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Auger SA, Venkatachalapathy S, Suazo KFG, Wang Y, Sarkis AW, Bernhagen K, Justyna K, Schaefer JV, Wollack JW, Plückthun A, Li L, Distefano MD. Broadening the Utility of Farnesyltransferase-Catalyzed Protein Labeling Using Norbornene-Tetrazine Click Chemistry. Bioconjug Chem 2024. [PMID: 38654427 DOI: 10.1021/acs.bioconjchem.4c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bioorthogonal chemistry has gained widespread use in the study of many biological systems of interest, including protein prenylation. Prenylation is a post-translational modification, in which one or two 15- or 20-carbon isoprenoid chains are transferred onto cysteine residues near the C-terminus of a target protein. The three main enzymes─protein farnesyltransferase (FTase), geranylgeranyl transferase I (GGTase I), and geranylgeranyl transferase II (GGTase II)─that catalyze this process have been shown to tolerate numerous structural modifications in the isoprenoid substrate. This feature has previously been exploited to transfer an array of farnesyl diphosphate analogues with a range of functionalities, including an alkyne-containing analogue for copper-catalyzed bioconjugation reactions. Reported here is the synthesis of an analogue of the isoprenoid substrate embedded with norbornene functionality (C10NorOPP) that can be used for an array of applications, ranging from metabolic labeling to selective protein modification. The probe was synthesized in seven steps with an overall yield of 7% and underwent an inverse electron demand Diels-Alder (IEDDA) reaction with tetrazine-containing tags, allowing for copper-free labeling of proteins. The use of C10NorOPP for the study of prenylation was explored in the metabolic labeling of prenylated proteins in HeLa, COS-7, and astrocyte cells. Furthermore, in HeLa cells, these modified prenylated proteins were identified and quantified using label-free quantification (LFQ) proteomics with 25 enriched prenylated proteins. Additionally, the unique chemistry of C10NorOPP was utilized for the construction of a multiprotein-polymer conjugate for the targeted labeling of cancer cells. That construct was prepared using a combination of norbornene-tetrazine conjugation and azide-alkyne cycloaddition, highlighting the utility of the additional degree of orthogonality for the facile assembly of new protein conjugates with novel structures and functions.
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Affiliation(s)
- Shelby A Auger
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Sneha Venkatachalapathy
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Kiall Francis G Suazo
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Yiao Wang
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Alexander W Sarkis
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Kaitlyn Bernhagen
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Katarzyna Justyna
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - James W Wollack
- Department of Chemistry and Biochemistry, St. Catherine University, 2004 Randolph Avenue, St. Paul, Minnesota 55105, United States
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - Ling Li
- Department of Experimental and Clinical Pharmacology, University of Minnesota─-Twin Cities, 2001 6th Street SE, Minneapolis, Minnesota 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
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Wang Y, Xu F, Nichols CB, Shi Y, Hellinga HW, Alspaugh JA, Distefano MD, Beese LS. Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase. J Med Chem 2022; 65:13753-13770. [PMID: 36218371 PMCID: PMC10755971 DOI: 10.1021/acs.jmedchem.2c00902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Infections by fungal pathogens are difficult to treat due to a paucity of antifungals and emerging resistances. Next-generation antifungals therefore are needed urgently. We have developed compounds that prevent farnesylation of Cryptoccoccus neoformans Ras protein by inhibiting protein farnesyltransferase with 3-4 nanomolar affinities. Farnesylation directs Ras to the cell membrane and is required for infectivity of this lethal pathogenic fungus. Our high-affinity compounds inhibit fungal growth with 3-6 micromolar minimum inhibitory concentrations (MICs), 4- to 8-fold better than Fluconazole, an antifungal commonly used in the clinic. Compounds bound with distinct inhibition mechanisms at two alternative, partially overlapping binding sites, accessed via different inhibitor conformations. We showed that antifungal potency depends critically on the selected inhibition mechanism because this determines the efficacy of an inhibitor at low in vivo levels of enzyme and farnesyl substrate. We elucidated how chemical modifications of the antifungals encode desired inhibitor conformation and concomitant inhibitory mechanism.
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Affiliation(s)
- You Wang
- Department of Biochemistry, Duke University School
of Medicine, Durham, North Carolina, USA 27710
| | - Feng Xu
- Department of Chemistry, University of Minnesota,
Minneapolis, Minnesota, USA 55455
| | - Connie B. Nichols
- Department of Medicine, Duke University School of
Medicine, Durham, North Carolina, USA 27710
- Department of Molecular Genetics and Microbiology,
Duke University School of Medicine, Durham, North Carolina, USA 27710
| | - Yuqian Shi
- Department of Biochemistry, Duke University School
of Medicine, Durham, North Carolina, USA 27710
| | - Homme W. Hellinga
- Department of Biochemistry, Duke University School
of Medicine, Durham, North Carolina, USA 27710
| | - J. Andrew Alspaugh
- Department of Medicine, Duke University School of
Medicine, Durham, North Carolina, USA 27710
- Department of Molecular Genetics and Microbiology,
Duke University School of Medicine, Durham, North Carolina, USA 27710
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota,
Minneapolis, Minnesota, USA 55455
| | - Lorena S. Beese
- Department of Biochemistry, Duke University School
of Medicine, Durham, North Carolina, USA 27710
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Pekel H, Guzel M, Sensoy O. Mechanistic insight into impact of phosphorylation on the enzymatic steps of farnesyltransferase. Protein Sci 2022; 31:e4414. [PMID: 36173156 PMCID: PMC9601885 DOI: 10.1002/pro.4414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/27/2022] [Accepted: 06/21/2022] [Indexed: 11/08/2022]
Abstract
Farnesyltransferase (FTase) is a heterodimeric enzyme, which catalyzes covalent attachment of the farnesyl group to target proteins, thus coordinating their trafficking in the cell. FTase has been demonstrated to be highly expressed in cancer and neurological diseases; hence considered as a hot target for therapeutic purposes. However, due to the nonspecific inhibition, there has been only one inhibitor that could be translated into the clinic. Importantly, it has been shown that phosphorylation of the α-subunit of FTase increases the activity of the enzyme in certain diseases. As such, understanding the impact of phosphorylation on dynamics of FTase provides a basis for targeting a specific state of the enzyme that emerges under pathological conditions. To this end, we performed 18 μs molecular dynamics (MD) simulations using complexes of (non)-phosphorylated FTase that are representatives of the farnesylation reaction. We demonstrated that phosphorylation modulated the catalytic site by rearranging interactions between farnesyl pyrophosphate (FPP)/peptide substrate, catalytic Zn2+ ion/coordinating residues and hot-spot residues at the interface of the subunits, all of which led to the stabilization of the substrate and facilitation of the release of the product, thus collectively expediting the reaction rate. Importantly, we also identified a likely allosteric pocket on the phosphorylated FTase, which might be used for specific targeting of the enzyme. To the best of our knowledge, this is the first study that systematically examines the impact of phosphorylation on the enzymatic reaction steps, hence opens up new avenues for drug discovery studies that focus on targeting phosphorylated FTase.
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Affiliation(s)
- Hanife Pekel
- Department of Pharmacy ServicesVocational School of Health Services, Istanbul Medipol UniversityIstanbulTurkey
- Regenerative and Restorative Medicine Research Center (REMER)Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
| | - Mustafa Guzel
- Department of Medical Pharmacology/International School of MedicineIstanbul Medipol UniversityIstanbulTurkey
- Center of Drug Discovery and DevelopmentResearch Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
| | - Ozge Sensoy
- Regenerative and Restorative Medicine Research Center (REMER)Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
- Department of Computer Engineering/School of Engineering and Natural SciencesIstanbul Medipol UniversityIstanbulTurkey
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Marchwicka A, Kamińska D, Monirialamdari M, Błażewska KM, Gendaszewska-Darmach E. Protein Prenyltransferases and Their Inhibitors: Structural and Functional Characterization. Int J Mol Sci 2022; 23:ijms23105424. [PMID: 35628237 PMCID: PMC9141697 DOI: 10.3390/ijms23105424] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
Protein prenylation is a post-translational modification controlling the localization, activity, and protein–protein interactions of small GTPases, including the Ras superfamily. This covalent attachment of either a farnesyl (15 carbon) or a geranylgeranyl (20 carbon) isoprenoid group is catalyzed by four prenyltransferases, namely farnesyltransferase (FTase), geranylgeranyltransferase type I (GGTase-I), Rab geranylgeranyltransferase (GGTase-II), and recently discovered geranylgeranyltransferase type III (GGTase-III). Blocking small GTPase activity, namely inhibiting prenyltransferases, has been proposed as a potential disease treatment method. Inhibitors of prenyltransferase have resulted in substantial therapeutic benefits in various diseases, such as cancer, neurological disorders, and viral and parasitic infections. In this review, we overview the structure of FTase, GGTase-I, GGTase-II, and GGTase-III and summarize the current status of research on their inhibitors.
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Affiliation(s)
- Aleksandra Marchwicka
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (A.M.); (D.K.)
| | - Daria Kamińska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (A.M.); (D.K.)
| | - Mohsen Monirialamdari
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (M.M.); (K.M.B.)
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (M.M.); (K.M.B.)
| | - Edyta Gendaszewska-Darmach
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (A.M.); (D.K.)
- Correspondence:
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6
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Chang HY, Cheng TH, Wang AHJ. Structure, catalysis, and inhibition mechanism of prenyltransferase. IUBMB Life 2020; 73:40-63. [PMID: 33246356 PMCID: PMC7839719 DOI: 10.1002/iub.2418] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/02/2020] [Accepted: 11/14/2020] [Indexed: 12/31/2022]
Abstract
Isoprenoids, also known as terpenes or terpenoids, represent a large family of natural products composed of five‐carbon isopentenyl diphosphate or its isomer dimethylallyl diphosphate as the building blocks. Isoprenoids are structurally and functionally diverse and include dolichols, steroid hormones, carotenoids, retinoids, aromatic metabolites, the isoprenoid side‐chain of ubiquinone, and isoprenoid attached signaling proteins. Productions of isoprenoids are catalyzed by a group of enzymes known as prenyltransferases, such as farnesyltransferases, geranylgeranyltransferases, terpenoid cyclase, squalene synthase, aromatic prenyltransferase, and cis‐ and trans‐prenyltransferases. Because these enzymes are key in cellular processes and metabolic pathways, they are expected to be potential targets in new drug discovery. In this review, six distinct subsets of characterized prenyltransferases are structurally and mechanistically classified, including (1) head‐to‐tail prenyl synthase, (2) head‐to‐head prenyl synthase, (3) head‐to‐middle prenyl synthase, (4) terpenoid cyclase, (5) aromatic prenyltransferase, and (6) protein prenylation. Inhibitors of those enzymes for potential therapies against several diseases are discussed. Lastly, recent results on the structures of integral membrane enzyme, undecaprenyl pyrophosphate phosphatase, are also discussed.
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Affiliation(s)
- Hsin-Yang Chang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Tien-Hsing Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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7
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Pantsar T. The current understanding of KRAS protein structure and dynamics. Comput Struct Biotechnol J 2019; 18:189-198. [PMID: 31988705 PMCID: PMC6965201 DOI: 10.1016/j.csbj.2019.12.004] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 01/10/2023] Open
Abstract
One of the most common drivers in human cancer is the mutant KRAS protein. Not so long ago KRAS was considered as an undruggable oncoprotein. After a long struggle, however, we finally see some light at the end of the tunnel as promising KRAS targeted therapies are in or approaching clinical trials. In recent years, together with the promising progress in RAS drug discovery, our understanding of KRAS has increased tremendously. This progress has been accompanied with a resurgence of publicly available KRAS structures, which were limited to nine structures less than ten years ago. Furthermore, the ever-increasing computational capacity has made biologically relevant timescales accessible, enabling molecular dynamics (MD) simulations to study the dynamics of KRAS protein in more detail at the atomistic level. In this minireview, my aim is to provide the reader an overview of the publicly available KRAS structural data, insights to conformational dynamics revealed by experiments and what we have learned from MD simulations. Also, I will discuss limitations of the current data and provide suggestions for future research related to KRAS, which would fill out the existing gaps in our knowledge and provide guidance in deciphering this enigmatic oncoprotein.
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Affiliation(s)
- Tatu Pantsar
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
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8
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Abdelkarim H, Banerjee A, Grudzien P, Leschinsky N, Abushaer M, Gaponenko V. The Hypervariable Region of K-Ras4B Governs Molecular Recognition and Function. Int J Mol Sci 2019; 20:ijms20225718. [PMID: 31739603 PMCID: PMC6888304 DOI: 10.3390/ijms20225718] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/09/2019] [Accepted: 11/11/2019] [Indexed: 12/25/2022] Open
Abstract
The flexible C-terminal hypervariable region distinguishes K-Ras4B, an important proto-oncogenic GTPase, from other Ras GTPases. This unique lysine-rich portion of the protein harbors sites for post-translational modification, including cysteine prenylation, carboxymethylation, phosphorylation, and likely many others. The functions of the hypervariable region are diverse, ranging from anchoring K-Ras4B at the plasma membrane to sampling potentially auto-inhibitory binding sites in its GTPase domain and participating in isoform-specific protein-protein interactions and signaling. Despite much research, there are still many questions about the hypervariable region of K-Ras4B. For example, mechanistic details of its interaction with plasma membrane lipids and with the GTPase domain require further clarification. The roles of the hypervariable region in K-Ras4B-specific protein-protein interactions and signaling are incompletely defined. It is also unclear why post-translational modifications frequently found in protein polylysine domains, such as acetylation, glycation, and carbamoylation, have not been observed in K-Ras4B. Expanding knowledge of the hypervariable region will likely drive the development of novel highly-efficient and selective inhibitors of K-Ras4B that are urgently needed by cancer patients.
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Affiliation(s)
- Hazem Abdelkarim
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago (UIC), Chicago, IL 60607, USA; (H.A.); (P.G.); (N.L.); (M.A.)
| | - Avik Banerjee
- Department of Chemistry, University of Illinois at Chicago (UIC), Chicago, IL 60612, USA;
| | - Patrick Grudzien
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago (UIC), Chicago, IL 60607, USA; (H.A.); (P.G.); (N.L.); (M.A.)
| | - Nicholas Leschinsky
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago (UIC), Chicago, IL 60607, USA; (H.A.); (P.G.); (N.L.); (M.A.)
| | - Mahmoud Abushaer
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago (UIC), Chicago, IL 60607, USA; (H.A.); (P.G.); (N.L.); (M.A.)
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago (UIC), Chicago, IL 60607, USA; (H.A.); (P.G.); (N.L.); (M.A.)
- Correspondence: ; Tel.: +312-355-4839
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Tsubamoto M, Le TK, Li M, Watanabe T, Matsumi C, Parvatkar P, Fujii H, Kato N, Sun J, Ohkanda J. A Guanidyl-Based Bivalent Peptidomimetic Inhibits K-Ras Prenylation and Association with c-Raf. Chemistry 2019; 25:13531-13536. [PMID: 31393030 DOI: 10.1002/chem.201903129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/07/2019] [Indexed: 01/06/2023]
Abstract
Unusual lipid modification of K-Ras makes Ras-directed cancer therapy a challenging task. Aiming to disrupt electrostatic-driven protein-protein interactions (PPIs) of K-Ras with FTase and GGTase I, a series of bivalent dual inhibitors that recognize the active pocket and the common acidic surface of FTase and GGTase I were designed. The structure-activity-relationship study resulted in 8 b, in which a biphenyl-based peptidomimetic FTI-277 was attached to a guanidyl-containing gallate moiety through an alkyl linker. Cell-based evaluation demonstrated that 8 b exhibited substantial inhibition of K-Ras processing without apparent interference with Rap-1A processing. Fluorescent imaging showed that 8 b disrupts localization of K-Ras to the plasma membrane and impairs interaction with c-Raf, whereas only FTI-277 was found to be inactive. These results suggest that targeting the PPI interface of K-Ras may provide an alternative method of inhibiting K-Ras.
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Affiliation(s)
- Mai Tsubamoto
- The Institute of Scientific Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Toan Khanh Le
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
| | - Minghua Li
- Department of Pharmaceutical Science, University of South Florida, Tampa, Florida, 33612, USA
| | - Taku Watanabe
- Ina Laboratory, Medical & Biological Laboratories, CO., Ltd., Ina, Nagano, 396-0002, Japan
| | - Chiemi Matsumi
- Ina Laboratory, Medical & Biological Laboratories, CO., Ltd., Ina, Nagano, 396-0002, Japan
| | - Prakash Parvatkar
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Hiroshi Fujii
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
| | - Nobuo Kato
- The Institute of Scientific Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Jiazhi Sun
- Department of Pharmaceutical Science, University of South Florida, Tampa, Florida, 33612, USA
| | - Junko Ohkanda
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
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Kuchay S, Wang H, Marzio A, Jain K, Homer H, Fehrenbacher N, Philips MR, Zheng N, Pagano M. GGTase3 is a newly identified geranylgeranyltransferase targeting a ubiquitin ligase. Nat Struct Mol Biol 2019; 26:628-636. [PMID: 31209342 PMCID: PMC6609460 DOI: 10.1038/s41594-019-0249-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 05/10/2019] [Indexed: 11/25/2022]
Abstract
Protein prenylation is believed to be catalyzed by three heterodimeric enzymes: FTase, GGTase1 and GGTase2. Here we report the identification of a previously unknown human prenyltransferase complex consisting of an orphan prenyltransferase α-subunit, PTAR1, and the catalytic β-subunit of GGTase2, RabGGTB. This enzyme, which we named GGTase3, geranylgeranylates FBXL2 to allow its localization at cell membranes, where this ubiquitin ligase mediates the polyubiquitylation of membrane-anchored proteins. In cells, FBXL2 is specifically recognized by GGTase3 despite having a typical carboxy-terminal CaaX prenylation motif that is predicted to be recognized by GGTase1. Our crystal structure analysis of the full-length GGTase3-FBXL2-SKP1 complex reveals an extensive multivalent interface specifically formed between the leucine-rich repeat domain of FBXL2 and PTAR1, which unmasks the structural basis of the substrate-enzyme specificity. By uncovering a missing prenyltransferase and its unique mode of substrate recognition, our findings call for a revision of the 'prenylation code'.
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Affiliation(s)
- Shafi Kuchay
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Hui Wang
- Department of Pharmacology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Antonio Marzio
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Kunj Jain
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Harrison Homer
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Nicole Fehrenbacher
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Mark R Philips
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA.
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11
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García-Torres D, Fierke CA. The chaperone SmgGDS-607 has a dual role, both activating and inhibiting farnesylation of small GTPases. J Biol Chem 2019; 294:11793-11804. [PMID: 31197034 DOI: 10.1074/jbc.ra119.007438] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/12/2019] [Indexed: 11/06/2022] Open
Abstract
Ras family small GTPases undergo prenylation (such as farnesylation) for proper localization to the plasma membrane, where they can initiate oncogenic signaling pathways. Small GTP-binding protein GDP-dissociation stimulator (SmgGDS) proteins are chaperones that bind and traffic small GTPases, although their exact cellular function is unknown. Initially, SmgGDS proteins were classified as guanine nucleotide exchange factors, but recent findings suggest that SmgGDS proteins also regulate prenylation of small GTPases in vivo in a substrate-selective manner. SmgGDS-607 recognizes the polybasic region and the CAAX box of several small GTPases and inhibits prenylation by impeding their entry into the geranylgeranylation pathway. Here, using recombinant and purified enzymes for prenylation and protein-binding assays, we demonstrate that SmgGDS-607 differentially regulates farnesylation of several small GTPases. SmgGDS-607 inhibited farnesylation of some proteins, such as DiRas1, by sequestering the protein and limiting modification catalyzed by protein farnesyltransferase (FTase). We found that the competitive binding affinities of the small GTPase for SmgGDS-607 and FTase dictate the extent of this inhibition. Additionally, we discovered that SmgGDS-607 increases the rate of farnesylation of HRas by enhancing product release from FTase. Our work indicates that SmgGDS-607 binds to a broad range of small GTPases and does not require a PBR for recognition. Together, these results provide mechanistic insight into SmgGDS-607-mediated regulation of farnesylation of small GTPases and suggest that SmgGDS-607 has multiple modes of substrate recognition.
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Affiliation(s)
| | - Carol A Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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12
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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: 263] [Impact Index Per Article: 43.8] [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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13
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Blanden MJ, Suazo KF, Hildebrandt ER, Hardgrove DS, Patel M, Saunders WP, Distefano MD, Schmidt WK, Hougland JL. Efficient farnesylation of an extended C-terminal C( x) 3X sequence motif expands the scope of the prenylated proteome. J Biol Chem 2017; 293:2770-2785. [PMID: 29282289 DOI: 10.1074/jbc.m117.805770] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/24/2017] [Indexed: 12/25/2022] Open
Abstract
Protein prenylation is a post-translational modification that has been most commonly associated with enabling protein trafficking to and interaction with cellular membranes. In this process, an isoprenoid group is attached to a cysteine near the C terminus of a substrate protein by protein farnesyltransferase (FTase) or protein geranylgeranyltransferase type I or II (GGTase-I and GGTase-II). FTase and GGTase-I have long been proposed to specifically recognize a four-amino acid CAAX C-terminal sequence within their substrates. Surprisingly, genetic screening reveals that yeast FTase can modify sequences longer than the canonical CAAX sequence, specifically C(x)3X sequences with four amino acids downstream of the cysteine. Biochemical and cell-based studies using both peptide and protein substrates reveal that mammalian FTase orthologs can also prenylate C(x)3X sequences. As the search to identify physiologically relevant C(x)3X proteins begins, this new prenylation motif nearly doubles the number of proteins within the yeast and human proteomes that can be explored as potential FTase substrates. This work expands our understanding of prenylation's impact within the proteome, establishes the biologically relevant reactivity possible with this new motif, and opens new frontiers in determining the impact of non-canonically prenylated proteins on cell function.
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Affiliation(s)
- Melanie J Blanden
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | - Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Emily R Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Daniel S Hardgrove
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Meet Patel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - William P Saunders
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Walter K Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - James L Hougland
- Department of Chemistry, Syracuse University, Syracuse, New York 13244.
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14
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Novotny CJ, Hamilton GL, McCormick F, Shokat KM. Farnesyltransferase-Mediated Delivery of a Covalent Inhibitor Overcomes Alternative Prenylation to Mislocalize K-Ras. ACS Chem Biol 2017; 12:1956-1962. [PMID: 28530791 DOI: 10.1021/acschembio.7b00374] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mutationally activated Ras is one of the most common oncogenic drivers found across all malignancies, and its selective inhibition has long been a goal in both pharma and academia. One of the oldest and most validated methods to inhibit overactive Ras signaling is by interfering with its post-translational processing and subsequent cellular localization. Previous attempts to target Ras processing led to the development of farnesyltransferase inhibitors, which can inhibit H-Ras localization but not K-Ras due to its ability to bypass farnesyltransterase inhibition through alternative prenylation by geranylgeranyltransferase. Here, we present the creation of a neo-substrate for farnesyltransferase that prevents the alternative prenlation by geranylgeranyltransferase and mislocalizes oncogenic K-Ras in cells.
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Affiliation(s)
- Chris J. Novotny
- Howard
Hughes Medical Institute and Department of Cellular and Molecular
Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Gregory L. Hamilton
- Howard
Hughes Medical Institute and Department of Cellular and Molecular
Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Frank McCormick
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National
Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21701, United States
- Diller Family Comprehensive
Cancer Center, University of California, San Francisco, California 94158, United States
| | - Kevan M. Shokat
- Howard
Hughes Medical Institute and Department of Cellular and Molecular
Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
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15
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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. [PMID: 28623230 DOI: 10.1074/jbc.m117.785063] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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16
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Temple KJ, Wright EN, Fierke CA, Gibbs RA. Exploration of GGTase-I substrate requirements. Part 1: Synthesis and biochemical evaluation of novel aryl-modified geranylgeranyl diphosphate analogs. Bioorg Med Chem Lett 2016; 26:3499-502. [PMID: 27342750 DOI: 10.1016/j.bmcl.2016.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 06/11/2016] [Accepted: 06/13/2016] [Indexed: 10/21/2022]
Abstract
Protein geranylgeranylation is a type of post-translational modification that aids in the localization of proteins to the plasma member where they elicit cellular signals. To better understand the isoprenoid requirements of GGTase-I, a series of aryl-modified geranylgeranyl diphosphate analogs were synthesized and screened against mammalian GGTase-I. Of our seven-member library of compounds, six analogs proved to be substrates of GGTase-I, with 6d having a krel=1.93 when compared to GGPP (krel=1.0).
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Affiliation(s)
- Kayla J Temple
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; The Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47909, USA.
| | - Elia N Wright
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carol A Fierke
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard A Gibbs
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; The Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47909, USA
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17
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Wang YC, Distefano MD. Synthetic isoprenoid analogues for the study of prenylated proteins: Fluorescent imaging and proteomic applications. Bioorg Chem 2016; 64:59-65. [PMID: 26709869 PMCID: PMC4731301 DOI: 10.1016/j.bioorg.2015.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/01/2015] [Accepted: 12/10/2015] [Indexed: 01/09/2023]
Abstract
Protein prenylation is a posttranslational modification catalyzed by prenyltransferases involving the attachment of farnesyl or geranylgeranyl groups to residues near the C-termini of proteins. This irreversible covalent modification is important for membrane localization and proper signal transduction. Here, the use of isoprenoid analogues for studying prenylated proteins is reviewed. First, experiments with analogues containing small fluorophores that are alternative substrates for prenyltransferases are described. Those analogues have been useful for quantifying binding affinity and for the production of fluorescently labeled proteins. Next, the use of analogues that incorporate biotin, bioorthogonal groups or antigenic moieties is described. Such probes have been particularly useful for identifying proteins that are naturally prenylated within mammalian cells. Overall, the use of isoprenoid analogues has contributed significantly to the understanding of protein prenlation.
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Affiliation(s)
- Yen-Chih Wang
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark D Distefano
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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18
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Lu S, Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R, Zhang J. Ras Conformational Ensembles, Allostery, and Signaling. Chem Rev 2016; 116:6607-65. [PMID: 26815308 DOI: 10.1021/acs.chemrev.5b00542] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ras proteins are classical members of small GTPases that function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states. Ras activation is regulated by guanine nucleotide exchange factors that catalyze the exchange of GDP by GTP, and inactivation is terminated by GTPase-activating proteins that accelerate the intrinsic GTP hydrolysis rate by orders of magnitude. In this review, we focus on data that have accumulated over the past few years pertaining to the conformational ensembles and the allosteric regulation of Ras proteins and their interpretation from our conformational landscape standpoint. The Ras ensemble embodies all states, including the ligand-bound conformations, the activated (or inactivated) allosteric modulated states, post-translationally modified states, mutational states, transition states, and nonfunctional states serving as a reservoir for emerging functions. The ensemble is shifted by distinct mutational events, cofactors, post-translational modifications, and different membrane compositions. A better understanding of Ras biology can contribute to therapeutic strategies.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine , Shanghai, 200025, China.,Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States
| | | | | | | | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute , Frederick, Maryland 21702, United States.,Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University , Tel Aviv 69978, Israel
| | - Jian Zhang
- Department of Pathophysiology, Shanghai Universities E-Institute for Chemical Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine , Shanghai, 200025, China
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19
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Ho MH, De Vivo M, Peraro MD, Klein ML. Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation. J Chem Theory Comput 2015; 5:1657-66. [PMID: 26609858 DOI: 10.1021/ct8004722] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protein farnesyltransferase (FTase) is a Zn(2+)-metalloenzyme that catalyzes the farnesylation reaction, i.e., the transfer of the 15-carbon atom farnesyl group from farnesyl diphosphate (FPP) to a specific cysteine of protein substrates. Oncogenic Ras proteins, which are among the FTase substrates, are observed in about 20-30% of human cancer cells. Thus, FTase represents a target for anticancer drug design. Herein, we present a classical force-field-based and quantum mechanics/molecular mechanics (QM/MM) computational study of the FTase reaction mechanism. Our findings offer a detailed picture of the FTase catalytic pathway, describing structural features and the energetics of its saddle points. A moderate dissociation of the diphosphate group from the FPP is observed during the nucleophilic attack of the zinc-bound thiolate. At the transition state, a resonance structure is observed, which indicates the formation of a metastable carbocation. However, no stable intermediate is found along the reaction pathway. Thus, the reaction occurs via an associative mechanism with dissociative character, in agreement with the mechanism proposed by Fierke et al. ( Biochemistry 2000, 39, 2593-2602 and Biochemistry 2003, 42, 9741-9748 ). Moreover, a fluorine-substituted FPP analogue (CF3-FPP) is used to investigate the inhibitory effect of fluorine, which in turn provides additional agreement with experimental data.
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Affiliation(s)
- Ming-Hsun Ho
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy, and Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Marco De Vivo
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy, and Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy, and Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
| | - Michael L Klein
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, Department of Drug Discovery and Development, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy, and Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, EPFL, CH-1015 Lausanne, Switzerland
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20
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Kubala MH, Norwood SJ, Gomez GA, Jones A, Johnston W, Yap AS, Mureev S, Alexandrov K. Mammalian farnesyltransferase α subunit regulates vacuolar protein sorting-associated protein 4A (Vps4A)--dependent intracellular trafficking through recycling endosomes. Biochem Biophys Res Commun 2015; 468:580-6. [PMID: 26551458 DOI: 10.1016/j.bbrc.2015.10.148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 11/19/2022]
Abstract
The protein farnesyltransferase (FTase) mediates posttranslational modification of proteins with isoprenoid lipids. FTase is a heterodimer and although the β subunit harbors the active site, it requires the α subunit for its activity. Here we explore the other functions of the FTase α subunit in addition to its established role in protein prenylation. We found that in the absence of the β subunit, the α subunit of FTase forms a stable autonomous dimeric structure in solution. We identify interactors of FTase α using mass spectrometry, followed by rapid in vitro analysis using the Leishmania tarentolae cell - free system. Vps4A was validated for direct binding to the FTase α subunit both in vitro and in vivo. Analysis of the interaction with Vps4A in Hek 293 cells demonstrated that FTase α controls trafficking of transferrin receptor upstream of this protein. These results point to the existence of previously undetected biological functions of the FTase α subunit that includes control of intracellular membrane trafficking.
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Affiliation(s)
- Marta H Kubala
- Institute for Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, Queensland, 4072, Australia
| | - Suzanne J Norwood
- Institute for Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, Queensland, 4072, Australia
| | - Guillermo A Gomez
- Institute for Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, Queensland, 4072, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, Queensland, 4072, Australia
| | - Wayne Johnston
- Institute for Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, Queensland, 4072, Australia
| | - Alpha S Yap
- Institute for Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, Queensland, 4072, Australia
| | - Sergey Mureev
- Institute for Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, Queensland, 4072, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience, University of Queensland, Brisbane, St. Lucia, Queensland, 4072, Australia.
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21
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Lu S, Banerjee A, Jang H, Zhang J, Gaponenko V, Nussinov R. GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site. J Biol Chem 2015; 290:28887-900. [PMID: 26453300 DOI: 10.1074/jbc.m115.664755] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Indexed: 12/22/2022] Open
Abstract
K-Ras4B, a frequently mutated oncogene in cancer, plays an essential role in cell growth, differentiation, and survival. Its C-terminal membrane-associated hypervariable region (HVR) is required for full biological activity. In the active GTP-bound state, the HVR interacts with acidic plasma membrane (PM) headgroups, whereas the farnesyl anchors in the membrane; in the inactive GDP-bound state, the HVR may interact with both the PM and the catalytic domain at the effector binding region, obstructing signaling and nucleotide exchange. Here, using molecular dynamics simulations and NMR, we aim to figure out the effects of nucleotides (GTP and GDP) and frequent (G12C, G12D, G12V, G13D, and Q61H) and infrequent (E37K and R164Q) oncogenic mutations on full-length K-Ras4B. The mutations are away from or directly at the HVR switch I/effector binding site. Our results suggest that full-length wild-type GDP-bound K-Ras4B (K-Ras4B(WT)-GDP) is in an intrinsically autoinhibited state via tight HVR-catalytic domain interactions. The looser association in K-Ras4B(WT)-GTP may release the HVR. Some of the oncogenic mutations weaken the HVR-catalytic domain association in the K-Ras4B-GDP/-GTP bound states, which may facilitate the HVR disassociation in a nucleotide-independent manner, thereby up-regulating oncogenic Ras signaling. Thus, our results suggest that mutations can exert their effects in more than one way, abolishing GTP hydrolysis and facilitating effector binding.
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Affiliation(s)
- Shaoyong Lu
- From the Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China, Cancer and Inflammation Program, Leidos Biomedical Research, Inc., NCI-Frederick, Frederick, Maryland 21702
| | | | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Jian Zhang
- From the Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China,
| | - Vadim Gaponenko
- Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, and
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., NCI-Frederick, Frederick, Maryland 21702, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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22
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Dozier JK, Khatwani SL, Wollack JW, Wang YC, Schmidt-Dannert C, Distefano MD. Engineering protein farnesyltransferase for enzymatic protein labeling applications. Bioconjug Chem 2014; 25:1203-12. [PMID: 24946229 PMCID: PMC4103756 DOI: 10.1021/bc500240p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Creating covalent protein conjugates is an active area of research due to the wide range of uses for protein conjugates spanning everything from biological studies to protein therapeutics. Protein Farnesyltransferase (PFTase) has been used for the creation of site-specific protein conjugates, and a number of PFTase substrates have been developed to facilitate that work. PFTase is an effective catalyst for protein modification because it transfers Farnesyl diphosphate (FPP) analogues to protein substrates on a cysteine four residues from the C-terminus. While much work has been done to synthesize various FPP analogues, there are few reports investigating how mutations in PFTase alter the kinetics with these unnatural analogues. Herein we examined how different mutations within the PFTase active site alter the kinetics of the PFTase reaction with a series of large FPP analogues. We found that mutating either a single tryptophan or tyrosine residue to alanine results in greatly improved catalytic parameters, particularly in kcat. Mutation of tryptophan 102β to alanine caused a 4-fold increase in kcat and a 10-fold decrease in KM for a benzaldehyde-containing FPP analogue resulting in an overall 40-fold increase in catalytic efficiency. Similarly, mutation of tyrosine 205β to alanine caused a 25-fold increase in kcat and a 10-fold decrease in KM for a coumarin-containing analogue leading to a 300-fold increase in catalytic efficiency. Smaller but significant changes in catalytic parameters were also obtained for cyclo-octene- and NBD-containing FPP analogues. The latter compound was used to create a fluorescently labeled form of Ciliary Neurotrophic Factor (CNTF), a protein of therapeutic importance. Additionally, computational modeling was performed to study how the large non-natural isoprenoid analogues can fit into the active sites enlarged via mutagenesis. Overall, these results demonstrate that PFTase can be improved via mutagenesis in ways that will be useful for protein engineering and the creation of site-specific protein conjugates.
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Affiliation(s)
- Jonathan K Dozier
- Department of Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
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23
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Mabanglo MF, Hast MA, Lubock NB, Hellinga HW, Beese LS. Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design. Protein Sci 2014; 23:289-301. [PMID: 24347326 PMCID: PMC3945837 DOI: 10.1002/pro.2411] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/11/2013] [Accepted: 12/11/2013] [Indexed: 11/07/2022]
Abstract
Species of the fungal genus Aspergillus are significant human and agricultural pathogens that are often refractory to existing antifungal treatments. Protein farnesyltransferase (FTase), a critical enzyme in eukaryotes, is an attractive potential target for antifungal drug discovery. We report high-resolution structures of A. fumigatus FTase (AfFTase) in complex with substrates and inhibitors. Comparison of structures with farnesyldiphosphate (FPP) bound in the absence or presence of peptide substrate, corresponding to successive steps in ordered substrate binding, revealed that the second substrate-binding step is accompanied by motions of a loop in the catalytic site. Re-examination of other FTase structures showed that this motion is conserved. The substrate- and product-binding clefts in the AfFTase active site are wider than in human FTase (hFTase). Widening is a consequence of small shifts in the α-helices that comprise the majority of the FTase structure, which in turn arise from sequence variation in the hydrophobic core of the protein. These structural effects are key features that distinguish fungal FTases from hFTase. Their variation results in differences in steady-state enzyme kinetics and inhibitor interactions and presents opportunities for developing selective anti-fungal drugs by exploiting size differences in the active sites. We illustrate the latter by comparing the interaction of ED5 and Tipifarnib with hFTase and AfFTase. In AfFTase, the wider groove enables ED5 to bind in the presence of FPP, whereas in hFTase it binds only in the absence of substrate. Tipifarnib binds similarly to both enzymes but makes less extensive contacts in AfFTase with consequently weaker binding.
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Affiliation(s)
- Mark F Mabanglo
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
| | - Michael A Hast
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
| | - Nathan B Lubock
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
| | - Lorena S Beese
- Department of Biochemistry, Duke University Medical CenterDurham, North Carolina, 27710
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24
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Gangopadhyay SA, Losito EL, Hougland JL. Targeted reengineering of protein geranylgeranyltransferase type I selectivity functionally implicates active-site residues in protein-substrate recognition. Biochemistry 2014; 53:434-46. [PMID: 24344934 DOI: 10.1021/bi4011732] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Posttranslational modifications are vital for the function of many proteins. Prenylation is one such modification, wherein protein geranylgeranyltransferase type I (GGTase-I) or protein farnesyltransferase (FTase) modify proteins by attaching a 20- or 15-carbon isoprenoid group, respectively, to a cysteine residue near the C-terminus of a target protein. These enzymes require a C-terminal Ca1a2X sequence on their substrates, with the a1, a2, and X residues serving as substrate-recognition elements for FTase and/or GGTase-I. While crystallographic structures of rat GGTase-I show a tightly packed and hydrophobic a2 residue binding pocket, consistent with a preference for moderately sized a2 residues in GGTase-I substrates, the functional impact of enzyme-substrate contacts within this active site remains to be determined. Using site-directed mutagenesis and peptide substrate structure-activity studies, we have identified specific active-site residues within rat GGTase-I involved in substrate recognition and developed novel GGTase-I variants with expanded/altered substrate selectivity. The ability to drastically alter GGTase-I selectivity mirrors similar behavior observed in FTase but employs mutation of a distinct set of structurally homologous active-site residues. Our work demonstrates that tunable selectivity may be a general phenomenon among multispecific enzymes involved in posttranslational modification and raises the possibility of variable substrate selectivity among GGTase-I orthologues from different organisms. Furthermore, the GGTase-I variants developed herein can serve as tools for studying GGTase-I substrate selectivity and the effects of prenylation pathway modifications on specific proteins.
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Ohkanda J. Module Assembly for Designing Multivalent Mid-Sized Inhibitors of Protein-Protein Interactions. CHEM REC 2013; 13:561-75. [DOI: 10.1002/tcr.201300026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Junko Ohkanda
- Institute for Chemical Research; Kyoto University; Gokasho, Uji Kyoto 611-0011 Japan
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26
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Yu X, Zhao X, Zhu L, Zou C, Liu X, Zhao Z, Huang J, Li H. Discovery of novel inhibitors for human farnesyltransferase (hFTase) via structure-based virtual screening. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00058c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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Kang CW, Sun Y, Del Valle JR. Substituted imidazo[1,2-a]pyridines as β-strand peptidomimetics. Org Lett 2012; 14:6162-5. [PMID: 23210770 DOI: 10.1021/ol302850n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New conformationally extended dipeptide surrogates based on an imidazo[1,2-a]pyridine scaffold are described. Efficient synthesis and incorporation into host peptides affords structures with native side-chain functionality and hydrogen bonding elements on one face of the backbone. Structural analysis by NMR suggests that model peptidomimetics adopt a β-strand-like conformation in solution.
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Affiliation(s)
- Chang Won Kang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
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28
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Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif. J Mol Model 2012; 19:673-88. [DOI: 10.1007/s00894-012-1590-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
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29
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Hast MA, Nichols CB, Armstrong SM, Kelly SM, Hellinga HW, Alspaugh JA, Beese LS. Structures of Cryptococcus neoformans protein farnesyltransferase reveal strategies for developing inhibitors that target fungal pathogens. J Biol Chem 2011; 286:35149-62. [PMID: 21816822 DOI: 10.1074/jbc.m111.250506] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cryptococcus neoformans is a fungal pathogen that causes life-threatening infections in immunocompromised individuals, including AIDS patients and transplant recipients. Few antifungals can treat C. neoformans infections, and drug resistance is increasing. Protein farnesyltransferase (FTase) catalyzes post-translational lipidation of key signal transduction proteins and is essential in C. neoformans. We present a multidisciplinary study validating C. neoformans FTase (CnFTase) as a drug target, showing that several anticancer FTase inhibitors with disparate scaffolds can inhibit C. neoformans and suggesting structure-based strategies for further optimization of these leads. Structural studies are an essential element for species-specific inhibitor development strategies by revealing similarities and differences between pathogen and host orthologs that can be exploited. We, therefore, present eight crystal structures of CnFTase that define the enzymatic reaction cycle, basis of ligand selection, and structurally divergent regions of the active site. Crystal structures of clinically important anticancer FTase inhibitors in complex with CnFTase reveal opportunities for optimization of selectivity for the fungal enzyme by modifying functional groups that interact with structurally diverse regions. A substrate-induced conformational change in CnFTase is observed as part of the reaction cycle, a feature that is mechanistically distinct from human FTase. Our combined structural and functional studies provide a framework for developing FTase inhibitors to treat invasive fungal infections.
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Affiliation(s)
- Michael A Hast
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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30
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Yang Y, Chakravorty DK, Merz KM. Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry 2011; 49:9658-66. [PMID: 20923173 DOI: 10.1021/bi1008358] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies aimed at elucidating the unknown Mg2+ binding site in protein farnesyltransferase (FTase) are reported. FTase catalyzes the transfer of a farnesyl group to a conserved cysteine residue (Cys1p) on a target protein, an important step for proteins in the signal transduction pathways (e.g., Ras). Mg2+ ions accelerate the protein farnesylation reaction by up to 700-fold. The exact function of Mg2+ in catalysis and the structural characteristics of its binding remain unresolved to date. Molecular dynamics (MD) simulations addressing the role of magnesium ions in FTase are presented, and relevant octahedral binding motifs for Mg2+ in wild-type (WT) FTase and the Dβ352A mutant are explored. Our simulations suggest that the addition of Mg2+ ions causes a conformational change to occur in the FTase active site, breaking interactions known to keep FPP in its inactive conformation. Two relevant Mg2+ ion binding motifs were determined in WT FTase. In the first binding motif, WT1, the Mg2+ ion is coordinated to D352β, zinc-bound D297β, two water molecules, and one oxygen atom from the α- and β-phosphates of farnesyl diphosphate (FPP). The second binding motif, WT2, is identical with the exception of the zinc-bound D297β being replaced by a water molecule in the Mg2+ coordination complex. In the Dβ352A mutant Mg2+ binding motif, D297β, three water molecules, and one oxygen atom from the α- and β-phosphates of FPP complete the octahedral coordination sphere of Mg2+. Simulations of WT FTase, in which Mg2+ was replaced by water in the active site, recreated the salt bridges and hydrogen-bonding patterns around FPP, validating these simulations. In all Mg2+ binding motifs, a key hydrogen bond was identified between a magnesium-bound water and Cys1p, bridging the two metallic binding sites and, thereby, reducing the equilibrium distance between the reacting atoms of FPP Cys1p. The free energy profiles calculated for these systems provide a qualitative understanding of experimental results. They demonstrate that the two reactive atoms approach each other more readily in the presence of Mg2+ in WT FTase and mutant. The flexible WT2 model was found to possess the lowest barrier toward the conformational change, suggesting it is the preferred Mg2+ binding motif in WT FTase. In the mutant, the absence of D352β makes the transition toward a conformational change harder. Our calculations find support for the proposal that D352β performs a critical role in Mg2+ binding and Mg2+ plays an important role in the conformational transition step.
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Affiliation(s)
- Yue Yang
- Department of Chemistry and the Quantum Theory Project, University of Florida, Gainesville, FL 32611-8435, USA
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31
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Global Identification of Protein Prenyltransferase Substrates. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/b978-0-12-381339-8.00012-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
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32
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Machida S, Kato N, Harada K, Ohkanda J. Bivalent Inhibitors for Disrupting Protein Surface-Substrate Interactions and for Dual Inhibition of Protein Prenyltransferases. J Am Chem Soc 2010; 133:958-63. [DOI: 10.1021/ja1086112] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Shinnosuke Machida
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Nobuo Kato
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuo Harada
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501, Japan
| | - Junko Ohkanda
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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33
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Jost M, Zocher G, Tarcz S, Matuschek M, Xie X, Li SM, Stehle T. Structure−Function Analysis of an Enzymatic Prenyl Transfer Reaction Identifies a Reaction Chamber with Modifiable Specificity. J Am Chem Soc 2010; 132:17849-58. [DOI: 10.1021/ja106817c] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Jost
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany, Institut für Pharmazeutische Biologie und Biotechnologie, Universität Marburg, Deutschhausstrasse 17a, 35037 Marburg, Germany, Fachbereich Chemie, Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany, and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Georg Zocher
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany, Institut für Pharmazeutische Biologie und Biotechnologie, Universität Marburg, Deutschhausstrasse 17a, 35037 Marburg, Germany, Fachbereich Chemie, Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany, and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Sylwia Tarcz
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany, Institut für Pharmazeutische Biologie und Biotechnologie, Universität Marburg, Deutschhausstrasse 17a, 35037 Marburg, Germany, Fachbereich Chemie, Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany, and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Marco Matuschek
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany, Institut für Pharmazeutische Biologie und Biotechnologie, Universität Marburg, Deutschhausstrasse 17a, 35037 Marburg, Germany, Fachbereich Chemie, Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany, and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Xiulan Xie
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany, Institut für Pharmazeutische Biologie und Biotechnologie, Universität Marburg, Deutschhausstrasse 17a, 35037 Marburg, Germany, Fachbereich Chemie, Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany, and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Shu-Ming Li
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany, Institut für Pharmazeutische Biologie und Biotechnologie, Universität Marburg, Deutschhausstrasse 17a, 35037 Marburg, Germany, Fachbereich Chemie, Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany, and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Thilo Stehle
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany, Institut für Pharmazeutische Biologie und Biotechnologie, Universität Marburg, Deutschhausstrasse 17a, 35037 Marburg, Germany, Fachbereich Chemie, Universität Marburg, Hans-Meerwein-Strasse, 35032 Marburg, Germany, and Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
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Nguyen UTT, Goody RS, Alexandrov K. Understanding and exploiting protein prenyltransferases. Chembiochem 2010; 11:1194-201. [PMID: 20432425 DOI: 10.1002/cbic.200900727] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Uyen T T Nguyen
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, NY 10065, USA
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35
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Ranatunga S, Liyanage W, Del Valle JR. Synthesis and conformational analysis of bicyclic extended dipeptide surrogates. J Org Chem 2010; 75:5113-25. [PMID: 20593836 PMCID: PMC2914495 DOI: 10.1021/jo1008433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regio- and diastereoselective reactions of a homoproline enolate enable the synthesis of novel extended dipeptide surrogates. Bicyclic carbamate 9 and fused beta-lactam scaffold 11 were prepared from L-pyroglutamic acid via substrate-controlled electrophilic azidation. Synthesis of orthogonally protected hexahydropyrrolizine, hexahydropyrrolizinone, and hexahydropyrroloazepinone dipeptide surrogates relied on allylation of proline derivative 5, followed by Curtius rearrangement to introduce the N-terminal carbamate group. A total of six azabicycloalkane derivatives were evaluated for conformational mimicry of extended dipeptides by a combination of X-ray diffraction and molecular modeling. Analysis of putative backbone dihedral angles and N- to C-terminal dipeptide distances indicate that compounds (alpha'S)-14b and 21 approximate the conformation of dipeptides found in beta-sheets, while tripeptide mimic 28 is also highly extended in the solid state. Structural data suggest that ring size and relative stereochemistry have a profound effect on the ability of these scaffolds to act as beta-strand mimetics and should inform the design of related conformational probes.
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36
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Hougland JL, Lamphear CL, Scott SA, Gibbs RA, Fierke CA. Context-dependent substrate recognition by protein farnesyltransferase. Biochemistry 2010; 48:1691-701. [PMID: 19199818 DOI: 10.1021/bi801710g] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Prenylation is a posttranslational modification whereby C-terminal lipidation leads to protein localization to membranes. A C-terminal "Ca(1)a(2)X" sequence has been proposed as the recognition motif for two prenylation enzymes, protein farnesyltransferase (FTase) and protein geranylgeranyltransferase type I. To define the parameters involved in recognition of the a(2) residue, we performed structure-activity analysis which indicates that FTase discriminates between peptide substrates based on both the hydrophobicity and steric volume of the side chain at the a(2) position. For nonpolar side chains, the dependence of the reactivity on side chain volume at this position forms a pyramidal pattern with a maximal activity near the steric volume of valine. This discrimination occurs at a step in the kinetic mechanism that is at or before the farnesylation step. Furthermore, a(2) selectivity is also affected by the identity of the adjacent X residue, leading to context-dependent substrate recognition. Context-dependent a(2) selectivity suggests that FTase recognizes the sequence downstream of the conserved cysteine as a set of two or three cooperative, interconnected recognition elements as opposed to three independent amino acids. These findings expand the pool of proposed FTase substrates in cells. A better understanding of the molecular recognition of substrates performed by FTase will aid in both designing new FTase inhibitors as therapeutic agents and characterizing proteins involved in prenylation-dependent cellular pathways.
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Affiliation(s)
- James L Hougland
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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37
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Andrews M, Huizinga DH, Crowell DN. The CaaX specificities of Arabidopsis protein prenyltransferases explain era1 and ggb phenotypes. BMC PLANT BIOLOGY 2010; 10:118. [PMID: 20565889 PMCID: PMC3017772 DOI: 10.1186/1471-2229-10-118] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 06/18/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND Protein prenylation is a common post-translational modification in metazoans, protozoans, fungi, and plants. This modification, which mediates protein-membrane and protein-protein interactions, is characterized by the covalent attachment of a fifteen-carbon farnesyl or twenty-carbon geranylgeranyl group to the cysteine residue of a carboxyl terminal CaaX motif. In Arabidopsis, era1 mutants lacking protein farnesyltransferase exhibit enlarged meristems, supernumerary floral organs, an enhanced response to abscisic acid (ABA), and drought tolerance. In contrast, ggb mutants lacking protein geranylgeranyltransferase type 1 exhibit subtle changes in ABA and auxin responsiveness, but develop normally. RESULTS We have expressed recombinant Arabidopsis protein farnesyltransferase (PFT) and protein geranylgeranyltransferase type 1 (PGGT1) in E. coli and characterized purified enzymes with respect to kinetic constants and substrate specificities. Our results indicate that, whereas PFT exhibits little specificity for the terminal amino acid of the CaaX motif, PGGT1 exclusively prenylates CaaX proteins with a leucine in the terminal position. Moreover, we found that different substrates exhibit similar K(m) but different k(cat) values in the presence of PFT and PGGT1, indicating that substrate specificities are determined primarily by reactivity rather than binding affinity. CONCLUSIONS The data presented here potentially explain the relatively strong phenotype of era1 mutants and weak phenotype of ggb mutants. Specifically, the substrate specificities of PFT and PGGT1 suggest that PFT can compensate for loss of PGGT1 in ggb mutants more effectively than PGGT1 can compensate for loss of PFT in era1 mutants. Moreover, our results indicate that PFT and PGGT1 substrate specificities are primarily due to differences in catalysis, rather than differences in substrate binding.
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Affiliation(s)
- Michelle Andrews
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA
| | - David H Huizinga
- Department of Biology, Indiana University-Purdue University, Indianapolis, IN 46202, USA
- Dow AgroSciences LLC, Indianapolis, IN 46268, USA
| | - Dring N Crowell
- Department of Biological Sciences, Idaho State University, Pocatello, ID 83209, USA
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38
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Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-90-481-3034-4_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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39
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Hast MA, Fletcher S, Cummings CG, Pusateri EE, Blaskovich MA, Rivas K, Gelb MH, Van Voorhis WC, Sebti SM, Hamilton AD, Beese LS. Structural basis for binding and selectivity of antimalarial and anticancer ethylenediamine inhibitors to protein farnesyltransferase. ACTA ACUST UNITED AC 2009; 16:181-92. [PMID: 19246009 DOI: 10.1016/j.chembiol.2009.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 01/21/2009] [Accepted: 01/26/2009] [Indexed: 11/24/2022]
Abstract
Protein farnesyltransferase (FTase) catalyzes an essential posttranslational lipid modification of more than 60 proteins involved in intracellular signal transduction networks. FTase inhibitors have emerged as a significant target for development of anticancer therapeutics and, more recently, for the treatment of parasitic diseases caused by protozoan pathogens, including malaria (Plasmodium falciparum). We present the X-ray crystallographic structures of complexes of mammalian FTase with five inhibitors based on an ethylenediamine scaffold, two of which exhibit over 1000-fold selective inhibition of P. falciparum FTase. These structures reveal the dominant determinants in both the inhibitor and enzyme that control binding and selectivity. Comparison to a homology model constructed for the P. falciparum FTase suggests opportunities for further improving selectivity of a new generation of antimalarial inhibitors.
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Affiliation(s)
- Michael A Hast
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710, USA
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40
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Sousa SF, Fernandes PA, Ramos MJ. Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme. Bioorg Med Chem 2009; 17:3369-78. [DOI: 10.1016/j.bmc.2009.03.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 03/16/2009] [Accepted: 03/20/2009] [Indexed: 10/20/2022]
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41
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Sousa S, Fernandes P, Ramos M. The Search for the Mechanism of the Reaction Catalyzed by Farnesyltransferase. Chemistry 2009; 15:4243-7. [DOI: 10.1002/chem.200802745] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Subramanian T, Liu S, Troutman JM, Andres DA, Spielmann HP. Protein farnesyltransferase-catalyzed isoprenoid transfer to peptide depends on lipid size and shape, not hydrophobicity. Chembiochem 2009; 9:2872-82. [PMID: 18985644 DOI: 10.1002/cbic.200800248] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein farnesyl transferase (FTase) catalyzes transfer of a 15-carbon farnesyl group from farnesyl diphosphate (FPP) to a conserved cysteine in the C-terminal Ca(1)a(2)X motif of a range of proteins, including the oncoprotein H-Ras ("C" refers to the cysteine, "a" to any aliphatic amino acid, and "X" to any amino acid) and the lipid chain interacts with, and forms part of the Ca(1)a(2)X peptide binding site. Previous studies have shown that H-Ras biological function is ablated when it is modified with lipids that are 3-5 orders of magnitude less hydrophobic than FPP. Here, we employed a library of anilinogeranyl diphosphate (AGPP) and phenoxygeranyl diphosphate (PGPP) derivatives with a range of polarities (log P (lipid alcohol) = 0.7-6.8, log P (farnesol) = 6.1) and shapes to examine whether FTase-catalyzed transfer to peptide is dependent on the hydrophobicity of the lipid. Analysis of steady-state transfer kinetics for analogues to dansyl-GCVLS peptide revealed that the efficiency of lipid transfer was highly dependent on both the shape and size, but was independent of the polarity of the analogue. These observations indicate that hydrophobic features of isoprenoids critical for their association with membranes and/or protein receptors are not required for efficient transfer to Ca(1)a(2)X peptides by FTase. Furthermore, the results of these studies indicate that the role played by the farnesyl lipid in the FTase mechanism is primarily structural. To explain these results we propose a model in which the FTase active site stabilizes a membrane interface-like environment.
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Affiliation(s)
- Thangaiah Subramanian
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536-0084, USA
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43
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DeGraw AJ, Hast MA, Xu J, Mullen D, Beese LS, Barany G, Distefano MD. Caged protein prenyltransferase substrates: tools for understanding protein prenylation. Chem Biol Drug Des 2008; 72:171-81. [PMID: 18844669 DOI: 10.1111/j.1747-0285.2008.00698.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Originally designed to block the prenylation of oncogenic Ras, inhibitors of protein farnesyltransferase currently in preclinical and clinical trials are showing efficacy in cancers with normal Ras. Blocking protein prenylation has also shown promise in the treatment of malaria, Chagas disease and progeria syndrome. A better understanding of the mechanism, targets and in vivo consequences of protein prenylation are needed to elucidate the mode of action of current PFTase (Protein Farnesyltransferase) inhibitors and to create more potent and selective compounds. Caged enzyme substrates are useful tools for understanding enzyme mechanism and biological function. Reported here is the synthesis and characterization of caged substrates of PFTase. The caged isoprenoid diphosphates are poor substrates prior to photolysis. The caged CAAX peptide is a true catalytically caged substrate of PFTase in that it is to not a substrate, yet is able to bind to the enzyme as established by inhibition studies and X-ray crystallography. Irradiation of the caged molecules with 350 nm light readily releases their cognate substrate and their photolysis products are benign. These properties highlight the utility of those analogs towards a variety of in vitro and in vivo applications.
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Affiliation(s)
- Amanda J DeGraw
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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44
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Hast MA, Beese LS. Structure of protein geranylgeranyltransferase-I from the human pathogen Candida albicans complexed with a lipid substrate. J Biol Chem 2008; 283:31933-40. [PMID: 18713740 DOI: 10.1074/jbc.m805330200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein geranylgeranyltransferase-I (GGTase-I) catalyzes the transfer of a 20-carbon isoprenoid lipid to the sulfur of a cysteine residue located near the C terminus of numerous cellular proteins, including members of the Rho superfamily of small GTPases and other essential signal transduction proteins. In humans, GGTase-I and the homologous protein farnesyltransferase (FTase) are targets of anticancer therapeutics because of the role small GTPases play in oncogenesis. Protein prenyltransferases are also essential for many fungal and protozoan pathogens that infect humans, and have therefore become important targets for treating infectious diseases. Candida albicans, a causative agent of systemic fungal infections in immunocompromised individuals, is one pathogen for which protein prenylation is essential for survival. Here we present the crystal structure of GGTase-I from C. albicans (CaGGTase-I) in complex with its cognate lipid substrate, geranylgeranylpyrophosphate. This structure provides a high-resolution picture of a non-mammalian protein prenyltransferase. There are significant variations between species in critical areas of the active site, including the isoprenoid-binding pocket, as well as the putative product exit groove. These differences indicate the regions where specific protein prenyltransferase inhibitors with antifungal activity can be designed.
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Affiliation(s)
- Michael A Hast
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Sousa SF, Fernandes PA, Ramos MJ. Enzyme Flexibility and the Catalytic Mechanism of Farnesyltransferase: Targeting the Relation. J Phys Chem B 2008; 112:8681-91. [DOI: 10.1021/jp711214j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sérgio F. Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria João Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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Machida S, Usuba K, Blaskovich MA, Yano A, Harada K, Sebti SM, Kato N, Ohkanda J. Module assembly for protein-surface recognition: geranylgeranyltransferase I bivalent inhibitors for simultaneous targeting of interior and exterior protein surfaces. Chemistry 2008; 14:1392-401. [PMID: 18200641 DOI: 10.1002/chem.200701634] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Synthetic chemical probes designed to simultaneously targeting multiple sites of protein surfaces are of interest owing to their potential application as site specific modulators of protein-protein interactions. A new approach toward bivalent inhibitors of mammalian type I geranylgeranyltransferase (GGTase I) based on module assembly for simultaneous recognition of both interior and exterior protein surfaces is reported. The inhibitors synthesized in this study consist of two modules linked by an alkyl spacer; one is the tetrapeptide CVIL module for binding to the interior protein surface (active pocket) and the other is a 3,4,5-alkoxy substituted benzoyl motif that contains three aminoalkyl groups designed to bind to the negatively charged protein exterior surface near the active site. The compounds were screened by two distinct enzyme inhibition assays based on fluorescence spectroscopy and incorporation of a [(3)H]-labeled prenyl group onto a protein substrate. The bivalent inhibitors block GGTase I enzymatic activity with K(i) values in the submicromolar range and are approximately one order of magnitude and more than 150 times more effective than the tetrapeptide CVIL and the methyl benzoate derivatives, respectively. The bivalent compounds 6 and 8 were shown to be competitive inhibitors, suggesting that the CVIL module anchors the whole molecule to the GGTase I active site and delivers the other module to the targeting protein surface. Thus, our module-assembly approach resulted in simultaneous multiple-site recognition, and as a consequence, synergetic inhibition of GGTase I activity, thereby providing a new approach in designing protein-surface-directed inhibitors for targeting protein-protein interactions.
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Affiliation(s)
- Shinnosuke Machida
- The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, Japan
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Raczyński P, Gburski Z. The dynamics of cholesterol molecules near the surface of protein farnesyltransferase - computer simulation. BIOMOLECULAR ENGINEERING 2007; 24:568-571. [PMID: 17977065 DOI: 10.1016/j.bioeng.2007.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have made the molecular dynamics (MD) simulations for the cluster of cholesterols localized near the protein farnesyltransferase (1FT2) at the physiological temperature T=309.75K. We have observed that the cholesterol molecules form a lodgment on the surface of protein. Several physical characteristics of the deposited cholesterol cluster have been calculated among those: the mean square displacement, diffusion coefficient, linear and angular velocity autocorrelation function and their Fourier transforms.
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Affiliation(s)
- Przemysław Raczyński
- Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice, Poland.
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Cui G, Merz KM. Computational studies of the farnesyltransferase ternary complex part II: the conformational activation of farnesyldiphosphate. Biochemistry 2007; 46:12375-81. [PMID: 17918965 DOI: 10.1021/bi701324t] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studies aimed at elucidating the reaction mechanism of farnesyltransferase (FTase), which catalyzes the prenylation of many cellular signaling proteins including Ras, has been an active area of research. Much is known regarding substrate binding and the impact of various catalytic site residues on catalysis. However, the molecular level details regarding the conformational rearrangement of farnesyldiphosphate (FPP), which has been proposed via structural analysis and mutagenesis studies to occur prior to the chemical step, is still poorly understood. Following on our previous computational characterization of the resting state of the FTase ternary complex, the thermodynamics of the conformational rearrangement step in the absence of magnesium was investigated for the wild type FTase and the Y300Fbeta mutant complexed with the peptide CVIM. In addition, we also explored the target dependence of the conformational activation step by perturbing isoleucine into a leucine (CVLM). The calculated free energy profiles of the proposed conformational transition confirm the presence of a stable intermediate state, which was identified only when the diphosphate is monoprotonated (FPP2-). The farnesyl group in the computed intermediate state assumes a conformation similar to that of the product complex, particularly for the first two isoprene units. We found that Y300beta can readily form hydrogen bonds with either of the phosphates of FPP. Removing the hydroxyl group on Y300beta does not significantly alter the thermodynamics of the conformational transition, but shifts the location of the intermediate farther away from the nucleophile by 0.5 A, which suggests that Y300beta facilitate the reaction by stabilizing the chemical step. Our results also showed an increased transition barrier height for CVLM (1.5 kcal/mol higher than that of CVIM). Although qualitatively consistent with the findings from the recent kinetic isotope experiments by Fierke and co-workers, the magnitude is not large enough to affect the rate-limiting step.
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Affiliation(s)
- Guanglei Cui
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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Penner-Hahn J. Zinc-promoted alkyl transfer: a new role for zinc. Curr Opin Chem Biol 2007; 11:166-71. [PMID: 17376731 DOI: 10.1016/j.cbpa.2007.02.038] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 02/20/2007] [Indexed: 10/23/2022]
Abstract
The roles of zinc in biology are often thought to be limited to activating water, as in hydrolytic enzymes, and conferring structure, as in the zinc finger proteins. Over the past 15 years, it has been shown that there are many zinc-containing proteins that have 'structural-like' zinc sites with multiple cysteine ligands but in which the site promotes the alkylation of a zinc-bound thiolate. Recent work continues to extend the range of proteins showing zinc-promoted alkytransfer activity, and has refined the structural details of these sites. Of particular interest are recent crystal structures suggesting that in most cases the endogenous ligand that is displaced when the substrate thiol bind is an endogenous amino acid and not water, as had been previously thought. Despite extensive study, it remains unclear whether these enzymes function via an associative mechanism (direct alkylation of a zinc-bound thiolate) or a dissociate mechanism (nucleophilic attack by a free thiolate that has dissociated from the zinc).
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Affiliation(s)
- James Penner-Hahn
- Department of Chemistry and Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055 USA.
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Hajdo-Milasinović A, Ellenbroek SIJ, van Es S, van der Vaart B, Collard JG. Rac1 and Rac3 have opposing functions in cell adhesion and differentiation of neuronal cells. J Cell Sci 2007; 120:555-66. [PMID: 17244648 DOI: 10.1242/jcs.03364] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rac1 and Rac3 are highly homologous members of the Rho small GTPase family. Rac1 is ubiquitously expressed and regulates cell adhesion, migration and differentiation in various cell types. Rac3 is primarily expressed in brain and may therefore have a specific function in neuronal cells. We found that depletion of Rac1 by short interference RNA leads to decreased cell-matrix adhesions and cell rounding in neuronal N1E-115 cells. By contrast, depletion of Rac3 induces stronger cell adhesions and dramatically increases the outgrowth of neurite-like protrusions, suggesting opposite functions for Rac1 and Rac3 in neuronal cells. Consistent with this, overexpression of Rac1 induces cell spreading, whereas overexpression of Rac3 results in a contractile round morphology. Rac1 is mainly found at the plasma membrane, whereas Rac3 is predominantly localized in the perinuclear region. Residues 185-187, present in the variable polybasic rich region at the carboxyl terminus are responsible for the difference in phenotype induced by Rac1 and Rac3 as well as for their different intracellular localization. The Rac1-opposing function of Rac3 is not mediated by or dependent on components of the RhoA signaling pathway. It rather seems that Rac3 exerts its function through negatively affecting integrin-mediated cell-matrix adhesions. Together, our data reveal that Rac3 opposes Rac1 in the regulation of cell adhesion and differentiation of neuronal cells.
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Affiliation(s)
- Amra Hajdo-Milasinović
- The Netherlands Cancer Institute, Division of Cell Biology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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