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Parise A, Cresca S, Magistrato A. Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins. Expert Opin Drug Discov 2024:1-21. [PMID: 39105536 DOI: 10.1080/17460441.2024.2387856] [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: 04/18/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
INTRODUCTION Molecular Dynamics (MD) simulations can support mechanism-based drug design. Indeed, MD simulations by capturing biomolecule motions at finite temperatures can reveal hidden binding sites, accurately predict drug-binding poses, and estimate the thermodynamics and kinetics, crucial information for drug discovery campaigns. Small-Guanosine Triphosphate Phosphohydrolases (GTPases) regulate a cascade of signaling events, that affect most cellular processes. Their deregulation is linked to several diseases, making them appealing drug targets. The broad roles of small-GTPases in cellular processes and the recent approval of a covalent KRas inhibitor as an anticancer agent renewed the interest in targeting small-GTPase with small molecules. AREA COVERED This review emphasizes the role of MD simulations in elucidating small-GTPase mechanisms, assessing the impact of cancer-related variants, and discovering novel inhibitors. EXPERT OPINION The application of MD simulations to small-GTPases exemplifies the role of MD simulations in the structure-based drug design process for challenging biomolecular targets. Furthermore, AI and machine learning-enhanced MD simulations, coupled with the upcoming power of quantum computing, are promising instruments to target elusive small-GTPases mutations and splice variants. This powerful synergy will aid in developing innovative therapeutic strategies associated to small-GTPases deregulation, which could potentially be used for personalized therapies and in a tissue-agnostic manner to treat tumors with mutations in small-GTPases.
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Affiliation(s)
- Angela Parise
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Sofia Cresca
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
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2
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Hutchins CM, Gorfe AA. From disorder comes function: Regulation of small GTPase function by intrinsically disordered lipidated membrane anchor. Curr Opin Struct Biol 2024; 87:102869. [PMID: 38943706 PMCID: PMC11283958 DOI: 10.1016/j.sbi.2024.102869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 07/01/2024]
Abstract
The intrinsically disordered, lipid-modified membrane anchor of small GTPases is emerging as a critical modulator of function through its ability to sort lipids in a conformation-dependent manner. We reviewed recent computational and experimental studies that have begun to shed light on the sequence-ensemble-function relationship in this unique class of lipidated intrinsically disordered regions (LIDRs).
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Affiliation(s)
- Chase M Hutchins
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA; Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6431 Fannin St., Houston, TX 77030, USA. https://twitter.com/chasedsims
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA; Biochemistry and Cell Biology Program & Therapeutics and Pharmacology Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6431 Fannin St., Houston, TX 77030, USA.
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3
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Arora N, Mu H, Liang H, Zhao W, Zhou Y. RAS G-domains allosterically contribute to the recognition of lipid headgroups and acyl chains. J Cell Biol 2024; 223:e202307121. [PMID: 38334958 PMCID: PMC10857904 DOI: 10.1083/jcb.202307121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/15/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Mutant RAS are major contributors to cancer and signal primarily from nanoclusters on the plasma membrane (PM). Their C-terminal membrane anchors are main features of membrane association. However, the same RAS isoform bound to different guanine nucleotides spatially segregate. Different RAS nanoclusters all enrich a phospholipid, phosphatidylserine (PS). These findings suggest more complex membrane interactions. Our electron microscopy-spatial analysis shows that wild-types, G12V mutants, and membrane anchors of isoforms HRAS, KRAS4A, and KRAS4B prefer distinct PS species. Mechanistically, reorientation of KRAS4B G-domain exposes distinct residues, such as Arg 135 in orientation state 1 (OS1) and Arg 73/Arg 102 in OS2, to the PM and differentially facilitates the recognition of PS acyl chains. Allele-specific oncogenic mutations of KRAS4B also shift G-domain reorientation equilibrium. Indeed, KRAS4BG12V, KRAS4BG12D, KRAS4BG12C, KRAS4BG13D, and KRAS4BQ61H associate with PM lipids with headgroup and acyl chain specificities. Distribution of these KRAS4B oncogenic mutants favors different nanoscale membrane topography. Thus, RAS G-domains allosterically facilitate membrane lateral distribution.
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Affiliation(s)
- Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Huanwen Mu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Wenting Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
- Program of Molecular and Translational Biology, Graduate School of Biological Sciences, M.D. Anderson Cancer Center and University of Texas Health Science Center, Houston, TX, USA
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4
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Gu X, Zhang Y, Long D. Conserved allosteric perturbation of the GTPase domains by region 1 of Ras hypervariable regions. Biophys J 2024; 123:839-846. [PMID: 38419331 PMCID: PMC10995424 DOI: 10.1016/j.bpj.2024.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
Ras proteins are important intracellular signaling hubs that can interact with numerous downstream effectors and upstream regulators through their GTPase domains (G-domains) anchored to plasma membranes by the C-terminal hypervariable regions (HVRs). The biological functions of Ras were proposed to be regulated at multiple levels including the intramolecular G-domain-HVR interactions, of which the exact mechanism and specificity are still controversial. Here, we demonstrate that the HVRs, instead of having direct contacts, can weakly perturb the G-domains via an allosteric interaction that is restricted to a ∼20 Å range and highly conserved in the tested Ras isoforms (HRas and KRas4B) and nucleotide-bound states. The origin of this allosteric perturbation has been localized to a short segment (residues 167-171) coinciding with region 1 of HVRs, which exhibits moderate to weak α-helical propensities. A charge-reversal mutation (E168K) of KRas4B in region 1, previously described in the Catalog of Somatic Mutations in Cancer database, was found to induce similar chemical shift perturbations as truncation of the HVR does. Further membrane paramagnetic relaxation enhancement (mPRE) data show that this region 1 mutation alters the membrane orientations of KRas4B and moderately increases the relative population of the signaling-compatible state.
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Affiliation(s)
- Xue Gu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yalong Zhang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Dong Long
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei, China; Department of Chemistry, University of Science and Technology of China, Hefei, China.
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5
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Erazo-Oliveras A, Muñoz-Vega M, Salinas ML, Wang X, Chapkin RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J 2024; 291:1299-1352. [PMID: 36282100 PMCID: PMC10126207 DOI: 10.1111/febs.16665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
- Center for Environmental Health Research; Texas A&M University; College Station, Texas, 77843; USA
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6
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Gu X, Liu D, Yu Y, Wang H, Long D. Quantitative Paramagnetic NMR-Based Analysis of Protein Orientational Dynamics on Membranes: Dissecting the KRas4B-Membrane Interactions. J Am Chem Soc 2023; 145:10295-10303. [PMID: 37116086 DOI: 10.1021/jacs.3c01597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Peripheral membrane proteins can adopt distinct orientations on the surfaces of lipid bilayers that are often short-lived and challenging to characterize by conventional experimental methods. Here we describe a robust approach for mapping protein orientational landscapes through quantitative interpretation of paramagnetic relaxation enhancement (PRE) data arising from membrane mimetics with spin-labeled lipids. Theoretical analysis, followed by experimental verification, reveals insights into the distinct properties of the PRE observables that are generally distorted in the case of stably membrane-anchored proteins. To suppress the artifacts, we demonstrate that undistorted Γ2 values can be obtained via transient membrane anchoring, based on which a computational framework is established for deriving accurate orientational ensembles obeying Boltzmann statistics. Application of the approach to KRas4B, a classical peripheral membrane protein whose orientations are critical for its functions and drug design, reveals four distinct orientational states that are close but not identical to those reported previously. Similar orientations are also found for a truncated KRas4B without the hypervariable region (HVR) that can sample a broader range of orientations, suggesting a confinement role of the HVR geometrically prohibiting severe tilting. Comparison of the KRas4B Γ2 rates measured using nanodiscs containing different types of anionic lipids reveals identical Γ2 patterns for the G-domain but different ones for the HVR, indicating only the latter is able to selectively interact with anionic lipids.
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Affiliation(s)
- Xue Gu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Dan Liu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yongkui Yu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Hui Wang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Dong Long
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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7
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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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8
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Ngo VA, Garcia AE. Millisecond molecular dynamics simulations of KRas-dimer formation and interfaces. Biophys J 2022; 121:3730-3744. [PMID: 35462078 PMCID: PMC9617078 DOI: 10.1016/j.bpj.2022.04.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/28/2022] [Accepted: 04/19/2022] [Indexed: 11/02/2022] Open
Abstract
Ras dimers have been proposed as building blocks for initiating the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) cellular signaling pathway. To better examine the structure of possible dimer interfaces, the dynamics of Ras dimerization, and its potential signaling consequences, we performed molecular dynamics simulations totaling 1 ms of sampling, using an all-atom model of two full-length, farnesylated, guanosine triphosphate (GTP)-bound, wild-type KRas4b proteins diffusing on 29%POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine)-mixed POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membranes. Our simulations unveil an ensemble of thermodynamically weak KRas dimers spanning multiple conformations. The most stable conformations, having the largest interface areas, involve helix α2 and a hypervariable region (HVR). Among the dimer conformations, we found that the HVR of each KRas has frequent interactions with various parts of the dimer, thus potentially mediating the dimerization. Some dimer configurations have one KRas G-domain elevated above the lipid bilayer surface by residing on top of the other G-domain, thus likely contributing to the recruitment of cytosolic Raf kinases in the context of a stably formed multi-protein complex. We identified a variant of the α4-α5 KRas-dimer interface that is similar to the interfaces obtained with fluorescence resonance energy transfer (FRET) data of HRas on lipid bilayers. Interestingly, we found two arginine fingers, R68 and R149, that directly interact with the beta-phosphate of the GTP bound in KRas, in a manner similar to what is observed in a crystal structure of GAP-HRas complex, which can facilitate the GTP hydrolysis via the arginine finger of GTPase-activating protein (GAP).
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Affiliation(s)
- Van A Ngo
- Advanced Computing for Life Sciences and Engineering Group, Science Engagement Section, National Center for Computational Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee; Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Angel E Garcia
- Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico.
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9
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Nguyen K, López CA, Neale C, Van QN, Carpenter TS, Di Natale F, Travers T, Tran TH, Chan AH, Bhatia H, Frank PH, Tonelli M, Zhang X, Gulten G, Reddy T, Burns V, Oppelstrup T, Hengartner N, Simanshu DK, Bremer PT, Chen D, Glosli JN, Shrestha R, Turbyville T, Streitz FH, Nissley DV, Ingólfsson HI, Stephen AG, Lightstone FC, Gnanakaran S. Exploring CRD mobility during RAS/RAF engagement at the membrane. Biophys J 2022; 121:3630-3650. [PMID: 35778842 PMCID: PMC9617161 DOI: 10.1016/j.bpj.2022.06.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Abstract
During the activation of mitogen-activated protein kinase (MAPK) signaling, the RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF bind to active RAS at the plasma membrane. The orientation of RAS at the membrane may be critical for formation of the RAS-RBDCRD complex and subsequent signaling. To explore how RAS membrane orientation relates to the protein dynamics within the RAS-RBDCRD complex, we perform multiscale coarse-grained and all-atom molecular dynamics (MD) simulations of KRAS4b bound to the RBD and CRD domains of RAF-1, both in solution and anchored to a model plasma membrane. Solution MD simulations describe dynamic KRAS4b-CRD conformations, suggesting that the CRD has sufficient flexibility in this environment to substantially change its binding interface with KRAS4b. In contrast, when the ternary complex is anchored to the membrane, the mobility of the CRD relative to KRAS4b is restricted, resulting in fewer distinct KRAS4b-CRD conformations. These simulations implicate membrane orientations of the ternary complex that are consistent with NMR measurements. While a crystal structure-like conformation is observed in both solution and membrane simulations, a particular intermolecular rearrangement of the ternary complex is observed only when it is anchored to the membrane. This configuration emerges when the CRD hydrophobic loops are inserted into the membrane and helices α3-5 of KRAS4b are solvent exposed. This membrane-specific configuration is stabilized by KRAS4b-CRD contacts that are not observed in the crystal structure. These results suggest modulatory interplay between the CRD and plasma membrane that correlate with RAS/RAF complex structure and dynamics, and potentially influence subsequent steps in the activation of MAPK signaling.
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Affiliation(s)
- Kien Nguyen
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Francesco Di Natale
- Applications, Simulations, and Quality, Lawrence Livermore National Laboratory, Livermore, California
| | | | - Timothy H Tran
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Albert H Chan
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Harsh Bhatia
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - Peter H Frank
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Gulcin Gulten
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Tyler Reddy
- CCS-7, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Violetta Burns
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Tomas Oppelstrup
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Nick Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Dhirendra K Simanshu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Peer-Timo Bremer
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California
| | - De Chen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - James N Glosli
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Rebika Shrestha
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Thomas Turbyville
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Dwight V Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico.
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10
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López CA, Zhang X, Aydin F, Shrestha R, Van QN, Stanley CB, Carpenter TS, Nguyen K, Patel LA, Chen D, Burns V, Hengartner NW, Reddy TJE, Bhatia H, Di Natale F, Tran TH, Chan AH, Simanshu DK, Nissley DV, Streitz FH, Stephen AG, Turbyville TJ, Lightstone FC, Gnanakaran S, Ingólfsson HI, Neale C. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. J Chem Theory Comput 2022; 18:5025-5045. [PMID: 35866871 DOI: 10.1021/acs.jctc.2c00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. Here, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (∼98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ∼1.5 million atoms is discussed in the context of MuMMI.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fikret Aydin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N Van
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Lara A Patel
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - De Chen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Violetta Burns
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tyler J E Reddy
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Albert H Chan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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11
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Araya MK, Gorfe AA. Phosphatidylserine and Phosphatidylethanolamine Asymmetry Have a Negligible Effect on the Global Structure, Dynamics, and Interactions of the KRAS Lipid Anchor. J Phys Chem B 2022; 126:4491-4500. [PMID: 35687481 DOI: 10.1021/acs.jpcb.2c01253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The intrinsically disordered C-terminus of the prominent oncogenic protein KRAS-4B (KRAS) selectively interacts and clusters with phosphatidylserine (PS) lipids in the plasma membrane (PM). This 11-residue segment, called tK, contains a polybasic domain (PBD) of six contiguous lysine residues and a farnesylated cysteine. Previous molecular dynamics (MD) simulation studies of tK in phosphatidylcholine (PC)/PS bilayers have suggested that backbone conformational dynamics modulate tK-PS interactions. These simulations have been conducted in symmetric membranes whereas the PM is compositionally asymmetric, with the inner leaflet, where KRAS is localized, being enriched with PS and phosphatidylethanolamine (PE) lipids. To examine if bilayer asymmetry affects tK conformational dynamics and interaction with lipids, we conducted two 10 μs long MD simulations of tK bound to a PC/PS and a PC/PS/PE bilayer in which the PS and PE lipids are distributed in one leaflet. We found that, first, these compositional asymmetries caused differences in acyl chain dynamics between leaflets, but the equilibrium structural and dynamic properties of the two asymmetric bilayers are similar; second, in both systems tK is highly dynamic and samples at least two distinct conformational states; third, PS-tK hydrogen-bonding interactions vary with peptide backbone conformations, and lysine side chains in the PBD predominantly interact with the serine oxygens of PS. These results are in good agreement with previous observations of tK in symmetric membranes. The effects of POPS asymmetry or the presence of POPE on tK are limited to modulating the relative contribution of individual side chains to interactions with lipids and redistributing conformational substates. Additional observations include the larger flexibility of tK in the current simulations, which we attribute to the longer duration of the simulations and the use of the CHARMM36m force field, which more accurately models intrinsically disordered peptides such as tK.
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Affiliation(s)
- Mussie K Araya
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas 77030, United States
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, Texas 77030, United States
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12
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Abstract
Both the mTORC2 and Ras-ERK pathways respond to growth factor stimulation and play critical roles in cell growth and proliferation, disarray of these pathways leads to many diseases, especially cancer. These two signaling pathways crosstalk at many levels; recently it's become clear that the SIN1 component of mTORC2 could interact with Ras family small GTPases, but how these two proteins interact at the molecular level and the functional outcomes of this interaction remain to be addressed. In this work we determined the high-resolution structure of Ras-SIN1 complexes and revealed the detailed interaction mechanism. We also showed that Ras-SIN1 association inhibits insulin-induced ERK activation. Insights from this work could improve our understanding of the disease-causing mechanism of errant mTORC2 or Ras proteins. Over the years it has been established that SIN1, a key component of mTORC2, could interact with Ras family small GTPases through its Ras-binding domain (RBD). The physical association of Ras and SIN1/mTORC2 could potentially affect both mTORC2 and Ras-ERK pathways. To decipher the precise molecular mechanism of this interaction, we determined the high-resolution structures of HRas/KRas-SIN1 RBD complexes, showing the detailed interaction interface. Mutation of critical interface residues abolished Ras-SIN1 interaction and in SIN1 knockout cells we demonstrated that Ras-SIN1 association promotes SGK1 activity but inhibits insulin-induced ERK activation. With structural comparison and competition fluorescence resonance energy transfer (FRET) assays we showed that HRas-SIN1 RBD association is much weaker than HRas-Raf1 RBD but is slightly stronger than HRas-PI3K RBD interaction, providing a possible explanation for the different outcome of insulin or EGF stimulation. We also found that SIN1 isoform lacking the PH domain binds stronger to Ras than other longer isoforms and the PH domain appears to have an inhibitory effect on Ras-SIN1 binding. In addition, we uncovered a Ras dimerization interface that could be critical for Ras oligomerization. Our results advance our understanding of Ras-SIN1 association and crosstalk between growth factor-stimulated pathways.
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13
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Nussinov R, Zhang M, Maloney R, Tsai C, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2022; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [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: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Chung‐Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of InformaticsMiddle East Technical UniversityAnkaraTurkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of InformaticsMiddle East Technical UniversityAnkaraTurkey
- Department of Chemical and Biological Engineering, College of EngineeringKoc UniversityIstanbulTurkey
- Koc University Research Center for Translational Medicine, School of MedicineKoc UniversityIstanbulTurkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
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14
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Bondos SE, Dunker AK, Uversky VN. Intrinsically disordered proteins play diverse roles in cell signaling. Cell Commun Signal 2022; 20:20. [PMID: 35177069 PMCID: PMC8851865 DOI: 10.1186/s12964-022-00821-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered.
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Affiliation(s)
- Sarah E. Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843 USA
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, Moscow Region, Russia 142290
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15
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Andreadelis I, Kiriakidi S, Lamprakis C, Theodoropoulou A, Doerr S, Chatzigoulas A, Manchester J, Velez-Vega C, Duca JS, Cournia Z. Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability. J Phys Chem B 2022; 126:1504-1519. [PMID: 35142524 DOI: 10.1021/acs.jpcb.1c01184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ras proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the properties of Ras in terms of dimerization/clustering on the cell membrane. To understand the effects of anionic lipids on key spatiotemporal properties of dimeric K-Ras4B, we perform all-atom molecular dynamics simulations of the dimer K-Ras4B in the presence and absence of Raf[RBD/CRD] effectors on two model anionic lipid membranes: one containing 78% mol DOPC, 20% mol DOPS, and 2% mol PIP2 and another one with enhanced concentration of anionic lipids containing 50% mol DOPC, 40% mol DOPS, and 10% mol PIP2. Analysis of our results unveils the orientational space of dimeric K-Ras4B and shows that the stability of the dimer is enhanced on the membrane containing a high concentration of anionic lipids in the absence of Raf effectors. This enhanced stability is also observed in the presence of Raf[RBD/CRD] effectors although it is not influenced by the concentration of anionic lipids in the membrane, but rather on the ability of Raf[CRD] to anchor to the membrane. We generate dominant K-Ras4B conformations by Markov state modeling and yield the population of states according to the K-Ras4B orientation on the membrane. For the membrane containing anionic lipids, we observe correlations between the diffusion of K-Ras4B and PIP2 and anchoring of anionic lipids to the Raf[CRD] domain. We conclude that the presence of effectors with the Raf[CRD] domain anchoring on the membrane as well as the membrane composition both influence the conformational stability of the K-Ras4B dimer, enabling the preservation of crucial interface interactions.
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Affiliation(s)
- Ioannis Andreadelis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Sofia Kiriakidi
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Christos Lamprakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | | | - Stefan Doerr
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Alexios Chatzigoulas
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - John Manchester
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - José S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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16
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Ozdemir ES, Koester AM, Nan X. Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Genes (Basel) 2022; 13:219. [PMID: 35205266 PMCID: PMC8872464 DOI: 10.3390/genes13020219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Formation of Ras multimers, including dimers and nanoclusters, has emerged as an exciting, new front of research in the 'old' field of Ras biomedicine. With significant advances made in the past few years, we are beginning to understand the structure of Ras multimers and, albeit preliminary, mechanisms that regulate their formation in vitro and in cells. Here we aim to synthesize the knowledge accrued thus far on Ras multimers, particularly the presence of multiple globular (G-) domain interfaces, and discuss how membrane nanodomain composition and structure would influence Ras multimer formation. We end with some general thoughts on the potential implications of Ras multimers in basic and translational biology.
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Affiliation(s)
- E. Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
| | - Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
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17
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Prakash P, Gorfe AA. Determinants of Membrane Orientation Dynamics in Lipid-Modified Small GTPases. JACS AU 2022; 2:128-135. [PMID: 35098229 PMCID: PMC8790735 DOI: 10.1021/jacsau.1c00426] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 05/30/2023]
Abstract
The transient membrane engagement and reorientation of the soluble catalytic domain of Ras proteins has emerged as an important modulator of their functions. However, there has been limited information on whether this phenomenon is applicable to other members of the Ras superfamily. To address this issue, we conducted long-time-scale atomistic molecular dynamics simulations (55 μs aggregate simulation time) on representatives of the Ras, Rho, and Arf family proteins that differ in sequence, lipid modification, and the rigidity of the linker between the lipid anchor and the catalytic G-domain. The results show that the concept of membrane reorientation is generalizable to most but not all members of the Ras superfamily. Specifically, C-terminally prenylated small GTPases that are anchored to membranes via a single flexible linker adopt multiple orientations, whereas those that are N-terminally myristoylated and harbor a rigid linker experience limited orientational dynamics. Combined with published reports on Ras proteins, these observations provide insights into the common principles and determinants of the orientational dynamics of lipidated small GTPases on membrane surfaces and offer new ways of thinking about the regulation and druggability of the Ras superfamily proteins.
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18
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Heinrich F, Van QN, Jean-Francois F, Stephen AG, Lösche M. Membrane-bound KRAS approximates an entropic ensemble of configurations. Biophys J 2021; 120:4055-4066. [PMID: 34384763 PMCID: PMC8510975 DOI: 10.1016/j.bpj.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/08/2021] [Accepted: 08/04/2021] [Indexed: 11/27/2022] Open
Abstract
KRAS4B is a membrane-anchored signaling protein and a primary target in cancer research. Predictions from molecular dynamics simulations that have previously shaped our mechanistic understanding of KRAS signaling disagree with recent experimental results from neutron reflectometry, NMR, and thermodynamic binding studies. To gain insight into these discrepancies, we compare this body of biophysical data to back-calculated experimental results from a series of molecular simulations that implement different subsets of molecular interactions. Our results show that KRAS4B approximates an entropic ensemble of configurations at model membranes containing 30% phosphatidylserine lipids, which is not significantly shaped by interactions between the globular G-domain of KRAS4B and the lipid membrane. These findings revise our understanding of KRAS signaling and promote a model in which the protein samples the accessible conformational space in a near-uniform manner while being available to bind to effector proteins.
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Affiliation(s)
- Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland.
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Frantz Jean-Francois
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland
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19
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Intrinsically disordered proteins and membranes: a marriage of convenience for cell signalling? Biochem Soc Trans 2021; 48:2669-2689. [PMID: 33155649 PMCID: PMC7752083 DOI: 10.1042/bst20200467] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023]
Abstract
The structure-function paradigm has guided investigations into the molecules involved in cellular signalling for decades. The peripheries of this paradigm, however, start to unravel when considering the co-operation between proteins and the membrane in signalling processes. Intrinsically disordered regions hold distinct advantages over folded domains in terms of their binding promiscuity, sensitivity to their particular environment and their ease of modulation through post-translational modifications. Low sequence complexity and bias towards charged residues are also favourable for the multivalent electrostatic interactions that occur at the surfaces of lipid bilayers. This review looks at the principles behind the successful marriage between protein disorder and membranes in addition to the role of this partnership in modifying and regulating signalling in cellular processes. The HVR (hypervariable region) of small GTPases is highlighted as a well-studied example of the nuanced role a short intrinsically disordered region can play in the fine-tuning of signalling pathways.
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20
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Zhou Y, Gorfe AA, Hancock JF. RAS Nanoclusters Selectively Sort Distinct Lipid Headgroups and Acyl Chains. Front Mol Biosci 2021; 8:686338. [PMID: 34222339 PMCID: PMC8245699 DOI: 10.3389/fmolb.2021.686338] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
RAS proteins are lipid-anchored small GTPases that switch between the GTP-bound active and GDP-bound inactive states. RAS isoforms, including HRAS, NRAS and splice variants KRAS4A and KRAS4B, are some of the most frequently mutated proteins in cancer. In particular, constitutively active mutants of KRAS comprise ∼80% of all RAS oncogenic mutations and are found in 98% of pancreatic, 45% of colorectal and 31% of lung tumors. Plasma membrane (PM) is the primary location of RAS signaling in biology and pathology. Thus, a better understanding of how RAS proteins localize to and distribute on the PM is critical to better comprehend RAS biology and to develop new strategies to treat RAS pathology. In this review, we discuss recent findings on how RAS proteins sort lipids as they undergo macromolecular assembly on the PM. We also discuss how RAS/lipid nanoclusters serve as signaling platforms for the efficient recruitment of effectors and signal transduction, and how perturbing the PM biophysical properties affect the spatial distribution of RAS isoforms and their functions.
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Affiliation(s)
- Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX, United States
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX, United States
| | - John F. Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX, United States
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21
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Ras Variant Biology and Contributions to Human Disease. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:3-18. [PMID: 33977468 DOI: 10.1007/978-1-0716-1190-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of cancer and RASopathy genetic databases reveals that ~19% of all cancer cases and ~4% of developmental disorders contain Ras mutations. Ras isoform and mutation variants differentially contribute to these diseases and provide an opportunity for deeper understanding of Ras function. The putative mechanisms underpinning these differences, new approaches that are being applied, and some of the key questions and challenges that remain are discussed.
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22
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Nair VV, Yin G, Zhang J, Hancock JF, Campbell SL, Gorfe AA. Monoubiquitination of KRAS at Lysine104 and Lysine147 Modulates Its Dynamics and Interaction with Partner Proteins. J Phys Chem B 2021; 125:4681-4691. [PMID: 33929846 DOI: 10.1021/acs.jpcb.1c01062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
KRAS, a 21 kDa guanine nucleotide-binding protein that functions as a molecular switch, plays a key role in regulating cellular growth. Dysregulation of this key signaling node leads to uncontrolled cell growth, a hallmark of cancer cells. KRAS undergoes post-translational modification by monoubiquitination at various locations, including at lysine104 (K104) and lysine147 (K147). Previous studies have suggested that K104 stabilizes helix-2/helix-3 interactions and K147 is involved in nucleotide binding. However, the impact of monoubiquitination at these residues on the overall structure, dynamics, or function of KRAS is not fully understood. In this study, we examined KRAS monoubiquitination at these sites using data from extensive (12 μs aggregate time) molecular dynamics simulations complemented by nuclear magnetic resonance spectroscopy data. We found that ubiquitin forms dynamic nonspecific interactions with various regions of KRAS and that ubiquitination at both sites modulates conformational fluctuations. In both cases, ubiquitin samples a broad range of conformational space and does not form long-lasting noncovalent contacts with KRAS but it adopts several preferred orientations relative to KRAS. To examine the functional impact of these preferred orientations, we performed a systematic comparison of the dominant configurations of the ubiquitin/KRAS simulated complex with experimental structures of KRAS bound to regulatory and effector proteins as well as a model membrane. Results from these analyses suggest that conformational selection and population shift may minimize the deleterious effects of KRAS ubiquitination at K104 and K147 on binding to some but not all interaction partners. Our findings thus provide new insights into the steric effects of ubiquitin and suggest a potential avenue for therapeutic targeting.
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Affiliation(s)
- Vinay V Nair
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States.,MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Guowei Yin
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, Guangdong, China
| | - Jerry Zhang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States.,MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Sharon L Campbell
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, United States
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States.,MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
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23
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López CA, Agarwal A, Van QN, Stephen AG, Gnanakaran S. Unveiling the Dynamics of KRAS4b on Lipid Model Membranes. J Membr Biol 2021; 254:201-216. [PMID: 33825026 PMCID: PMC8052243 DOI: 10.1007/s00232-021-00176-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/16/2021] [Indexed: 12/23/2022]
Abstract
Small GTPase proteins are ubiquitous and responsible for regulating several processes related to cell growth and differentiation. Mutations that stabilize their active state can lead to uncontrolled cell proliferation and cancer. Although these proteins are well characterized at the cellular scale, the molecular mechanisms governing their functions are still poorly understood. In addition, there is limited information about the regulatory function of the cell membrane which supports their activity. Thus, we have studied the dynamics and conformations of the farnesylated KRAS4b in various membrane model systems, ranging from binary fluid mixtures to heterogeneous raft mimics. Our approach combines long time-scale coarse-grained (CG) simulations and Markov state models to dissect the membrane-supported dynamics of KRAS4b. Our simulations reveal that protein dynamics is mainly modulated by the presence of anionic lipids and to some extent by the nucleotide state (activation) of the protein. In addition, our results suggest that both the farnesyl and the polybasic hypervariable region (HVR) are responsible for its preferential partitioning within the liquid-disordered (Ld) domains in membranes, potentially enhancing the formation of membrane-driven signaling platforms.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
| | - Animesh Agarwal
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation. Nat Commun 2021; 12:1176. [PMID: 33608534 PMCID: PMC7895934 DOI: 10.1038/s41467-021-21422-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
The first step of RAF activation involves binding to active RAS, resulting in the recruitment of RAF to the plasma membrane. To understand the molecular details of RAS-RAF interaction, we present crystal structures of wild-type and oncogenic mutants of KRAS complexed with the RAS-binding domain (RBD) and the membrane-interacting cysteine-rich domain (CRD) from the N-terminal regulatory region of RAF1. Our structures reveal that RBD and CRD interact with each other to form one structural entity in which both RBD and CRD interact extensively with KRAS. Mutations at the KRAS-CRD interface result in a significant reduction in RAF1 activation despite only a modest decrease in binding affinity. Combining our structures and published data, we provide a model of RAS-RAF complexation at the membrane, and molecular insights into RAS-RAF interaction during the process of RAS-mediated RAF activation. The molecular details of the RAS-RAF interaction are still not fully understood. Here, the authors present crystal structures of wild-type and mutant KRAS in complex with the RAS-binding and membrane-interacting cysteine-rich domains of RAF1, and propose a model of the membrane-bound RAS-RAF complex.
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Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V. Inhibition of Nonfunctional Ras. Cell Chem Biol 2021; 28:121-133. [PMID: 33440168 PMCID: PMC7897307 DOI: 10.1016/j.chembiol.2020.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Intuitively, functional states should be targeted; not nonfunctional ones. So why could drugging the inactive K-Ras4BG12Cwork-but drugging the inactive kinase will likely not? The reason is the distinct oncogenic mechanisms. Kinase driver mutations work by stabilizing the active state and/or destabilizing the inactive state. Either way, oncogenic kinases are mostly in the active state. Ras driver mutations work by quelling its deactivation mechanisms, GTP hydrolysis, and nucleotide exchange. Covalent inhibitors that bind to the inactive GDP-bound K-Ras4BG12C conformation can thus work. By contrast, in kinases, allosteric inhibitors work by altering the active-site conformation to favor orthosteric drugs. From the translational standpoint this distinction is vital: it expedites effective pharmaceutical development and extends the drug classification based on the mechanism of action. Collectively, here we postulate that drug action relates to blocking the mechanism of activation, not to whether the protein is in the active or inactive state.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Migliori AD, Patel LA, Neale C. The RIT1 C-terminus associates with lipid bilayers via charge complementarity. Comput Biol Chem 2021; 91:107437. [PMID: 33517146 DOI: 10.1016/j.compbiolchem.2021.107437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/30/2020] [Accepted: 01/14/2021] [Indexed: 12/13/2022]
Abstract
RIT1 is a member of the Ras superfamily of small GTPases involved in regulation of cellular signaling. Mutations to RIT1 are involved in cancer and developmental disorders. Like many Ras subfamily members, RIT1 is localized to the plasma membrane. However, RIT1 lacks the C-terminal prenylation that helps many other subfamily members adhere to cellular membranes. We used molecular dynamics simulations to examine the mechanisms by which the C-terminal peptide (CTP) of RIT1 associates with lipid bilayers. We show that the CTP is unstructured and that its membrane interactions depend on lipid composition. While a 12-residue region of the CTP binds strongly to anionic bilayers containing phosphatidylserine lipids, the CTP termini fray from the membrane allowing for accommodation of the RIT1 globular domain at the membrane-water interface.
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Affiliation(s)
- Amy D Migliori
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States
| | - Lara A Patel
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, United States.
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Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
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Pálfy G, Menyhárd DK, Perczel A. Dynamically encoded reactivity of Ras enzymes: opening new frontiers for drug discovery. Cancer Metastasis Rev 2020; 39:1075-1089. [PMID: 32815102 PMCID: PMC7680338 DOI: 10.1007/s10555-020-09917-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022]
Abstract
Decoding molecular flexibility in order to understand and predict biological processes-applying the principles of dynamic-structure-activity relationships (DSAR)-becomes a necessity when attempting to design selective and specific inhibitors of a protein that has overlapping interaction surfaces with its upstream and downstream partners along its signaling cascade. Ras proteins are molecular switches that meet this definition perfectly. The close-lying P-loop and the highly flexible switch I and switch II regions are the site of nucleotide-, assisting-, and effector-protein binding. Oncogenic mutations that also appear in this region do not cause easily characterized overall structural changes, due partly to the inherent conformational heterogeneity and pliability of these segments. In this review, we present an overview of the results obtained using approaches targeting Ras dynamics, such as nuclear magnetic resonance (NMR) measurements and experiment-based modeling calculations (mostly molecular dynamics (MD) simulations). These methodologies were successfully used to decipher the mutant- and isoform-specific nature of certain transient states, far-lying allosteric sites, and the internal interaction networks, as well as the interconnectivity of the catalytic and membrane-binding regions. This opens new therapeutic potential: the discovered interaction hotspots present hitherto not targeted, selective sites for drug design efforts in diverse locations of the protein matrix.
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Affiliation(s)
- Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary
- Protein Modeling Group HAS-ELTE, Institute of Chemistry, Eötvös Loránd University, P.O.B. 32, Budapest, 1538, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary.
- Protein Modeling Group HAS-ELTE, Institute of Chemistry, Eötvös Loránd University, P.O.B. 32, Budapest, 1538, Hungary.
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE, Eötvös Loránd University, Pázmány Péter sétány 1/A, 1117, Budapest, Hungary.
- Protein Modeling Group HAS-ELTE, Institute of Chemistry, Eötvös Loránd University, P.O.B. 32, Budapest, 1538, Hungary.
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29
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Abankwa D, Gorfe AA. Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again. Biomolecules 2020; 10:E1522. [PMID: 33172116 PMCID: PMC7694788 DOI: 10.3390/biom10111522] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/17/2022] Open
Abstract
Ras is the most frequently mutated oncogene and recent drug development efforts have spurred significant new research interest. Here we review progress toward understanding how Ras functions in nanoscale, proteo-lipid signaling complexes on the plasma membrane, called nanoclusters. We discuss how G-domain reorientation is plausibly linked to Ras-nanoclustering and -dimerization. We then look at how these mechanistic features could cooperate in the engagement and activation of RAF by Ras. Moreover, we show how this structural information can be integrated with microscopy data that provide nanoscale resolution in cell biological experiments. Synthesizing the available data, we propose to distinguish between two types of Ras nanoclusters, an active, immobile RAF-dependent type and an inactive/neutral membrane anchor-dependent. We conclude that it is possible that Ras reorientation enables dynamic Ras dimerization while the whole Ras/RAF complex transits into an active state. These transient di/oligomer interfaces of Ras may be amenable to pharmacological intervention. We close by highlighting a number of open questions including whether all effectors form active nanoclusters and whether there is an isoform specific composition of Ras nanocluster.
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Affiliation(s)
- Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA
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30
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Ueda S, Tamura N, Mima J. Membrane Tethering Potency of Rab-Family Small GTPases Is Defined by the C-Terminal Hypervariable Regions. Front Cell Dev Biol 2020; 8:577342. [PMID: 33102484 PMCID: PMC7554592 DOI: 10.3389/fcell.2020.577342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane tethering is a crucial step to determine the spatiotemporal specificity of secretory and endocytic trafficking pathways in all eukaryotic endomembrane systems. Recent biochemical studies by a chemically-defined reconstitution approach reveal that, in addition to the structurally-diverse classic tethering factors such as coiled-coil tethering proteins and multisubunit tethering complexes, Rab-family small GTPases also retain the inherent membrane tethering functions to directly and physically bridge two distinct lipid bilayers by themselves. Although Rab-mediated membrane tethering reactions are fairly efficient and specific in the physiological context, its mechanistic basis is yet to be understood. Here, to explore whether and how the intrinsic tethering potency of Rab GTPases is controlled by their C-terminal hypervariable region (HVR) domains that link the conserved small GTPase domains (G-domains) to membrane anchors at the C-terminus, we quantitatively compared tethering activities of two representative Rab isoforms in humans (Rab5a, Rab4a) and their HVR-deleted mutant forms. Strikingly, deletion of the HVR linker domains enabled both Rab5a and Rab4a isoforms to enhance their intrinsic tethering potency, exhibiting 5- to 50-fold higher initial velocities of tethering for the HVR-deleted mutants than those for the full-length, wild-type Rabs. Furthermore, we revealed that the tethering activity of full-length Rab5a was significantly reduced by the omission of anionic lipids and cholesterol from membrane lipids and, however, membrane tethering driven by HVR-deleted Rab5a mutant was completely insensitive to the headgroup composition of lipids. Reconstituted membrane tethering assays with the C-terminally-truncated mutants of Rab4a further uncovered that the N-terminal residues in the HVR linker, located adjacent to the G-domain, are critical for regulating the intrinsic tethering activity. In conclusion, our current findings establish that the non-conserved, flexible C-terminal HVR linker domains define membrane tethering potency of Rab-family small GTPases through controlling the close attachment of the globular G-domains to membrane surfaces, which confers the active tethering-competent state of the G-domains on lipid bilayers.
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Affiliation(s)
- Sanae Ueda
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Naoki Tamura
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Joji Mima
- Institute for Protein Research, Osaka University, Suita, Japan
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31
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Van QN, López CA, Tonelli M, Taylor T, Niu B, Stanley CB, Bhowmik D, Tran TH, Frank PH, Messing S, Alexander P, Scott D, Ye X, Drew M, Chertov O, Lösche M, Ramanathan A, Gross ML, Hengartner NW, Westler WM, Markley JL, Simanshu DK, Nissley DV, Gillette WK, Esposito D, McCormick F, Gnanakaran S, Heinrich F, Stephen AG. Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane. Proc Natl Acad Sci U S A 2020; 117:24258-24268. [PMID: 32913056 PMCID: PMC7533834 DOI: 10.1073/pnas.2006504117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as "membrane-distal" and estimate to comprise ∼90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.
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Affiliation(s)
- Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Troy Taylor
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Ben Niu
- National Mass Spectrometry Resource, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Debsindhu Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Timothy H Tran
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Peter H Frank
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Simon Messing
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Patrick Alexander
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Daniel Scott
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Xiaoying Ye
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Matt Drew
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Oleg Chertov
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Mathias Lösche
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Michael L Gross
- National Mass Spectrometry Resource, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - William M Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Dhirendra K Simanshu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dwight V Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - William K Gillette
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dominic Esposito
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Frank McCormick
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702;
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702;
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How to make an undruggable enzyme druggable: lessons from ras proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020. [PMID: 32951811 DOI: 10.1016/bs.apcsb.2020.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Significant advances have been made toward discovering allosteric inhibitors for challenging drug targets such as the Ras family of membrane-associated signaling proteins. Malfunction of Ras proteins due to somatic mutations is associated with up to a quarter of all human cancers. Computational techniques have played critical roles in identifying and characterizing allosteric ligand-binding sites on these proteins, and to screen ligand libraries against those sites. These efforts, combined with a wide range of biophysical, structural, biochemical and cell biological experiments, are beginning to yield promising inhibitors to treat malignancies associated with mutated Ras proteins. In this chapter, we discuss some of these developments and how the lessons learned from Ras might be applied to similar other challenging drug targets.
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Travers T, López CA, Agamasu C, Hettige JJ, Messing S, García AE, Stephen AG, Gnanakaran S. Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD. Biophys J 2020; 119:525-538. [PMID: 32649863 PMCID: PMC7399501 DOI: 10.1016/j.bpj.2020.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 11/25/2022] Open
Abstract
CRAF activation requires binding to membrane-anchored and active GTP-bound RAS. Whereas its RAS-binding domain (RBD) contains the main binding interface to the RAS G domain, its cysteine-rich domain (CRD) is responsible for association to anionic lipid-rich membranes. Both RAF domains are connected by a short linker, and it remains unclear if the two domains act independently or if one domain can impact the function of the other. Here, we used a combination of coarse-grained and all-atom molecular dynamics simulations of a CRAF RBD-CRD construct to investigate the dynamics of the RBD when it is tethered to CRD that is anchored to a POPC:POPS model membrane. First, we show that the RBD positioning is very dynamic with a preferential localization near the membrane surface. Next, we show that membrane-localized RBD has its RAS-binding interface mostly inaccessible because of its proximity to the membrane. Several positively charged residues in this interface were identified from simulations as important for driving RBD association to the membrane. Surface plasmon resonance (SPR) measurements confirmed that mutations of these RBD residues reduced the liposome partitioning of RBD-CRD. Last, simulations indicated that the presence of RBD near the membrane led to a local enrichment of anionic lipids that could potentially enhance the membrane affinity of the entire RBD-CRD construct. This was supported by SPR measurements that showed stronger liposome partitioning of RBD-CRD relative to CRD alone. These findings thus suggest that the RBD and CRD have synergistic effects on their membrane dynamics, with CRD bringing RBD closer to the membrane that impacts its accessibility to RAS and with RBD causing local anionic lipid enrichment that enhances the overall affinity between the membrane and RBD-CRD. These mechanisms have potential implications on the order of events of the interactions between RAS and CRAF at the membrane.
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Affiliation(s)
- Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico
| | - Constance Agamasu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | | | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Reseach, Inc., Frederick, Maryland
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos, New Mexico.
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KRAS(G12C)-AMG 510 interaction dynamics revealed by all-atom molecular dynamics simulations. Sci Rep 2020; 10:11992. [PMID: 32686745 PMCID: PMC7371895 DOI: 10.1038/s41598-020-68950-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/03/2020] [Indexed: 01/02/2023] Open
Abstract
The first KRAS(G12C) targeting inhibitor in clinical development, AMG 510, has shown promising antitumor activity in clinical trials. On the molecular level, however, the interaction dynamics of this covalently bound drug–protein complex has been undetermined. Here, we disclose the interaction dynamics of the KRAS(G12C)–AMG 510 complex by long timescale all-atom molecular dynamics (MD) simulations (total of 75 μs). Moreover, we investigated the influence of the recently reported post-translational modification (PTM) of KRAS’ N-terminus, removal of initiator methionine (iMet1) with acetylation of Thr2, to this complex. Our results demonstrate that AMG 510 does not entrap KRAS into a single conformation, as one would expect based on the crystal structure, but rather into an ensemble of conformations. AMG 510 binding is extremely stable regardless of highly dynamic interface of KRAS’ switches. Overall, KRAS(G12C)–AMG 510 complex partially mimic the native dynamics of GDP bound KRAS; however, AMG 510 stabilizes the α3-helix region. N-terminally modified KRAS displays similar interaction dynamics with AMG 510 as when Met1 is present, but this PTM appears to stabilize β2–β3-loop. These results provide novel conformational insights on the molecular level to KRAS(G12C)–AMG 510 interactions and dynamics, providing new perspectives to RAS related drug discovery.
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35
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Prakash P. A regulatory role of membrane by direct modulation of the catalytic kinase domain. Small GTPases 2020; 12:246-256. [PMID: 32663062 DOI: 10.1080/21541248.2020.1788886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cell membrane modulates the function and activity of specific proteins and acts more than just a non-specific scaffolding machinery. In this review, I focus on studies that highlight a direct membrane-mediated modulation of the catalytic kinase domain of a variety of kinases thereby regulating the kinase activity. It emerges that membrane provides a second level of regulation once kinase domain is relieved of its inactive auto-inhibitory state. For the first time a generalized regulatory role of membrane is proposed that governs the kinase activity by modulating the catalytic kinase domain. Striking similarities among a variety of multi-domain kinases as well as single-domain lipidated enzymes such as RAS proteins are presented.
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Affiliation(s)
- Priyanka Prakash
- Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
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36
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Ngo VA, Sarkar S, Neale C, Garcia AE. How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes. J Phys Chem B 2020; 124:5434-5453. [PMID: 32438809 DOI: 10.1021/acs.jpcb.0c02642] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RAS proteins are small membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the spatiotemporal properties of RAS through dimerization/clustering and signaling fidelity. To understand the effects of anionic lipids on key spatiotemporal properties of RAS, we dissected 1 ms of data from all-atom molecular dynamics simulations for KRAS4B on two model anionic lipid membranes that have 30% of POPS mixed with neutral POPC and 8% of PIP2 mixed with POPC. We unveiled the orientation space of KRAS4B, whose kinetics were slower and more distinguishable on the membrane containing PIP2 than the membrane containing POPS. Particularly, the PIP2-mixed membrane can differentiate a third kinetic orientation state from the other two known orientation states. We observed that each orientation state may yield different binding modes with an RAF kinase, which is required for activating the MAPK/ERK signaling pathway. However, an overall occluded probability, for which RAF kinases cannot bind KRAS4B, remains unchanged on the two different membranes. We identified rare fast diffusion modes of KRAS4B that appear coupled with orientations exposed to cytosolic RAF. Particularly, on the membrane having PIP2, we found nonlinear correlations between the orientation states and the conformations of the cationic farnesylated hypervariable region, which acts as an anchor in the membrane. Using diffusion coefficients estimated from the all-atom simulations, we quantified the effect of PIP2 and POPS on the KRAS4B dimerization via Green's function reaction dynamics simulations, in which the averaged dimerization rate is 12.5% slower on PIP2-mixed membranes.
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Affiliation(s)
- Van A Ngo
- Center for Nonlinear Studies (CNLS), Los Alamos National Lab, Los Alamos, New Mexico 87545, United States
| | - Sumantra Sarkar
- Center for Nonlinear Studies (CNLS), Los Alamos National Lab, Los Alamos, New Mexico 87545, United States
| | - Chris Neale
- Theoretical Biology and Biophysics Group, T-6, Los Alamos National Lab, Los Alamos, New Mexico 87545, United States
| | - Angel E Garcia
- Center for Nonlinear Studies (CNLS), Los Alamos National Lab, Los Alamos, New Mexico 87545, United States
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Gorfe AA, Sligar SG. Membrane-Bound Ras as a Conformational Clock. Biophys J 2020; 118:991-993. [PMID: 32023437 DOI: 10.1016/j.bpj.2020.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/14/2020] [Indexed: 01/18/2023] Open
Affiliation(s)
- Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas.
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, Illinois.
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