Catalonia, Spain
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2
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Fink JC, Landry D, Webb LJ. Probing the Electrostatic Effects of H-Ras Tyrosine 32 Mutations on Intrinsic GTP Hydrolysis Using Vibrational Stark Effect Spectroscopy of a Thiocyanate Probe. Biochemistry 2024; 63:1752-1760. [PMID: 38967549 DOI: 10.1021/acs.biochem.4c00075] [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: 07/06/2024]
Abstract
The wildtype H-Ras protein functions as a molecular switch in a variety of cell signaling pathways, and mutations to key residues result in a constitutively active oncoprotein. However, there is some debate regarding the mechanism of the intrinsic GTPase activity of H-Ras. It has been hypothesized that ordered water molecules are coordinated at the active site by Q61, a highly transforming amino acid site, and Y32, a position that has not previously been investigated. Here, we examine the electrostatic contribution of the Y32 position to GTP hydrolysis by comparing the rate of GTP hydrolysis of Y32X mutants to the vibrational energy shift of each mutation measured by a nearby thiocyanate vibrational probe to estimate changes in the electrostatic environment caused by changes at the Y32 position. We further compared vibrational energy shifts for each mutation to the hydration potential of the respective side chain and demonstrated that Y32 is less critical for recruiting water molecules into the active site to promote hydrolysis than Q61. Our results show a clear interplay between a steric contribution from Y32 and an electrostatic contribution from Q61 that are both critical for intrinsic GTP hydrolysis.
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Affiliation(s)
- Jackson C Fink
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Danielle Landry
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
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3
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Tagad A, Patwari GN. Unraveling the Significance of Mg 2+ Dependency and Nucleotide Binding Specificity of H-RAS. J Phys Chem B 2024; 128:1618-1626. [PMID: 38351706 DOI: 10.1021/acs.jpcb.3c06998] [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: 02/23/2024]
Abstract
RAS is a small GTPase and acts as a binary molecular switch; the transition from its active to inactive state plays a crucial role in various cell signaling processes. Molecular dynamics simulations at the atomistic level suggest that the absence of cofactor Mg2+ ion generally leads to pronounced structural changes in the Switch-I than Switch-II regions and assists GTP binding. The presence of the Mg2+ ion also restricts the rotation of ϒ phosphate and enhances the hydrolysis rate of GTP. Further, the simulations reveal that the stability of the protein is almost uncompromised when Mg2+ is replaced with Zn2+ and not the Ca2+ ion. The specificity of H-RAS to GTP was evaluated by substituting with ATP and CTP, which indicates that the binding pocket tolerates purine bases over pyrimidine bases. However, the D119 residue specifically interacts with the guanine base and serves as one of the primary interactions that leads to the selectivity of GTP over ATP. The ring displacement of 32Y serves as gate dynamics in H-RAS which are important for its interaction with GAP for the nucleotide exchange and is restricted in the presence of ATP. Finally, the point mutations 61, 16, and 32 influence the structural changes, specifically in the Switch-II region, which are expected to impact the GTP hydrolysis and thus are termed oncogenic mutations.
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Affiliation(s)
- Amol Tagad
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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4
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Baumann P, Jin Y. Far-reaching effects of tyrosine64 phosphorylation on Ras revealed with BeF 3- complexes. Commun Chem 2024; 7:19. [PMID: 38297137 PMCID: PMC10830474 DOI: 10.1038/s42004-024-01105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Tyrosine phosphorylation on Ras by Src kinase is known to uncouple Ras from upstream regulation and downstream communication. However, the mechanisms by which phosphorylation modulates these interactions have not been detailed. Here, the major mono-phosphorylation level on tyrosine64 is quantified by 31P NMR and mutagenesis. Crystal structures of unphosphorylated and tyrosine64-phosphorylated Ras in complex with a BeF3- ground state analogue reveal "closed" Ras conformations very different from those of the "open" conformations previously observed for non-hydrolysable GTP analogue structures of Ras. They deliver new mechanistic and conformational insights into intrinsic GTP hydrolysis. Phosphorylation of tyrosine64 delivers conformational changes distant from the active site, showing why phosphorylated Ras has reduced affinity to its downstream effector Raf. 19F NMR provides evidence for changes in the intrinsic GTPase and nucleotide exchange rate and identifies the concurrent presence of a major "closed" conformation alongside a minor yet functionally important "open" conformation at the ground state of Ras. This study expands the application of metal fluoride complexes in revealing major and minor conformational changes of dynamic and modified Ras proteins.
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Affiliation(s)
- Patrick Baumann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yi Jin
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK.
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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5
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Jermusek FA, Webb LJ. Electrostatic Impact of Brefeldin A on Thiocyanate Probes Surrounding the Interface of Arf1-BFA-ARNO4M, a Protein-Drug-Protein Complex. Biochemistry 2024; 63:27-41. [PMID: 38078826 DOI: 10.1021/acs.biochem.3c00366] [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: 01/03/2024]
Abstract
Protein-protein interactions regulate many cellular processes, making them ideal drug candidates. Design of such drugs, however, is hindered by a lack of understanding of the factors that contribute to the interaction specificity. Specific protein-protein complexes possess both structural and electrostatic complementarity, and while structural complementarity of protein complexes has been extensively investigated, fundamental understanding of the complicated networks of electrostatic interactions at these interfaces is lacking, thus hindering the rational design of orthosterically binding small molecules. To better understand the electrostatic interactions at protein interfaces and how a small molecule could contribute to and fit within that environment, we used a model protein-drug-protein system, Arf1-BFA-ARNO4M, to investigate how small molecule brefeldin A (BFA) perturbs the Arf1-ARNO4M interface. By using nitrile probe labeled Arf1 sites and measuring vibrational Stark effects as well as temperature dependent infrared shifts, we measured changes in the electric field and hydrogen bonding at this interface upon BFA binding. At all five probe locations of Arf1, we found that the vibrational shifts resulting from BFA binding corroborate trends found in Poisson-Boltzmann calculations of surface potentials of Arf1-ARNO4M and Arf1-BFA-ARNO4M, where BFA contributes negative electrostatic potential to the protein interface. The data also corroborate previous hypotheses about the mechanism of interfacial binding and confirm that alternating patches of hydrophobic and polar interactions lead to BFA binding specificity. These findings demonstrate the impact of BFA on this protein-protein interface and have implications for the design of other interfacial drug candidates.
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Affiliation(s)
- Frank A Jermusek
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry and Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, Texas 78712, United States
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6
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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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7
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Yang Y, Feng RR, Gai F. 4-Cyanotryptophan as a Sensitive Fluorescence Probe of Local Electric Field of Proteins. J Phys Chem B 2023; 127:514-519. [PMID: 36598839 DOI: 10.1021/acs.jpcb.2c07605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Electrostatic interactions are key determinants of protein structure, dynamics, and function. Since protein electrostatics are nonuniform, assessment of the internal electric fields (EFs) of proteins requires spatial resolution at the amino acid residue level. In this regard, vibrational Stark spectroscopy, in conjunction with various unnatural amino acid-based vibrational probes, has become a common method for site-specific interrogation of protein EFs. However, application of this method is often limited to proteins with relatively high solubility, due to the intrinsically low oscillator strength of vibrational transitions. Therefore, it would be useful to develop an alternative method that can overcome this limitation. To this end, we show that, using solvatochromic study and molecular dynamics simulations, the frequency of maximum emission intensity of the fluorophore of 4-cyanotryptophan (4CN-Trp), 3-methyl-1H-indole-4-carbonitrile, exhibits a linear dependence on the local EF. Since the absorption and emission spectra of 4CN-Trp are easily distinguishable from those of naturally occurring aromatic amino acids, we believe that this linear relationship provides an easier and more sensitive means to determine the local EF of proteins.
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Affiliation(s)
- Yuyao Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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8
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Cheng R, Li F, Zhang M, Xia X, Wu J, Gao X, Zhou H, Zhang Z, Huang N, Yang X, Zhang Y, Shen S, Kang T, Liu Z, Xiao F, Yao H, Xu J, Yan C, Zhang N. A novel protein RASON encoded by a lncRNA controls oncogenic RAS signaling in KRAS mutant cancers. Cell Res 2023; 33:30-45. [PMID: 36241718 PMCID: PMC9810732 DOI: 10.1038/s41422-022-00726-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/05/2022] [Indexed: 01/07/2023] Open
Abstract
Mutations of the RAS oncogene are found in around 30% of all human cancers yet direct targeting of RAS is still considered clinically impractical except for the KRASG12C mutant. Here we report that RAS-ON (RASON), a novel protein encoded by the long intergenic non-protein coding RNA 00673 (LINC00673), is a positive regulator of oncogenic RAS signaling. RASON is aberrantly overexpressed in pancreatic ductal adenocarcinoma (PDAC) patients, and it promotes proliferation of human PDAC cell lines in vitro and tumor growth in vivo. CRISPR/Cas9-mediated knockout of Rason in mouse embryonic fibroblasts inhibits KRAS-mediated tumor transformation. Genetic deletion of Rason abolishes oncogenic KRAS-driven pancreatic and lung cancer tumorigenesis in LSL-KrasG12D; Trp53R172H/+ mice. Mechanistically, RASON directly binds to KRASG12D/V and inhibits both intrinsic and GTPase activating protein (GAP)-mediated GTP hydrolysis, thus sustaining KRASG12D/V in the GTP-bound hyperactive state. Therapeutically, deprivation of RASON sensitizes KRAS mutant pancreatic cancer cells and patient-derived organoids to EGFR inhibitors. Our findings identify RASON as a critical regulator of oncogenic KRAS signaling and a promising therapeutic target for KRAS mutant cancers.
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Affiliation(s)
- Rongjie Cheng
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, School of life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Fanying Li
- grid.412615.50000 0004 1803 6239Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Maolei Zhang
- grid.412615.50000 0004 1803 6239Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Xin Xia
- grid.412615.50000 0004 1803 6239Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Jianzhuang Wu
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, School of life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Xinya Gao
- grid.412615.50000 0004 1803 6239Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Huangkai Zhou
- grid.412615.50000 0004 1803 6239Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Zhi Zhang
- grid.263761.70000 0001 0198 0694Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu China
| | - Nunu Huang
- grid.412615.50000 0004 1803 6239Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Xuesong Yang
- grid.412615.50000 0004 1803 6239Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Yaliang Zhang
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, School of life Sciences, Nanjing University, Nanjing, Jiangsu China
| | - Shunli Shen
- grid.412615.50000 0004 1803 6239Department of Hepatological surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Tiebang Kang
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong China
| | - Zexian Liu
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong China
| | - Feizhe Xiao
- grid.412615.50000 0004 1803 6239Department of Scientific Research Section, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong China
| | - Hongwei Yao
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, China.
| | - Jianbo Xu
- Department of Gastrointestinal surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Chao Yan
- State Key Laboratory of Pharmaceutical Biotechnology, School of life Sciences, Nanjing University, Nanjing, Jiangsu, China. .,Chemistry and Biomedicine Innovation Center, Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China. .,Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, Jiangsu, China. .,Institute of Pancreatology, Nanjing University, Nanjing, China.
| | - Nu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China. .,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China. .,Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou, Guangdong, China.
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9
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Chen S, Zhang Z, Zhang Y, Choi T, Zhao Y. Activation Mechanism of RhoA Caused by Constitutively Activating Mutations G14V and Q63L. Int J Mol Sci 2022; 23:ijms232415458. [PMID: 36555100 PMCID: PMC9778661 DOI: 10.3390/ijms232415458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
RhoA, a member of Rho GTPases, regulates myriad cellular processes. Abnormal expression of RhoA has been implicated in various diseases, including cancers, developmental disorders and bacterial infections. RhoA mutations G14V and Q63L have been reported to constitutively activate RhoA. To figure out the mechanisms, in total, 1.8 μs molecular dynamics (MD) simulations were performed here on RhoAWT and mutants G14V and Q63L in GTP-bound forms, followed by dynamic analysis. Both mutations were found to affect the conformational dynamics of RhoA switch regions, especially switch I, shifting the whole ensemble from the wild type's open inactive state to different active-like states, where T37 and Mg2+ played important roles. In RhoAG14V, both switches underwent thorough state transition, whereas in RhoAQ63L, only switch I was sustained in a much more closed conformation with additional hydrophobic interactions introduced by L63. Moreover, significantly decreased solvent exposure of the GTP-binding site was observed in both mutants with the surrounding hydrophobic regions expanded, which furnished access to water molecules required for hydrolysis more difficult and thereby impaired GTP hydrolysis. These structural and dynamic differences first suggested the potential activation mechanism of RhoAG14V and RhoAQ63L. Together, our findings complemented the understanding of RhoA activation at the atomic level and can be utilized in the development of novel therapies for RhoA-related diseases.
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Chau JE, Vish KJ, Boggon TJ, Stiegler AL. SH3 domain regulation of RhoGAP activity: Crosstalk between p120RasGAP and DLC1 RhoGAP. Nat Commun 2022; 13:4788. [PMID: 35970859 PMCID: PMC9378701 DOI: 10.1038/s41467-022-32541-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/04/2022] [Indexed: 11/10/2022] Open
Abstract
RhoGAP proteins are key regulators of Rho family GTPases and influence a variety of cellular processes, including cell migration, adhesion, and cytokinesis. These GTPase activating proteins (GAPs) downregulate Rho signaling by binding and enhancing the intrinsic GTPase activity of Rho proteins. Deleted in liver cancer 1 (DLC1) is a tumor suppressor and ubiquitously expressed RhoGAP protein; its activity is regulated in part by binding p120RasGAP, a GAP protein for the Ras GTPases. In this study, we report the co-crystal structure of the p120RasGAP SH3 domain bound directly to DLC1 RhoGAP, at a site partially overlapping the RhoA binding site and impinging on the catalytic arginine finger. We demonstrate biochemically that mutation of this interface relieves inhibition of RhoGAP activity by the SH3 domain. These results reveal the mechanism for inhibition of DLC1 RhoGAP activity by p120RasGAP and demonstrate the molecular basis for direct SH3 domain modulation of GAP activity.
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Affiliation(s)
- Jocelyn E Chau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kimberly J Vish
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Titus J Boggon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, CT, USA.
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11
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Weberg AB, Murphy RP, Tomson NC. Oriented internal electrostatic fields: an emerging design element in coordination chemistry and catalysis. Chem Sci 2022; 13:5432-5446. [PMID: 35694353 PMCID: PMC9116365 DOI: 10.1039/d2sc01715f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 11/21/2022] Open
Abstract
The power of oriented electrostatic fields (ESFs) to influence chemical bonding and reactivity is a phenomenon of rapidly growing interest. The presence of strong ESFs has recently been implicated as one of the most significant contributors to the activity of select enzymes, wherein alignment of a substrate's changing dipole moment with a strong, local electrostatic field has been shown to be responsible for the majority of the enzymatic rate enhancement. Outside of enzymology, researchers have studied the impacts of "internal" electrostatic fields via the addition of ionic salts to reactions and the incorporation of charged functional groups into organic molecules (both experimentally and computationally), and "externally" via the implementation of bulk fields between electrode plates. Incorporation of charged moieties into homogeneous inorganic complexes to generate internal ESFs represents an area of high potential for novel catalyst design. This field has only begun to materialize within the past 10 years but could be an area of significant impact moving forward, since it provides a means for tuning the properties of molecular complexes via a method that is orthogonal to traditional strategies, thereby providing possibilities for improved catalytic conditions and novel reactivity. In this perspective, we highlight recent developments in this area and offer insights, obtained from our own research, on the challenges and future directions of this emerging field of research.
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Affiliation(s)
- Alexander B Weberg
- R, oy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia Pennsylvania 19104 USA
| | - Ryan P Murphy
- R, oy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia Pennsylvania 19104 USA
| | - Neil C Tomson
- R, oy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia Pennsylvania 19104 USA
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12
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Burge RA, Hobbs GA. Not all RAS mutations are equal: A detailed review of the functional diversity of RAS hot spot mutations. Adv Cancer Res 2022; 153:29-61. [PMID: 35101234 DOI: 10.1016/bs.acr.2021.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The RAS family of small GTPases are among the most frequently mutated oncogenes in human cancer. Approximately 20% of cancers harbor a RAS mutation, and >150 different missense mutations have been detected. Many of these mutations have mutant-specific biochemical defects that alter nucleotide binding and hydrolysis, effector interactions and cell signaling, prompting renewed efforts in the development of anti-RAS therapies, including the mutation-specific strategies. Previously viewed as undruggable, the recent FDA approval of a KRASG12C-selective inhibitor has offered real promise to the development of allele-specific RAS therapies. A broader understanding of the mutational consequences on RAS function must be developed to exploit additional allele-specific vulnerabilities. Approximately 94% of RAS mutations occur at one of three mutational "hot spots" at Gly12, Gly13 and Gln61. Further, the single-nucleotide substitutions represent >99% of these mutations. Within this scope, we discuss the mutational frequencies of RAS isoforms in cancer, mutant-specific effector interactions and biochemical properties. By limiting our analysis to this mutational subset, we simplify the analysis while only excluding a small percentage of total mutations. Combined, these data suggest that the presence or absence of select RAS mutations in human cancers can be linked to their biochemical properties. Continuing to examine the biochemical differences in each RAS-mutant protein will continue to provide additional breakthroughs in allele-specific therapeutic strategies.
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Affiliation(s)
- Rachel A Burge
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - G Aaron Hobbs
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
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13
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Tang W, Wang L, Liu Y, Xiao D. RasGRP exacerbates lipopolysaccharides-induced acute kidney injury through regulating ERKs activation. Open Forum Infect Dis 2022; 9:ofac041. [PMID: 35198649 PMCID: PMC8860163 DOI: 10.1093/ofid/ofac041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background Excessive inflammatory activities are reported to be the primary cause of sepsis-induced acute kidney injury (AKI). Ras guanyl nucleotide-releasing protein (RasGRP) could prevent inflammatory response. However, its role in the regulation of inflammatory response in sepsis-associated AKI remains unclear. Methods Wild-type or RasGRP1-deficient mice were treated with lipopolysaccharide intraperitoneally in combination with D-galactosamine to establish a mouse model of sepsis-associated AKI. Serum inflammatory cytokines were measured using enzyme-linked immunosorbent assay. The messenger RNA (mRNA) levels of interleukin 6, tumor necrosis factor, nitric oxide synthase 2, and interleukin 1β were measured using quantitative reverse-transcription polymerase chain reaction. The morphological change in kidney tubule was determined by hematoxylin-and-eosin staining. The protein levels of RasGRP, extracellular signal-regulated kinases 1 and 2 (ERK1/2), and c-Jun N-terminal kinase (JNK) were determined using Western blot. Results RasGRP1 mRNA and protein levels were significantly increased in patients with sepsis-related AKI compared to those in healthy subjects. RasGRP knockout markedly reduced inflammatory cytokines induced by AKI in sepsis when compared with wild-type mice. Additionally, RasGRP deficiency inhibited the phosphorylation of ERK1/2 without altering JNK expression. In conclusion, we demonstrate that RasGRP1 plays a pivotal role in sepsis-associated AKI. Downregulation of RasGRP1 could significantly inhibit inflammatory response by inhibiting the activation of ERK1/2 and mitogen-activated protein kinase pathway, thereby reducing AKI induced by sepsis. Conclusions Our data suggest that RasGRP exacerbates lipopolysaccharide-induced acute kidney injury through regulating ERK activation, which reveals a potential therapeutic target for the treatment of sepsis-induced AKI.
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Affiliation(s)
- Wen Tang
- Department of Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Tianshan District, Urumqi 830001, Xinjiang Uygur Autonomous Region, China
| | - Lu Wang
- Department of Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Tianshan District, Urumqi 830001, Xinjiang Uygur Autonomous Region, China
| | - Yan Liu
- Department of Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Tianshan District, Urumqi 830001, Xinjiang Uygur Autonomous Region, China
| | - Dong Xiao
- Department of Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, No.91 Tianchi Road, Tianshan District, Urumqi 830001, Xinjiang Uygur Autonomous Region, China
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14
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Zeng J, Weng J, Zhang Y, Xia F, Cui Q, Xu X. Conformational Features of Ras: Key Hydrogen-Bonding Interactions of Gln61 in the Intermediate State during GTP Hydrolysis. J Phys Chem B 2021; 125:8805-8813. [PMID: 34324329 DOI: 10.1021/acs.jpcb.1c04679] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Ras protein is one of the most important drug targets for battling cancers. To effectively design novel drugs of Ras, we characterize here its conformational ensembles for the hydrolysis intermediate state RasGDP·Pi and the product state RasGDP by extensive replica-exchange molecular dynamics simulations. Several substates for RasGDP·Pi have been identified, while structural analyses have revealed an unrecognized hydrogen-bonding network that stabilizes the hydrolysis intermediate state. More interestingly, Gln61, which is involved in numerous oncogenic mutations, was found to be engaged in this hydrogen-bonding network, adopting a specific conformation that always points to Pi in contrast to that in the RasGTP state. The simulations also reveal that RasGDP has more than one substate, suggesting a conformational selection mechanism for the interaction between Ras and the guanine nucleotide exchange factors (GEFs). These findings offer new opportunities for the drug design of Ras by stabilizing the hydrolysis intermediate or disrupting its interaction with the GEFs.
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Affiliation(s)
- Juan Zeng
- School of Biomedical Engineering, Guangdong Medical University, Dongguan 523808, China
| | - Jingwei Weng
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Departments of Chemistry, Fudan University, Shanghai 200433, China
| | - Yuwei Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Fei Xia
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Departments of Chemistry, Fudan University, Shanghai 200433, China
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15
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Zhao J, Sun H, Wang W, Zhang L, Chen J. Theoretical insights into mutation-mediated conformational changes of the GNP-bound H-RAS. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.138042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Zhou ZW, Ambrogio C, Bera AK, Li Q, Li XX, Li L, Son J, Gondi S, Li J, Campbell E, Jin H, Okoro JJ, Xu CX, Janne PA, Westover KD. KRAS Q61H Preferentially Signals through MAPK in a RAF Dimer-Dependent Manner in Non-Small Cell Lung Cancer. Cancer Res 2020; 80:3719-3731. [PMID: 32605999 DOI: 10.1158/0008-5472.can-20-0448] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022]
Abstract
Assembly of RAS molecules into complexes at the cell membrane is critical for RAS signaling. We previously showed that oncogenic KRAS codon 61 mutations increase its affinity for RAF, raising the possibility that KRASQ61H, the most common KRAS mutation at codon 61, upregulates RAS signaling through mechanisms at the level of RAS assemblies. We show here that KRASQ61H exhibits preferential binding to RAF relative to PI3K in cells, leading to enhanced MAPK signaling in in vitro models and human NSCLC tumors. X-ray crystallography of KRASQ61H:GTP revealed that a hyperdynamic switch 2 allows for a more stable interaction with switch 1, suggesting that enhanced RAF activity arises from a combination of absent intrinsic GTP hydrolysis activity and increased affinity for RAF. Disruption of KRASQ61H assemblies by the RAS oligomer-disrupting D154Q mutation impaired RAF dimerization and altered MAPK signaling but had little effect on PI3K signaling. However, KRASQ61H oligomers but not KRASG12D oligomers were disrupted by RAF mutations that disrupt RAF-RAF interactions. KRASQ61H cells show enhanced sensitivity to RAF and MEK inhibitors individually, whereas combined treatment elicited synergistic growth inhibition. Furthermore, KRASQ61H tumors in mice exhibited high vulnerability to MEK inhibitor, consistent with cooperativity between KRASQ61H and RAF oligomerization and dependence on MAPK signaling. These findings support the notion that KRASQ61H and functionally similar mutations may serve as predictive biomarkers for targeted therapies against the MAPK pathway. SIGNIFICANCE: These findings show that oncogenic KRASQ61H forms a cooperative RAS-RAF ternary complex, which renders RAS-driven tumors vulnerable to MEKi and RAFi, thus establishing a framework for evaluating RAS biomarker-driven targeted therapies.
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Affiliation(s)
- Zhi-Wei Zhou
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Chiara Ambrogio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Molecular Biotechnology and Health Science, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Asim K Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Qing Li
- Cancer Center, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing, China
| | - Xing-Xiao Li
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jieun Son
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jiaqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Emily Campbell
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah
| | - Hua Jin
- Department of Thoracic Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing, China
| | - Jeffrey J Okoro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cheng-Xiong Xu
- Cancer Center, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing, China.
| | - Pasi A Janne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.
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17
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Bera AK, Lu J, Lu C, Li L, Gondi S, Yan W, Nelson A, Zhang G, Westover KD. GTP hydrolysis is modulated by Arg34 in the RASopathy-associated KRAS P34R. Birth Defects Res 2020; 112:708-717. [PMID: 32187889 PMCID: PMC7495839 DOI: 10.1002/bdr2.1647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/08/2020] [Indexed: 01/07/2023]
Abstract
RAS proteins are commonly mutated in cancerous tumors, but germline RAS mutations are also found in RASopathy syndromes such as Noonan syndrome (NS) and cardiofaciocutaneous (CFC) syndrome. Activating RAS mutations can be subclassified based on their activating mechanisms. Understanding the structural basis for these mechanisms may provide clues for how to manage associated health conditions. We determined high-resolution X-ray structures of the RASopathy mutant KRASP34R seen in NS and CFCS. GTP and GDP-bound KRASP34R crystallized in multiple forms, with each lattice consisting of multiple protein conformations. In all GTP-bound conformations, the switch regions are not compatible with GAP binding, suggesting a structural mechanism for the GAP insensitivity of this RAS mutant. However, GTP-bound conformations are compatible with intrinsic nucleotide hydrolysis, including one that places R34 in a position analogous to the GAP arginine finger or intrinsic arginine finger found in heterotrimeric G proteins, which may support intrinsic GTP hydrolysis. We also note that the affinity between KRASP34R and RAF-RBD is decreased, suggesting another possible mechanism for dampening of RAS signaling. These results may provide a foothold for development of new mutation-specific strategies to address KRASP34R -driven diseases.
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Affiliation(s)
- Asim K. Bera
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jia Lu
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Chunya Lu
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lianbo Li
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Sudershan Gondi
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Wei Yan
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | | | - Goujun Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Kenneth D. Westover
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
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18
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Gao Z, Xing K, Zhang C, Qi J, Wang L, Gao S, Lai R. Crystal structure and function of Rbj: A constitutively GTP-bound small G protein with an extra DnaJ domain. Protein Cell 2020; 10:760-763. [PMID: 30945136 PMCID: PMC6776491 DOI: 10.1007/s13238-019-0622-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Zhengrong Gao
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keke Xing
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Chang Zhang
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shan Gao
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
| | - Ren Lai
- Key Laboratory of Bioactive Peptides of Yunnan Province/Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China.
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19
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First JT, Novelli ET, Webb LJ. Beyond pKa: Experiments and Simulations of Nitrile Vibrational Probes in Staphylococcal Nuclease Show the Importance of Local Interactions. J Phys Chem B 2020; 124:3387-3399. [DOI: 10.1021/acs.jpcb.0c00747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy T. First
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology The University of Texas at Austin 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| | - Elisa T. Novelli
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology The University of Texas at Austin 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology The University of Texas at Austin 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
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20
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Post JB, Roodhart JML, Snippert HJG. Colorectal Cancer Modeling with Organoids: Discriminating between Oncogenic RAS and BRAF Variants. Trends Cancer 2020; 6:111-129. [PMID: 32061302 DOI: 10.1016/j.trecan.2019.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022]
Abstract
RAS and BRAF proteins are frequently mutated in colorectal cancer (CRC) and have been associated with therapy resistance in metastatic CRC patients. RAS isoforms are considered to act as redundant entities in physiological and pathological settings. However, there is compelling evidence that mutant variants of RAS and BRAF have different oncogenic potentials and therapeutic outcomes. In this review we describe similarities and differences between various RAS and BRAF oncogenes in CRC development, histology, and therapy resistance. In addition, we discuss the potential of patient-derived tumor organoids for personalized therapy, as well as CRC modeling using genome editing in preclinical model systems to study similarities and discrepancies between the effects of oncogenic MAPK pathway mutations on tumor growth and drug response.
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Affiliation(s)
- Jasmin B Post
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, CX Utrecht, The Netherlands; Oncode Institute Netherlands, Office Jaarbeurs Innovation Mile, Utrecht, The Netherlands
| | - Jeanine M L Roodhart
- Department of Medical Oncology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands; Oncode Institute Netherlands, Office Jaarbeurs Innovation Mile, Utrecht, The Netherlands
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, CX Utrecht, The Netherlands; Oncode Institute Netherlands, Office Jaarbeurs Innovation Mile, Utrecht, The Netherlands.
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21
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Grigorenko BL, Kots ED, Nemukhin AV. Diversity of mechanisms in Ras-GAP catalysis of guanosine triphosphate hydrolysis revealed by molecular modeling. Org Biomol Chem 2020; 17:4879-4891. [PMID: 31041977 DOI: 10.1039/c9ob00463g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mechanism of the deceptively simple reaction of guanosine triphosphate (GTP) hydrolysis catalyzed by the cellular protein Ras in complex with the activating protein GAP is an important issue because of the significance of this reaction in cancer research. We show that molecular modeling of GTP hydrolysis in the Ras-GAP active site reveals a diversity of mechanisms of the intrinsic chemical reaction depending on molecular groups at position 61 in Ras occupied by glutamine in the wild-type enzyme. First, a comparison of reaction energy profiles computed at the quantum mechanics/molecular mechanics (QM/MM) level shows that an assignment of the Gln61 side chain in the wild-type Ras either to QM or to MM parts leads to different scenarios corresponding to the glutamine-assisted or the substrate-assisted mechanisms. Second, replacement of Gln61 by the nitro-analog of glutamine (NGln) or by Glu, applied in experimental studies, results in two more scenarios featuring the so-called two-water and the concerted-type mechanisms. The glutamine-assisted mechanism in the wild-type Ras-GAP, in which the conserved Gln61 plays a decisive role, switching between the amide and imide tautomer forms, is consistent with the known experimental results of structural, kinetic and spectroscopy studies. The results emphasize the role of the Ras residue Gln61 in Ras-GAP catalysis and explain the retained catalytic activity of the Ras-GAP complex towards GTP hydrolysis in the Gln61NGln and Gln61Glu mutants of Ras.
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Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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22
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Goswami D, Chen D, Yang Y, Gudla PR, Columbus J, Worthy K, Rigby M, Wheeler M, Mukhopadhyay S, Powell K, Burgan W, Wall V, Esposito D, Simanshu DK, Lightstone FC, Nissley DV, McCormick F, Turbyville T. Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior. eLife 2020; 9:47654. [PMID: 31958057 PMCID: PMC7060043 DOI: 10.7554/elife.47654] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/02/2020] [Indexed: 01/16/2023] Open
Abstract
The RAS proteins are GTP-dependent switches that regulate signaling pathways and are frequently mutated in cancer. RAS proteins concentrate in the plasma membrane via lipid-tethers and hypervariable region side-chain interactions in distinct nano-domains. However, little is known about RAS membrane dynamics and the details of RAS activation of downstream signaling. Here, we characterize RAS in live human and mouse cells using single-molecule-tracking methods and estimate RAS mobility parameters. KRAS4b exhibits confined mobility with three diffusive states distinct from the other RAS isoforms (KRAS4a, NRAS, and HRAS); and although most of the amino acid differences between RAS isoforms lie within the hypervariable region, the additional confinement of KRAS4b is largely determined by the protein’s globular domain. To understand the altered mobility of an oncogenic KRAS4b, we used complementary experimental and molecular dynamics simulation approaches to reveal a detailed mechanism.
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Affiliation(s)
- Debanjan Goswami
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Yue Yang
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, United States
| | - Prabhakar R Gudla
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - John Columbus
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Karen Worthy
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Megan Rigby
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Madeline Wheeler
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Suman Mukhopadhyay
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Katie Powell
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - William Burgan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Vanessa Wall
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Felice C Lightstone
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, San Francisco, United States
| | - Thomas Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States
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23
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Nussinov R, Tsai C, Jang H. Autoinhibition can identify rare driver mutations and advise pharmacology. FASEB J 2019; 34:16-29. [DOI: 10.1096/fj.201901341r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/18/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section Basic Science Program Frederick National Laboratory for Cancer Research Frederick MD USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine Tel Aviv University Tel Aviv Israel
| | - Chung‐Jung Tsai
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine Tel Aviv University Tel Aviv Israel
| | - Hyunbum Jang
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine Tel Aviv University Tel Aviv Israel
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24
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Moghadamchargari Z, Huddleston J, Shirzadeh M, Zheng X, Clemmer DE, M Raushel F, Russell DH, Laganowsky A. Intrinsic GTPase Activity of K-RAS Monitored by Native Mass Spectrometry. Biochemistry 2019; 58:3396-3405. [PMID: 31306575 DOI: 10.1021/acs.biochem.9b00532] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mutations in RAS are associated with many different cancers and have been a therapeutic target for more than three decades. RAS cycles from an active to inactive state by both intrinsic and GTPase-activating protein (GAP)-stimulated hydrolysis. The activated enzyme interacts with downstream effectors, leading to tumor proliferation. Mutations in RAS associated with cancer are insensitive to GAP, and the rate of inactivation is limited to their intrinsic hydrolysis rate. Here, we use high-resolution native mass spectrometry (MS) to determine the kinetics and transition state thermodynamics of intrinsic hydrolysis for K-RAS and its oncogenic mutants. MS data reveal heterogeneity where both 2'-deoxy and 2'-hydroxy forms of GDP (guanosine diphosphate) and GTP (guanosine triphosphate) are bound to the recombinant enzyme. Intrinsic GTPase activity is directly monitored by the loss in mass of K-RAS bound to GTP, which corresponds to the release of phosphate. The rates determined from MS are in direct agreement with those measured using an established solution-based assay. Our results show that the transition state thermodynamics for the intrinsic GTPase activity of K-RAS is both enthalpically and entropically unfavorable. The oncogenic mutants G12C, Q61H, and G13D unexpectedly exhibit a 2'-deoxy GTP intrinsic hydrolysis rate higher than that for GTP.
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Affiliation(s)
- Zahra Moghadamchargari
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Jamison Huddleston
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Mehdi Shirzadeh
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Xueyun Zheng
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , Indiana , 47405 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - David H Russell
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Arthur Laganowsky
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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25
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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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