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Lee J, Lee HJ, Lee Y, Lim B, Gam J, Oh DC, Lee J. Development of PD3 and PD3-B for PDEδ inhibition to modulate KRAS activity. J Enzyme Inhib Med Chem 2022; 37:1656-1666. [PMID: 35695156 PMCID: PMC9225715 DOI: 10.1080/14756366.2022.2086865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Despite extensive efforts over 40 years, few effective KRAS inhibitors have been developed to date, mainly due to the undruggable features of KRAS proteins. In addition to the direct approach to KRAS via covalent inhibition, modulation of the prenyl-binding protein PDEδ that binds with farnesylated KRAS has emerged as an alternative strategy to abrogate KRAS activity. For the verification of new therapeutic strategies, chemical probes with the dual functions of visualisation and pharmacological inhibition against oncogenic proteins are enormously valuable to understand cellular events related to cancer. Here, we report indolizino[3,2-c]quinoline (IQ)-based fluorescent probes (PD3 and PD3-B) for PDEδ inhibition. By using the unique fluorescent characteristics of the IQ scaffold, a fluorescence polarisation (FP)-based binding assay identified PD3 as the most effective PDEδ probe among the tested PD analogues, with a low Kd value of 0.491 µM and long retention time in the binding site of PDEδ. In particular, a FP-based competition assay using deltarasin verified that PD3 occupies the farnesylation binding site of PDEδ, excluding the possibility that the FP signals resulted from non-specific hydrophobic interactions between the ligand and protein in the assay. We also designed and synthesised PD3-B (5), an affinity-based probe (ABP) from the PD3 structure, which enabled us to pull down PDEδ from bacterial lysates containing a large number of intrinsic bacterial proteins. Finally, KRAS relocalization was verified in PANC-1 cells by treatment with PD3, suggesting its potential as an effective probe to target PDEδ.
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Affiliation(s)
- Jungeun Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ho Jin Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yeongcheol Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Bumhee Lim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jongsik Gam
- Department of Medicinal Bioscience, College of Interdisciplinary & Creative Studies, Konyang University, Nonsan, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Jeeyeon Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
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2
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Zhang H, Ni D, Fan J, Li M, Zhang J, Hua C, Nussinov R, Lu S. Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation. J Chem Inf Model 2022; 62:4222-4231. [PMID: 35994329 DOI: 10.1021/acs.jcim.2c00591] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
K-Ras4B, the most frequently mutated Ras isoform in human tumors, plays a vital part in cell growth, differentiation, and survival. Its tail, the C-terminal hypervariable region (HVR), is involved in anchoring K-Ras4B at the cellular plasma membrane and in isoform-specific protein-protein interactions and signaling. In the inactive guanosine diphosphate-bound state, the intrinsically disordered HVR interacts with the catalytic domain at the effector-binding region, rendering K-Ras4B in its autoinhibited state. Activation releases the HVR from the catalytic domain, with its ensemble favoring an ordered α-helical structure. The large-scale conformational transition of the HVR from the intrinsically disordered to the ordered conformation remains poorly understood. Here, we deploy a computational scheme that integrates a transition path-generation algorithm, extensive molecular dynamics simulation, and Markov state model analysis to investigate the conformational landscape of the HVR transition pathway. Our findings reveal a stepwise pathway for the HVR transition and uncover several key conformational substates along the transition pathway. Importantly, key interactions between the HVR and the catalytic domain are unraveled, highlighting the pathogenesis of K-Ras4B mild mutations in several congenital developmental anomaly syndromes. Together, these findings provide a deeper understanding of the HVR transition mechanism and the regulation of K-Ras4B activity at an atomic level.
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Affiliation(s)
- Hao Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jigang Fan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Minyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Chen Hua
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, China
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States.,Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China.,Medicinal Chemistry and Bioinformatics Centre, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
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3
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Ingólfsson HI, Neale C, Carpenter TS, Shrestha R, López CA, Tran TH, Oppelstrup T, Bhatia H, Stanton LG, Zhang X, Sundram S, Di Natale F, Agarwal A, Dharuman G, Kokkila Schumacher SIL, Turbyville T, Gulten G, Van QN, Goswami D, Jean-Francois F, Agamasu C, Chen D, Hettige JJ, Travers T, Sarkar S, Surh MP, Yang Y, Moody A, Liu S, Van Essen BC, Voter AF, Ramanathan A, Hengartner NW, Simanshu DK, Stephen AG, Bremer PT, Gnanakaran S, Glosli JN, Lightstone FC, McCormick F, Nissley DV, Streitz FH. Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins. Proc Natl Acad Sci U S A 2022; 119:e2113297119. [PMID: 34983849 PMCID: PMC8740753 DOI: 10.1073/pnas.2113297119] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2021] [Indexed: 01/17/2023] Open
Abstract
RAS is a signaling protein associated with the cell membrane that is mutated in up to 30% of human cancers. RAS signaling has been proposed to be regulated by dynamic heterogeneity of the cell membrane. Investigating such a mechanism requires near-atomistic detail at macroscopic temporal and spatial scales, which is not possible with conventional computational or experimental techniques. We demonstrate here a multiscale simulation infrastructure that uses machine learning to create a scale-bridging ensemble of over 100,000 simulations of active wild-type KRAS on a complex, asymmetric membrane. Initialized and validated with experimental data (including a new structure of active wild-type KRAS), these simulations represent a substantial advance in the ability to characterize RAS-membrane biology. We report distinctive patterns of local lipid composition that correlate with interfacially promiscuous RAS multimerization. These lipid fingerprints are coupled to RAS dynamics, predicted to influence effector binding, and therefore may be a mechanism for regulating cell signaling cascades.
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Affiliation(s)
- Helgi I Ingólfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Chris Neale
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Timothy S Carpenter
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Rebika Shrestha
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Timothy H Tran
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Tomas Oppelstrup
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Harsh Bhatia
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Liam G Stanton
- Department of Mathematics and Statistics, San José State University, San José, CA 95192
| | - Xiaohua Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Shiv Sundram
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Francesco Di Natale
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Animesh Agarwal
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Gautham Dharuman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | | | - Thomas Turbyville
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Gulcin Gulten
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Que N Van
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Debanjan Goswami
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Frantz Jean-Francois
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Constance Agamasu
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - De Chen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Jeevapani J Hettige
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Sumantra Sarkar
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Michael P Surh
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Yue Yang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Adam Moody
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Shusen Liu
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Brian C Van Essen
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Arthur F Voter
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Arvind Ramanathan
- Computing, Environment & Life Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Dhirendra K Simanshu
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Andrew G Stephen
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701
| | - Peer-Timo Bremer
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - James N Glosli
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Felice C Lightstone
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Frank McCormick
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701;
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94115
| | - Dwight V Nissley
- RAS Initiative, The Cancer Research Technology Program, Frederick National Laboratory, Frederick, MD 21701;
| | - Frederick H Streitz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550;
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Electrostatic Forces Mediate the Specificity of RHO GTPase-GDI Interactions. Int J Mol Sci 2021; 22:ijms222212493. [PMID: 34830380 PMCID: PMC8622166 DOI: 10.3390/ijms222212493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
Three decades of research have documented the spatiotemporal dynamics of RHO family GTPase membrane extraction regulated by guanine nucleotide dissociation inhibitors (GDIs), but the interplay of the kinetic mechanism and structural specificity of these interactions is as yet unresolved. To address this, we reconstituted the GDI-controlled spatial segregation of geranylgeranylated RHO protein RAC1 in vitro. Various biochemical and biophysical measurements provided unprecedented mechanistic details for GDI function with respect to RHO protein dynamics. We determined that membrane extraction of RHO GTPases by GDI occurs via a 3-step mechanism: (1) GDI non-specifically associates with the switch regions of the RHO GTPases; (2) an electrostatic switch determines the interaction specificity between the C-terminal polybasic region of RHO GTPases and two distinct negatively-charged clusters of GDI1; (3) a non-specific displacement of geranylgeranyl moiety from the membrane sequesters it into a hydrophobic cleft, effectively shielding it from the aqueous milieu. This study substantially extends the model for the mechanism of GDI-regulated RHO GTPase extraction from the membrane, and could have implications for clinical studies and drug development.
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Tawfeeq N, Jin Y, Lamango NS. Synthetic Optimization and MAPK Pathway Activation Anticancer Mechanism of Polyisoprenylated Cysteinyl Amide Inhibitors. Cancers (Basel) 2021; 13:cancers13225757. [PMID: 34830912 PMCID: PMC8616522 DOI: 10.3390/cancers13225757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary RAS G-protein genes are frequently mutated and drive the progression of about 30% of human cancers. Polyisoprenylated cysteinyl amide inhibitors (PCAIs) offer a novel approach to address the decades-long anti-RAS drug development challenge. This manuscript reports on the continuous development of the PCAIs and their anticancer molecular mechanisms that involve strong activation of MAP kinase pathway enzymes. Abstract Abnormalities of the MAPK pathway play vital roles in cancer initiation and progression. RAS GTPases that are key upstream mediators of the pathway are mutated in 30% of human cancers. Polyisoprenylated cysteinyl amide inhibitors (PCAIs) were designed as potential targeted therapies against the RAS-driven cancers. The current study reports on the optimization of the PCAIs and the determination of their mechanisms of action in KRAS-mutant cancer cells. They display ClogP values ranging from 3.01 to 6.35, suppressing the viabilities of KRAS-mutant MDA-MB-231, A549, MIA PaCa-2, and NCI-H1299 cells in 2D and 3D cultures with EC50 values of 2.2 to 6.8, 2.2 to 7.6, 2.3 to 6.5 and 5.0 to 14 µM, respectively. When A549 cells were treated with the PCAIs, NSL-YHJ-2-27, for 48 h, no significant difference was observed in the levels of total or phosphorylated B- and C-Raf proteins. However, at 5 µM, it stimulated the phosphorylation of MEK1/2, ERK1/2, and p90RSK by 84%, 59%, and 160%, respectively, relative to controls. A non-farnesylated analog, NSL-YHJ-2-62, did not elicit similar effects. These data reveal that effects on the RAS-MAPK signaling axis most likely contribute to the anticancer effects of the PCAIs, possibly through the proapoptotic isoforms of p90RSK. The PCAIs may thus have the potential to serve the unmet therapeutic needs of patients with aberrant hyperactive G-protein signaling.
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Busquets-Hernández C, Triola G. Palmitoylation as a Key Regulator of Ras Localization and Function. Front Mol Biosci 2021; 8:659861. [PMID: 33816563 PMCID: PMC8010249 DOI: 10.3389/fmolb.2021.659861] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/22/2021] [Indexed: 11/27/2022] Open
Abstract
Ras proteins require membrane association for proper function. This process is tightly regulated by reversible palmitoylation that controls not only the distribution over different subcellular compartments but also Ras compartmentalization within membrane subdomains. As a result, there is a growing interest in protein palmitoylation and the enzymes that control this process. In this minireview, we discuss how palmitoylation affects the localization and function of Ras proteins. A better understanding of the regulatory mechanism controlling protein lipidation is expected to provide new insights into the functional role of these modifications and may ultimately lead to the development of novel therapeutic approaches.
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Affiliation(s)
| | - Gemma Triola
- Department of Biological Chemistry, Laboratory of Chemical Biology, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
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7
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Lamango NS, Nkembo AT, Ntantie E, Tawfeeq N. Polyisoprenylated Cysteinyl Amide Inhibitors: A Novel Approach to Controlling Cancers with Hyperactive Growth Signaling. Curr Med Chem 2021; 28:3476-3489. [PMID: 33176634 PMCID: PMC9175089 DOI: 10.2174/0929867327666201111140825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 11/22/2022]
Abstract
Aberrant activation of monomeric G-protein signaling pathways drives some of the most aggressive cancers. Suppressing these hyperactivities has been the focus of efforts to obtain targeted therapies. Polyisoprenylated methylated protein methyl esterase (PMPMEase) is overexpressed in various cancers. Its inhibition induces the death of cancer cells that harbor the constitutively active K-Ras proteins. Furthermore, the viability of cancer cells driven by factors upstream of K-Ras, such as overexpressed growth factors and their receptors or the mutationally-activated receptors, is also susceptible to PMPMEase inhibition. Polyisoprenylated cysteinyl amide inhibitors (PCAIs) were thus designed to target cancers with hyperactive signaling pathways involving the G-proteins. The PCAIs were, however, poor inhibitors of PMPMEase, with Ki values ranging from 3.7 to 20 μM. On the other hand, they inhibited cell viability, proliferation, colony formation, induced apoptosis in cells with mutant K-Ras and inhibited cell migration and invasion with EC50 values of 1 to 3 μM. HUVEC tube formation was inhibited at submicromolar concentrations through their disruption of actin filament organization. At the molecular level, the PCAIs at 2 to 5 μM depleted monomeric G-proteins such as K-Ras, RhoA, Cdc42 and Rac1. The PCAIs also deplete vinculin and fascin that are involved in actin organization and function while disrupting vinculin punctates in the process. These demonstrate a polyisoprenylation-dependent mechanism that explains the observed PCAIs' inhibition of the proliferative, invasive and angiogenic processes that promote both tumor growth and metastasis.
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Affiliation(s)
- Nazarius S. Lamango
- College of Pharmacy and Pharmaceutical Sciences Institute of Public Health, Florida A&M University, Tallahassee FL32307, USA
| | - Augustine T. Nkembo
- College of Pharmacy and Pharmaceutical Sciences Institute of Public Health, Florida A&M University, Tallahassee FL32307, USA
| | - Elizabeth Ntantie
- College of Pharmacy and Pharmaceutical Sciences Institute of Public Health, Florida A&M University, Tallahassee FL32307, USA
| | - Nada Tawfeeq
- College of Pharmacy and Pharmaceutical Sciences Institute of Public Health, Florida A&M University, Tallahassee FL32307, USA
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8
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Jang H, Banerjee A, Marcus K, Makowski L, Mattos C, Gaponenko V, Nussinov R. The Structural Basis of the Farnesylated and Methylated KRas4B Interaction with Calmodulin. Structure 2019; 27:1647-1659.e4. [PMID: 31495533 DOI: 10.1016/j.str.2019.08.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/31/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023]
Abstract
Ca2+-calmodulin (CaM) extracts KRas4B from the plasma membrane, suggesting that KRas4B/CaM interaction plays a role in regulating Ras signaling. To gain mechanistic insight, we provide a computational model, supported by experimental structural data, of farnesylated/methylated KRas4B1-185 interacting with CaM in solution and at anionic membranes including signaling lipids. Due to multiple interaction modes, we observe diverse conformational ensembles of the KRas4B-CaM complex. A highly populated conformation reveals the catalytic domain interacting with the N-lobe and the hypervariable region (HVR) wrapping around the linker with the farnesyl docking to the extended CaM's C-lobe pocket. Alternatively, KRas4B can interact with collapsed CaM with the farnesyl penetrating CaM's center. At anionic membranes, CaM interacts with the catalytic domain with large fluctuations, drawing the HVR. Signaling lipids establishing strong salt bridges with CaM prevent membrane departure. Membrane-interacting KRas4B-CaM complex can productively recruit phosphatidylinositol 3-kinase α (PI3Kα) to the plasma membrane, serving as a coagent in activating PI3Kα/Akt signaling.
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Affiliation(s)
- Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Avik Banerjee
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kendra Marcus
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Lee Makowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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9
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Membrane Dynamics in Health and Disease: Impact on Cellular Signalling. J Membr Biol 2019; 252:213-226. [PMID: 31435696 DOI: 10.1007/s00232-019-00087-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022]
Abstract
Biological membranes display a staggering complexity of lipids and proteins orchestrating cellular functions. Superior analytical tools coupled with numerous functional cellular screens have enabled us to query their role in cellular signalling, trafficking, guiding protein structure and function-all of which rely on the dynamic membrane lipid properties indispensable for proper cellular functions. Alteration of these has led to emergence of various pathological conditions, thus opening an area of lipid-centric therapeutic approaches. This perspective is a short summary of the dynamic properties of membranes essential for proper cellular functions, dictating both protein and lipid functions, and mis-regulated in diseases. Towards the end, we focus on some challenges lying ahead and potential means to tackle the same, mainly underscored by multi-disciplinary approaches.
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10
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Li L, Dwivedi M, Patra S, Erwin N, Möbitz S, Winter R. Probing Colocalization of N-Ras and K-Ras4B Lipoproteins in Model Biomembranes. Chembiochem 2019; 20:1190-1195. [PMID: 30604476 DOI: 10.1002/cbic.201800776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Indexed: 12/28/2022]
Abstract
Signaling of N-Ras and K-Ras4B proteins depends strongly on their correct localization in the cell membrane. In vivo studies suggest that intermolecular interactions foster the self-association of both N-Ras and K-Ras4B and the formation of nanoclusters in the cell membrane. As sites for effector binding, nanocluster formation is thought to be essential for effective signal transmission of both N-Ras and K-Ras4B. To shed more light on the spatial arrangement and mechanism underlying the proposed cross-talk between spatially segregated Ras proteins, the simultaneous localization of N-Ras and K-Ras4B and their effect on the lateral organization of a heterogeneous model biomembrane has been studied by using AFM and FRET methodology. It is shown that, owing to the different natures of their membrane anchor systems, N-Ras and K-Ras4B not only avoid assembly in bulk solution and do not colocalize, but rather form individual nanoclusters that diffuse independently in the fluid membrane plane.
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Affiliation(s)
- Lei Li
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.,International Max Planck Research School (IMPRS), in Chemical and Molecular Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Mridula Dwivedi
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Satyajit Patra
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Nelli Erwin
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.,International Max Planck Research School (IMPRS), in Chemical and Molecular Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Simone Möbitz
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I, Technical University of Dortmund, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
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11
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Oliva R, Del Vecchio P, Grimaldi A, Notomista E, Cafaro V, Pane K, Schuabb V, Winter R, Petraccone L. Membrane disintegration by the antimicrobial peptide (P)GKY20: lipid segregation and domain formation. Phys Chem Chem Phys 2019; 21:3989-3998. [PMID: 30706924 DOI: 10.1039/c8cp06280c] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial peptides (AMPs) are membrane-active peptides with a broad spectrum of activity against different pathogenic organisms and they represent promising new drugs to overcome the emergence of resistance to antibiotics in bacteria. (P)GKY20 is an antimicrobial peptide with a low hemolytic effect on eukaryotic cells and a strong antimicrobial activity especially against Gram-negative bacteria. However, its mechanism of action is still unknown. Here, we use fluorescence spectroscopy and differential scanning calorimetry combined with atomic force microscopy to characterise the binding of (P)GKY20 with model biomembranes and its effect on the membrane's microstructure and thermotropic properties. We found that (P)GKY20 selectively perturbs the bacterial-like membrane via a carpet-like mechanism employing peptide conformational changes, lipid segregation and domain formation as key steps in promoting membrane disruption. These results shed a first light on the action mechanism of (P)GKY20 and could represent an important contribution to the development of new peptides serving as antimicrobial agents.
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Affiliation(s)
- Rosario Oliva
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia 4, 80126 Napoli, Italy.
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12
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Lakshman B, Messing S, Schmid EM, Clogston JD, Gillette WK, Esposito D, Kessing B, Fletcher DA, Nissley DV, McCormick F, Stephen AG, Jean-Francois FL. Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane. J Biol Chem 2019; 294:2193-2207. [PMID: 30559287 PMCID: PMC6369290 DOI: 10.1074/jbc.ra118.005669] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/28/2018] [Indexed: 11/06/2022] Open
Abstract
The gene encoding the GTPase KRAS is frequently mutated in pancreatic, lung, and colorectal cancers. The KRAS fraction in the plasma membrane (PM) correlates with activation of the mitogen-activated protein kinase (MAPK) pathway and subsequent cellular proliferation. Understanding KRAS's interaction with the PM is challenging given the complexity of the cellular environment. To gain insight into key components necessary for KRAS signal transduction at the PM, we used synthetic membranes such as liposomes and giant unilamellar vesicles. Using surface plasmon resonance (SPR) spectroscopy, we demonstrated that KRAS and Raf-1 proto-oncogene Ser/Thr kinase (RAF1) domains interact with these membranes primarily through electrostatic interactions with negatively charged lipids reinforced by additional interactions involving phosphatidyl ethanolamine and cholesterol. We found that the RAF1 region spanning RBD through CRD (RBDCRD) interacts with the membrane significantly more strongly than the isolated RBD or CRD domains and synergizes KRAS partitioning to the membrane. We also found that calmodulin and phosphodiesterase 6 delta (PDE6δ), but not galectin3 previously proposed to directly interact with KRAS, passively sequester KRAS and prevent it from partitioning into the PM. RAF1 RBDCRD interacted with membranes preferentially at nonraft lipid domains. Moreover, a C-terminal O-methylation was crucial for KRAS membrane localization. These results contribute to a better understanding of how the KRAS-membrane interaction is tuned by multiple factors whose identification could inform drug discovery efforts to disrupt this critical interaction in diseases such as cancer.
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Affiliation(s)
- Bindu Lakshman
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Simon Messing
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Eva M Schmid
- Department of Bioengineering, University of California Berkeley, Berkeley, California 94720
| | - Jeffrey D Clogston
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702
| | - William K Gillette
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Dominic Esposito
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Bailey Kessing
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Daniel A Fletcher
- Department of Bioengineering, University of California Berkeley, Berkeley, California 94720
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Chan Zuckerberg Biohub, San Francisco, California 94158
| | - Dwight V Nissley
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Frank McCormick
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158
| | - Andrew G Stephen
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702
| | - Frantz L Jean-Francois
- From the NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21702,
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13
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Oncogenic KRas mobility in the membrane and signaling response. Semin Cancer Biol 2019; 54:109-113. [DOI: 10.1016/j.semcancer.2018.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 12/12/2022]
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14
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Role of epigenetic factors in the selection of the alternative splicing isoforms of human KRAS in colorectal cancer cell lines. Oncotarget 2018; 9:20578-20589. [PMID: 29755673 PMCID: PMC5945503 DOI: 10.18632/oncotarget.25016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/17/2018] [Indexed: 01/10/2023] Open
Abstract
Mutation-driven activation of KRAS is crucial to cancer development. The human gene yields four mRNA splicing isoforms, 4A and 4B being translated to protein. Their different properties and oncogenic potential have been studied, but the mechanisms deciding the ratio 4A/4B are not known. To address this issue, the expression of the four KRAS isoforms was determined in 9 human colorectal cancer cell lines. HCT116 and SW48 were further selected because they present the highest difference in the ratio 4A/4B (twice as much in HCT116 than in SW48). Chromatin structure was analysed at the exon 4A, characteristic of isoform 4A, at its intronic borders and at the two flanking exons. The low nucleosome occupancy at exon 4A in both cell lines may result in a fast transcriptional rate, which would explain the general lower abundance of isoform 4A, also found in cells and tissues by other authors, but due to its similarity between both cell lines, chromatin structure does not influence alternative splicing. DNA methylation downstream exon 4A significantly differs in HCT116 and SW48 cells, but the CCCTC-binding factor, which affects the processivity of RNA polymerase and the alternative splicing, does not bind the differentially methylated sequences. Quantitative epigenetic analysis at mononucleosomal level revealed significant differences between both cell lines in H3K4me3, H3K27me3, H3K36me3, H3K9ac, H3K27ac and H4K20me1, and the inhibition of some histone-modifying enzymes alters the ratio 4A/4B. It can be concluded that the epigenetic modification of histones has an influence on the selection of isoforms 4A and 4B.
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15
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Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland. .,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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16
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Nussinov R, Tsai CJ, Jang H. Oncogenic Ras Isoforms Signaling Specificity at the Membrane. Cancer Res 2018; 78:593-602. [PMID: 29273632 PMCID: PMC5811325 DOI: 10.1158/0008-5472.can-17-2727] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/13/2017] [Accepted: 11/10/2017] [Indexed: 01/21/2023]
Abstract
How do Ras isoforms attain oncogenic specificity at the membrane? Oncogenic KRas, HRas, and NRas (K-Ras, H-Ras, and N-Ras) differentially populate distinct cancers. How they selectively activate effectors and why is KRas4B the most prevalent are highly significant questions. Here, we consider determinants that may bias isoform-specific effector activation and signaling at the membrane. We merge functional data with a conformational view to provide mechanistic insight. Cell-specific expression levels, pathway cross-talk, and distinct interactions are the key, but conformational trends can modulate selectivity. There are two major pathways in oncogenic Ras-driven proliferation: MAPK (Raf/MEK/ERK) and PI3Kα/Akt/mTOR. All membrane-anchored, proximally located, oncogenic Ras isoforms can promote Raf dimerization and fully activate MAPK signaling. So why the differential statistics of oncogenic isoforms in distinct cancers and what makes KRas so highly oncogenic? Many cell-specific factors may be at play, including higher KRAS mRNA levels. As a key factor, we suggest that because only KRas4B binds calmodulin, only KRas can fully activate PI3Kα/Akt signaling. We propose that full activation of both MAPK and PI3Kα/Akt proliferative pathways by oncogenic KRas4B-but not by HRas or NRas-may help explain why the KRas4B isoform is especially highly populated in certain cancers. We further discuss pharmacologic implications. Cancer Res; 78(3); 593-602. ©2017 AACR.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland
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17
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Qureshi BM, Schmidt A, Behrmann E, Bürger J, Mielke T, Spahn CMT, Heck M, Scheerer P. Mechanistic insights into the role of prenyl-binding protein PrBP/δ in membrane dissociation of phosphodiesterase 6. Nat Commun 2018; 9:90. [PMID: 29311697 PMCID: PMC5758567 DOI: 10.1038/s41467-017-02569-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/11/2017] [Indexed: 01/01/2023] Open
Abstract
Isoprenylated proteins are associated with membranes and their inter-compartmental distribution is regulated by solubilization factors, which incorporate lipid moieties in hydrophobic cavities and thereby facilitate free diffusion during trafficking. Here we report the crystal structure of a solubilization factor, the prenyl-binding protein (PrBP/δ), at 1.81 Å resolution in its ligand-free apo-form. Apo-PrBP/δ harbors a preshaped, deep hydrophobic cavity, capacitating apo-PrBP/δ to readily bind its prenylated cargo. To investigate the molecular mechanism of cargo solubilization we analyzed the PrBP/δ-induced membrane dissociation of rod photoreceptor phosphodiesterase (PDE6). The results suggest that PrBP/δ exclusively interacts with the soluble fraction of PDE6. Depletion of soluble species in turn leads to dissociation of membrane-bound PDE6, as both are in equilibrium. This “solubilization by depletion” mechanism of PrBP/δ differs from the extraction of prenylated proteins by the similar folded solubilization factor RhoGDI, which interacts with membrane bound cargo via an N-terminal structural element lacking in PrBP/δ. The prenyl-binding protein PrBP/δ is a solubilization factor involved in trafficking of prenylated proteins. Here the authors present the ligand-free apo-PrBP/δ structure and propose a "solubilization by depletion" mechanism, where PrBP/δ sequesters only soluble rod photoreceptor phosphodiesterase (PDE6), leading to a dissociation of membrane-bound PDE6.
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Affiliation(s)
- Bilal M Qureshi
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Cryo Electron Microscopy, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Enzyme Kinetics, Charitéplatz 1, D-10117, Berlin, Germany.,Division of Biological & Environmental Sciences & Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Andrea Schmidt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117, Berlin, Germany
| | - Elmar Behrmann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Cryo Electron Microscopy, Charitéplatz 1, D-10117, Berlin, Germany.,Research Group Structural Dynamics of Proteins, Center of Advanced European Studies and Research (Caesar), Ludwig-Erhard-Allee 2, D-53175, Bonn, Germany.,Institute of Biochemistry-Structural Biochemistry, University of Cologne, Zuelpicher Straße 47, D-50674, Cologne, Germany
| | - Jörg Bürger
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Cryo Electron Microscopy, Charitéplatz 1, D-10117, Berlin, Germany.,UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195, Berlin, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195, Berlin, Germany
| | - Christian M T Spahn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Cryo Electron Microscopy, Charitéplatz 1, D-10117, Berlin, Germany
| | - Martin Heck
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Enzyme Kinetics, Charitéplatz 1, D-10117, Berlin, Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117, Berlin, Germany.
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18
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Jiang H, Zhang X, Chen X, Aramsangtienchai P, Tong Z, Lin H. Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies. Chem Rev 2018; 118:919-988. [PMID: 29292991 DOI: 10.1021/acs.chemrev.6b00750] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein lipidation, including cysteine prenylation, N-terminal glycine myristoylation, cysteine palmitoylation, and serine and lysine fatty acylation, occurs in many proteins in eukaryotic cells and regulates numerous biological pathways, such as membrane trafficking, protein secretion, signal transduction, and apoptosis. We provide a comprehensive review of protein lipidation, including descriptions of proteins known to be modified and the functions of the modifications, the enzymes that control them, and the tools and technologies developed to study them. We also highlight key questions about protein lipidation that remain to be answered, the challenges associated with answering such questions, and possible solutions to overcome these challenges.
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Affiliation(s)
- Hong Jiang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiaoyu Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiao Chen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Pornpun Aramsangtienchai
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Zhen Tong
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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19
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Jang H, Banerjee A, Chavan T, Gaponenko V, Nussinov R. Flexible-body motions of calmodulin and the farnesylated hypervariable region yield a high-affinity interaction enabling K-Ras4B membrane extraction. J Biol Chem 2017; 292:12544-12559. [PMID: 28623230 PMCID: PMC5535030 DOI: 10.1074/jbc.m117.785063] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/05/2017] [Indexed: 01/01/2023] Open
Abstract
In calmodulin (CaM)-rich environments, oncogenic KRAS plays a critical role in adenocarcinomas by promoting PI3K/Akt signaling. We previously proposed that at elevated calcium levels in cancer, CaM recruits PI3Kα to the membrane and extracts K-Ras4B from the membrane, organizing a K-Ras4B-CaM-PI3Kα ternary complex. CaM can thereby replace a missing receptor-tyrosine kinase signal to fully activate PI3Kα. Recent experimental data show that CaM selectively promotes K-Ras signaling but not of N-Ras or H-Ras. How CaM specifically targets K-Ras and how it extracts it from the membrane in KRAS-driven cancer is unclear. Obtaining detailed structural information for a CaM-K-Ras complex is still challenging. Here, using molecular dynamics simulations and fluorescence experiments, we observed that CaM preferentially binds unfolded K-Ras4B hypervariable regions (HVRs) and not α-helical HVRs. The interaction involved all three CaM domains including the central linker and both lobes. CaM specifically targeted the highly polybasic anchor region of the K-Ras4B HVR that stably wraps around CaM's acidic linker. The docking of the farnesyl group to the hydrophobic pockets located at both CaM lobes further enhanced CaM-HVR complex stability. Both CaM and K-Ras4B HVR are highly flexible molecules, suggesting that their interactions permit highly dynamic flexible-body motions. We, therefore, anticipate that the flexible-body interaction is required to extract K-Ras4B from the membrane, as conformational plasticity enables CaM to orient efficiently to the polybasic HVR anchor, which is partially diffused into the liquid-phase membrane. Our structural model of the CaM-K-Ras4B HVR association provides plausible clues to CaM's regulatory action in PI3Kα activation involving the ternary complex in cell proliferation signaling by oncogenic K-Ras.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI-Frederick, Frederick, Maryland 21702
| | - Avik Banerjee
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Tanmay Chavan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607.
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, NCI-Frederick, Frederick, Maryland 21702; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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20
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Muratcioglu S, Jang H, Gursoy A, Keskin O, Nussinov R. PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization. J Phys Chem B 2017; 121:5917-5927. [PMID: 28540724 PMCID: PMC7891760 DOI: 10.1021/acs.jpcb.7b03035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
To signal, Ras isoforms must be enriched at the plasma membrane (PM). It was suggested that phosphodiesterase-δ (PDEδ) can bind and shuttle some farnesylated Ras isoforms to the PM, but not all. Among these, interest focused on K-Ras4B, the most abundant oncogenic Ras isoform. To study PDEδ/Ras interactions, we modeled and simulated the PDEδ/K-Ras4B complex. We obtained structures, which were similar to two subsequently determined crystal structures. We next modeled and simulated complexes of PDEδ with the farnesylated hypervariable regions of K-Ras4A and N-Ras. Earlier data suggested that PDEδ extracts K-Ras4B and N-Ras from the PM, but surprisingly not K-Ras4A. Earlier analysis of the crystal structures advanced that the presence of large/charged residues adjacent to the farnesylated site precludes the PDEδ interaction. Here, we show that PDEδ can bind to farnesylated K-Ras4A and N-Ras like K-Ras4B, albeit not as strongly. This weaker binding, coupled with the stronger anchoring of K-Ras4A in the membrane (but not of electrostatically neutral N-Ras), can explain the observation why PDEδ is unable to effectively extract K-Ras4A. We thus propose that farnesylated Ras isoforms can bind PDEδ to fulfill the required PM enrichment, and argue that the different environments, PM versus solution, can resolve apparently puzzling Ras observations. These are novel insights that would not be expected based on the crystal structures alone, which provide an elegant rationale for previously puzzling observations of the differential effects of PDEδ on farnesylated Ras family proteins.
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Affiliation(s)
- Serena Muratcioglu
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick and Basic Science Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, United States
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick and Basic Science Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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21
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Zhang SY, Sperlich B, Li FY, Al-Ayoubi S, Chen HX, Zhao YF, Li YM, Weise K, Winter R, Chen YX. Phosphorylation Weakens but Does Not Inhibit Membrane Binding and Clustering of K-Ras4B. ACS Chem Biol 2017; 12:1703-1710. [PMID: 28448716 DOI: 10.1021/acschembio.7b00165] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
K-Ras4B is one of the most frequently mutated Ras isoforms in cancer. The signaling activity of K-Ras4B depends on its localization to the plasma membrane (PM), which is mainly mediated by its polybasic farnesylated C-terminus. On top of the constitutive cycles that maintain the PM enrichment of K-Ras4B, conditional phosphorylation at Ser181 located within this motif has been found to be involved in regulating K-Ras4B's cell distribution and signaling activity. However, discordant observations have undermined our understanding of the role this phosphorylation plays. Here, we report an efficient strategy for producing K-Ras4B simultaneously bearing phosphate, farnesyl, and methyl modifications on a preparative scale, a very useful in vitro system when used in concert with model biomembranes. By using this system, we determined that phosphorylation at Ser181 does not fully inhibit membrane binding and clustering of K-Ras4B but reduces its membrane binding affinity, depending on membrane fluidity. In addition, phosphorylated K-Ras4B maintains tight association with its cytosolic shuttle protein PDEδ. After delivering K-Ras4B containing nonhydrolyzable phosphoserine mimetic into cells, the protein displayed a decreasing PM distribution compared with nonphosphorylable K-Ras4B, implying that phosphorylation might facilitate the dissociation of K-Ras4B from the PM. In addition, phosphorylation does not alter the localization of K-Ras4B in the liquid-disordered lipid subdomains of the membrane but slightly alters the thermotropic properties of K-Ras4B-incorporated membranes probably due to minor differences in membrane partitioning and dynamics. These results provide novel mechanistic insights into the role that phosphorylation at Ser181 plays in regulating K-Ras4B's distribution and activity.
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Affiliation(s)
- Si-Yu Zhang
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Benjamin Sperlich
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
| | - Fang-Yi Li
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Samy Al-Ayoubi
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
| | - Hong-Xue Chen
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu-Fen Zhao
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yan-Mei Li
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Katrin Weise
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
| | - Roland Winter
- Physical
Chemistry I − Biophysical Chemistry, Faculty of Chemistry and
Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, D-44227 Dortmund, Germany
| | - Yong-Xiang Chen
- Key
Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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22
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Sperlich B, Kapoor S, Waldmann H, Winter R, Weise K. Regulation of K-Ras4B Membrane Binding by Calmodulin. Biophys J 2017; 111:113-22. [PMID: 27410739 DOI: 10.1016/j.bpj.2016.05.042] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/03/2016] [Accepted: 05/24/2016] [Indexed: 12/28/2022] Open
Abstract
K-Ras4B is a membrane-bound small GTPase with a prominent role in cancer development. It contains a polybasic farnesylated C-terminus that is required for the correct localization and clustering of K-Ras4B in distinct membrane domains. PDEδ and the Ca(2+)-binding protein calmodulin (CaM) are known to function as potential binding partners for farnesylated Ras proteins. However, they differ in the number of interaction sites with K-Ras4B, leading to different modes of interaction, and thus affect the subcellular distribution of K-Ras4B in different ways. Although it is clear that Ca(2+)-bound CaM can play a role in the dynamic spatial cycle of K-Ras4B in the cell, the exact molecular mechanism is only partially understood. In this biophysical study, we investigated the effect of Ca(2+)/CaM on the interaction of GDP- and GTP-loaded K-Ras4B with heterogeneous model biomembranes by using a combination of different spectroscopic and imaging techniques. The results show that Ca(2+)/CaM is able to extract K-Ras4B from negatively charged membranes in a nucleotide-independent manner. Moreover, the data demonstrate that the complex of Ca(2+)/CaM and K-Ras4B is stable in the presence of anionic membranes and shows no membrane binding. Finally, the influence of Ca(2+)/CaM on the interaction of K-Ras4B with membranes is compared with that of PDEδ, which was investigated in a previous study. Although both CaM and PDEδ exhibit a hydrophobic binding pocket for farnesyl, they have different effects on membrane binding of K-Ras4B and hence should be capable of regulating K-Ras4B plasma membrane localization in the cell.
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Affiliation(s)
- Benjamin Sperlich
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Shobhna Kapoor
- Chemical Biology, TU Dortmund University, Dortmund, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Herbert Waldmann
- Chemical Biology, TU Dortmund University, Dortmund, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany.
| | - Katrin Weise
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany.
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Erwin N, Sperlich B, Garivet G, Waldmann H, Weise K, Winter R. Lipoprotein insertion into membranes of various complexity: lipid sorting, interfacial adsorption and protein clustering. Phys Chem Chem Phys 2017; 18:8954-62. [PMID: 26960984 DOI: 10.1039/c6cp00563b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In a combined chemical-biological and biophysical approach we explored the membrane partitioning of the lipidated signaling proteins N-Ras and K-Ras4B into membrane systems of different complexity, ranging from one-component lipid bilayers and anionic binary and ternary heterogeneous membrane systems even up to partitioning studies on protein-free and protein-containing giant plasma membrane vesicles (GPMVs). To yield a pictorial view of the localization process, imaging using confocal laser scanning and atomic force microscopy was performed. The results reveal pronounced isoform-specific differences regarding the lateral distribution and formation of protein-rich membrane domains. Line tension is one of the key parameters controlling not only the size and dynamic properties of segregated lipid domains but also the partitioning process of N-Ras that acts as a lineactant. The formation of N-Ras protein clusters is even recorded for almost vanishing hydrophobic mismatch. Conversely, for K-Ras4B, selective localization and clustering are electrostatically mediated by its polybasic farnesylated C-terminus. The formation of K-Ras4B clusters is also observed for the multi-component GPMV membrane, i.e., it seems to be a general phenomenon, largely independent of the details of the membrane composition, including the anionic charge density of lipid headgroups. Our data indicate that unspecific and entropy-driven membrane-mediated interactions play a major role in the partitioning behavior, thus relaxing the need for a multitude of fine-tuned interactions. Such a scenario seems also to be reasonable recalling the high dynamic nature of cellular membranes. Finally, we note that even relatively simple models of heterogeneous membranes are able to reproduce many of the properties of much more complex biological membranes.
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Affiliation(s)
- Nelli Erwin
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, D-44221 Dortmund, Germany.
| | - Benjamin Sperlich
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, D-44221 Dortmund, Germany.
| | - Guillaume Garivet
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany and Faculty of Chemistry and Chemical Biology, Department of Chemical Biology, TU Dortmund University, D-44221 Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, D-44227 Dortmund, Germany and Faculty of Chemistry and Chemical Biology, Department of Chemical Biology, TU Dortmund University, D-44221 Dortmund, Germany
| | - Katrin Weise
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, D-44221 Dortmund, Germany.
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, D-44221 Dortmund, Germany.
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Dharmaiah S, Bindu L, Tran TH, Gillette WK, Frank PH, Ghirlando R, Nissley DV, Esposito D, McCormick F, Stephen AG, Simanshu DK. Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ. Proc Natl Acad Sci U S A 2016; 113:E6766-E6775. [PMID: 27791178 PMCID: PMC5098621 DOI: 10.1073/pnas.1615316113] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Farnesylation and carboxymethylation of KRAS4b (Kirsten rat sarcoma isoform 4b) are essential for its interaction with the plasma membrane where KRAS-mediated signaling events occur. Phosphodiesterase-δ (PDEδ) binds to KRAS4b and plays an important role in targeting it to cellular membranes. We solved structures of human farnesylated-methylated KRAS4b in complex with PDEδ in two different crystal forms. In these structures, the interaction is driven by the C-terminal amino acids together with the farnesylated and methylated C185 of KRAS4b that binds tightly in the central hydrophobic pocket present in PDEδ. In crystal form II, we see the full-length structure of farnesylated-methylated KRAS4b, including the hypervariable region. Crystal form I reveals structural details of farnesylated-methylated KRAS4b binding to PDEδ, and crystal form II suggests the potential binding mode of geranylgeranylated-methylated KRAS4b to PDEδ. We identified a 5-aa-long sequence motif (Lys-Ser-Lys-Thr-Lys) in KRAS4b that may enable PDEδ to bind both forms of prenylated KRAS4b. Structure and sequence analysis of various prenylated proteins that have been previously tested for binding to PDEδ provides a rationale for why some prenylated proteins, such as KRAS4a, RalA, RalB, and Rac1, do not bind to PDEδ. Comparison of all four available structures of PDEδ complexed with various prenylated proteins/peptides shows the presence of additional interactions due to a larger protein-protein interaction interface in KRAS4b-PDEδ complex. This interface might be exploited for designing an inhibitor with minimal off-target effects.
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Affiliation(s)
- Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701
| | - Lakshman Bindu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701
| | - William K Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701
| | - Peter H Frank
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701;
- Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701;
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25
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Mid-infrared spectroscopy for protein analysis: potential and challenges. Anal Bioanal Chem 2016; 408:2875-89. [PMID: 26879650 DOI: 10.1007/s00216-016-9375-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/22/2016] [Accepted: 01/28/2016] [Indexed: 12/11/2022]
Abstract
Mid-infrared (MIR) spectroscopy investigates the interaction of MIR photons with both organic and inorganic molecules via the excitation of vibrational and rotational modes, providing inherent molecular selectivity. In general, infrared (IR) spectroscopy is particularly sensitive to protein structure and structural changes via vibrational resonances originating from the polypeptide backbone or side chains; hence information on the secondary structure of proteins can be obtained in a label-free fashion. In this review, the challenges for IR spectroscopy for protein analysis are discussed as are the potential and limitations of different IR spectroscopic techniques enabling protein analysis. In particular, the amide I spectral range has been widely used to study protein secondary structure, conformational changes, protein aggregation, protein adsorption, and the formation of amyloid fibrils. In addition to representative examples of the potential of IR spectroscopy in various fields related to protein analysis, the potential of protein analysis taking advantage of miniaturized MIR systems, including waveguide-enhanced MIR sensors, is detailed.
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26
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Gillette WK, Esposito D, Abreu Blanco M, Alexander P, Bindu L, Bittner C, Chertov O, Frank PH, Grose C, Jones JE, Meng Z, Perkins S, Van Q, Ghirlando R, Fivash M, Nissley DV, McCormick F, Holderfield M, Stephen AG. Farnesylated and methylated KRAS4b: high yield production of protein suitable for biophysical studies of prenylated protein-lipid interactions. Sci Rep 2015; 5:15916. [PMID: 26522388 PMCID: PMC4629113 DOI: 10.1038/srep15916] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022] Open
Abstract
Prenylated proteins play key roles in several human diseases including cancer, atherosclerosis and Alzheimer's disease. KRAS4b, which is frequently mutated in pancreatic, colon and lung cancers, is processed by farnesylation, proteolytic cleavage and carboxymethylation at the C-terminus. Plasma membrane localization of KRAS4b requires this processing as does KRAS4b-dependent RAF kinase activation. Previous attempts to produce modified KRAS have relied on protein engineering approaches or in vitro farnesylation of bacterially expressed KRAS protein. The proteins produced by these methods do not accurately replicate the mature KRAS protein found in mammalian cells and the protein yield is typically low. We describe a protocol that yields 5-10 mg/L highly purified, farnesylated, and methylated KRAS4b from insect cells. Farnesylated and methylated KRAS4b is fully active in hydrolyzing GTP, binds RAF-RBD on lipid Nanodiscs and interacts with the known farnesyl-binding protein PDEδ.
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Affiliation(s)
- William K. Gillette
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Dominic Esposito
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Maria Abreu Blanco
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Patrick Alexander
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Lakshman Bindu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Cammi Bittner
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Oleg Chertov
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Peter H. Frank
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Carissa Grose
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Jane E. Jones
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Zhaojing Meng
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Shelley Perkins
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Que Van
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 5 Memorial Drive, Bethesda MD 20892
| | - Matthew Fivash
- Data Management Systems, NCI at Frederick, PO Box B, Frederick, MD 21702
| | - Dwight V. Nissley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Frank McCormick
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Matthew Holderfield
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
| | - Andrew G. Stephen
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD 21702
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27
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Kapoor S, Fansa EK, Möbitz S, Ismail SA, Winter R, Wittinghofer A, Weise K. Effect of the N-Terminal Helix and Nucleotide Loading on the Membrane and Effector Binding of Arl2/3. Biophys J 2015; 109:1619-29. [PMID: 26488653 PMCID: PMC4624342 DOI: 10.1016/j.bpj.2015.08.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/05/2015] [Accepted: 08/10/2015] [Indexed: 01/02/2023] Open
Abstract
The small GTP-binding proteins Arl2 and Arl3, which are close homologs, share a number of interacting partners and act as displacement factors for prenylated and myristoylated cargo. Nevertheless, both proteins have distinct biological functions. Whereas Arl3 is considered a ciliary protein, Arl2 has been reported to be involved in tubulin folding, mitochondrial function, and Ras signaling. How these different roles are attained by the two homolog proteins is not fully understood. Recently, we showed that the N-terminal amphipathic helix of Arl3, but not that of Arl2, regulates the release of myristoylated ciliary proteins from the GDI-like solubilizing factor UNC119a/b. In the biophysical study presented here, both proteins are shown to exhibit a preferential localization and clustering in liquid-disordered domains of phase-separated membranes. However, the membrane interaction behavior differs significantly between both proteins with regard to their nucleotide loading. Whereas Arl3 and other Arf proteins with an N-terminal amphipathic helix require GTP loading for the interaction with membranes, Arl2 binds to membranes in a nucleotide-independent manner. In contrast to Arl2, the N-terminal helix of Arl3 increases the binding affinity to UNC119a. Furthermore, UNC119a impedes membrane binding of Arl3, but not of Arl2. Taken together, these results suggest an interplay among the nucleotide status of Arl3, the location of the N-terminal helix, membrane fluidity and binding, and the release of lipid modified cargos from carriers such as UNC119a. Since a specific Arl3-GEF is postulated to reside inside cilia, the N-terminal helix of Arl3•GTP would be available for allosteric regulation of UNC119a cargo release only inside cilia.
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Affiliation(s)
- Shobhna Kapoor
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Eyad K Fansa
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Simone Möbitz
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Shehab A Ismail
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany; Structural Biology of Cilia, CR-UK Beatson Institute, Glasgow, United Kingdom
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Katrin Weise
- Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Dortmund, Germany.
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Nussinov R, Jang H, Tsai CJ. Oligomerization and nanocluster organization render specificity. Biol Rev Camb Philos Soc 2015; 90:587-98. [PMID: 24917483 PMCID: PMC4263682 DOI: 10.1111/brv.12124] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 04/30/2014] [Accepted: 05/14/2014] [Indexed: 12/11/2022]
Abstract
Nanoclusters are anchored to membranes, either within them or in the cytoplasm latched onto the cytoskeleton, whose reorganization can regulate their activity. Nanoclusters have been viewed in terms of cooperativity and activation; here we perceive nanocluster organization from a conformational standpoint. This leads us to suggest that while single molecules encode activity, nanoclusters induce specificity, and that this is their main evolutionary aim. Distinct, isoform-specific nanocluster organization can drive the preferred effector (and ligand) interactions and thereby designate signalling pathways. The absence of detailed structural information across the nanocluster, due to size and dynamics, hinders an in-depth grasp of its mechanistic features; however, available data already capture some of the principles and their functional 'raison d'être'. Collectively, clustering lends stability and reduces the likelihood of proteolytic cleavage; it also increases the effective local concentration and enables efficient cooperative activation. However, clustering does not determine the ability of the single molecule to function. Drugs targeting nanoclusters can attenuate activity by hampering cooperativity; however, this may not perturb activation and signalling, which originate from the molecules themselves, and as such, are likely to endure. What then is the major role of nanoclustering? Assuming that single molecules evolved first, with a subsequent increase in cellular complexity and emergence of highly similar isoform variants, evolution faced the threat of signalling promiscuity. We reason that this potential risk was thwarted by oligomerization and clustering; clustering confers higher specificity, and a concomitant extra layer of cellular control. In our Ras example, signalling will be more accurate as a dimer than as a monomer, where its isomer specificity could be compromised.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD 21702, USA
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29
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Zhang SC, Gremer L, Heise H, Janning P, Shymanets A, Cirstea IC, Krause E, Nürnberg B, Ahmadian MR. Liposome reconstitution and modulation of recombinant prenylated human Rac1 by GEFs, GDI1 and Pak1. PLoS One 2014; 9:e102425. [PMID: 25014207 PMCID: PMC4094549 DOI: 10.1371/journal.pone.0102425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/18/2014] [Indexed: 11/19/2022] Open
Abstract
Small Rho GTPases are well known to regulate a variety of cellular processes by acting as molecular switches. The regulatory function of Rho GTPases is critically dependent on their posttranslational modification at the carboxyl terminus by isoprenylation and association with proper cellular membranes. Despite numerous studies, the mechanisms of recycling and functional integration of Rho GTPases at the biological membranes are largely unclear. In this study, prenylated human Rac1, a prominent member of the Rho family, was purified in large amount from baculovirus-infected Spodoptera frugiperda insect cells using a systematic detergent screening. In contrast to non-prenylated human Rac1 purified from Escherichia coli, prenylated Rac1 from insect cells was able to associate with synthetic liposomes and to bind Rho-specific guanine nucleotide dissociation inhibitor 1 (GDI1). Subsequent liposome reconstitution experiments revealed that GDI1 efficiently extracts Rac1 from liposomes preferentially in the inactive GDP-bound state. The extraction was prevented when Rac1 was activated to its GTP-bound state by Rac-specific guanine nucleotide exchange factors (GEFs), such as Vav2, Dbl, Tiam1, P-Rex1 and TrioN, and bound by the downstream effector Pak1. We found that dissociation of Rac1-GDP from its complex with GDI1 strongly correlated with two distinct activities of especially Dbl and Tiam1, including liposome association and the GDP/GTP exchange. Taken together, our results provided first detailed insights into the advantages of the in vitro liposome-based reconstitution system to study both the integration of the signal transducing protein complexes and the mechanisms of regulation and signaling of small GTPases at biological membranes.
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Affiliation(s)
- Si-Cai Zhang
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
| | - Lothar Gremer
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
- Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
- Institute of Complex Systems, ICS-6, Research Center Jülich GmbH, Jülich, Germany
| | - Henrike Heise
- Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
- Institute of Complex Systems, ICS-6, Research Center Jülich GmbH, Jülich, Germany
| | - Petra Janning
- Department of Chemical Biology, Max-Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Aliaksei Shymanets
- Institute of Experimental and Clinical Pharmacology and Toxicology, Tübingen Medical School, Tübingen, Germany
| | - Ion C. Cirstea
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
- Leibniz Institute for Age Research, Jena, Germany
| | - Eberhard Krause
- Laboratory of Mass Spectrometry, Leibniz Institute of Molecular Pharmacology, Berlin, Germany
| | - Bernd Nürnberg
- Institute of Experimental and Clinical Pharmacology and Toxicology, Tübingen Medical School, Tübingen, Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich-Heine University, Düsseldorf, Germany
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30
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Suladze S, Ismail S, Winter R. Thermodynamic, dynamic and solvational properties of PDEδ binding to farnesylated cystein: a model study for uncovering the molecular mechanism of PDEδ interaction with prenylated proteins. J Phys Chem B 2014; 118:966-75. [PMID: 24401043 DOI: 10.1021/jp411466r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The protein PDEδ is an important solubilizing factor for several prenylated proteins including the Ras subfamily members. The binding occurs mainly through the farnesyl anchor of Ras proteins, which is recognized by a hydrophobic pocket of PDEδ. In this study, we carried out a detailed study of the thermodynamic and solvational properties of PDEδ binding to farnesyl-cystein, which serves as a model for PDEδ association to prenylated proteins. Using various biophysical approaches in conjunction with theoretical considerations, we show here that binding of the largely hydrophobic ligand surprisingly has enthalpy-driven signature, and the entropy change is largely controlled by the fine balance between the hydrational and conformational terms. Moreover, binding of PDEδ to farnesyl-cystein is accompanied by an increase in thermal stability, the release of about 150 water molecules from the interacting species, a decrease in solvent accessible surface area, and a marked decrease of the volume fluctuations and hence dynamics of the protein. Altogether, our results shed more light on the molecular mechanism of PDEδ interaction with prenylated Ras proteins, which is also prerequisite for an optimization of the structure-based molecular design of drugs against Ras related diseases and for understanding the multitude of biological functions of PDEδ.
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Affiliation(s)
- S Suladze
- TU Dortmund University , Department of Chemistry and Chemical Biology, D-44221 Dortmund, Germany
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31
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Werkmüller A, Triola G, Waldmann H, Winter R. Rotational and translational dynamics of ras proteins upon binding to model membrane systems. Chemphyschem 2013; 14:3698-705. [PMID: 24115726 DOI: 10.1002/cphc.201300617] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Indexed: 01/16/2023]
Abstract
Plasma-membrane-associated Ras proteins typically control signal transduction processes. As nanoclustering and membrane viscosity sensing provide plausible signaling mechanisms, determination of the rotational and translational dynamics of membrane-bound Ras isoforms can help to link their dynamic mobility to their function. Herein, by using time-resolved fluorescence anisotropy and correlation spectroscopic measurements, we obtain the rotational-correlation time and the translational diffusion coefficient of lipidated boron-dipyrromethene-labeled Ras, both in bulk Ras and upon membrane binding. The results show that the second lipidation motif of N-Ras triggers dimer formation in bulk solution, whereas K-Ras4B is monomeric. Upon membrane binding, an essentially free rotation of the G-domain is observed, along with a high lateral mobility; the latter is essentially limited by the viscosity of the membrane and by lipid-mediated electrostatic interactions. This high diffusional mobility warrants rapid recognition-binding sequences in the membrane-bound state, thereby facilitating efficient interactions between the Ras proteins and scaffolding or effector proteins. The lipid-like rapid lateral diffusion observed here complies with in vivo data.
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Affiliation(s)
- Alexander Werkmüller
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund (Germany), Fax: (+49) 231 755 3901
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32
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Blume A, Kerth A. Peptide and protein binding to lipid monolayers studied by FT-IRRA spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2294-305. [PMID: 23816442 DOI: 10.1016/j.bbamem.2013.04.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/12/2013] [Indexed: 12/30/2022]
Abstract
Lipid monolayers at the air-water interface represent half of a lipid bilayer and are therefore suitable model systems for studying the binding of peripheral proteins and polypeptides as well as proteins containing hydrophobic membrane anchors to membrane interfaces. Infrared reflection-absorption spectroscopy (IRRAS) of these monolayer films at the air-water interface provides information on the state of the lipid monolayers as well as on the conformational and orientational order of the film constituents. We will review shortly the experimental set-up and the possibilities for obtaining structural information before several applications of the method to lipid-protein monolayers will be described. We will focus on examples where the analysis of the protein and peptide bands for pure monolayers of these compounds are combined with experiments where the same compounds are bound to lipid monolayers. Combination of these experiments leads to detailed information about the conformational properties and the orientation of the molecules at the air-water interface in contrast to being bound to the lipid-water interface. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Alfred Blume
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, von-Danckelmann-Platz 4, D-06120, Halle Saale, Germany.
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Weise K, Huster D, Kapoor S, Triola G, Waldmann H, Winter R. Gibbs energy determinants of lipoprotein insertion into lipid membranes: the case study of Ras proteins. Faraday Discuss 2013; 161:549-61; discussion 563-89. [DOI: 10.1039/c2fd20100c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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