1
|
Ma W, Liu H, Li X. Chemical Synthesis of Peptides and Proteins Bearing Base-Labile Post-Translational Modifications: Evolution of the Methods in Four Decades. Chembiochem 2023; 24:e202300348. [PMID: 37380612 DOI: 10.1002/cbic.202300348] [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: 05/08/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
The S-palmitoylation on Cys residue and O-acetylation on Ser/Thr residues are two types of base-labile post-translational modifications (PTMs) in cells. The lability of these PTMs to bases and nucleophiles makes the peptides/proteins bearing S-palmitoyl or O-acetyl groups challenging synthetic targets, which cannot be prepared via the standard Fmoc-SPPS and native chemical ligation. In this review, we summarized the efforts towards their preparation in the past 40 years, with the focus on the evolution of synthetic methods.
Collapse
Affiliation(s)
- Wenjie Ma
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| |
Collapse
|
2
|
Chuh KN, Batt AR, Pratt MR. Chemical Methods for Encoding and Decoding of Posttranslational Modifications. Cell Chem Biol 2016; 23:86-107. [PMID: 26933738 DOI: 10.1016/j.chembiol.2015.11.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/25/2015] [Accepted: 11/25/2015] [Indexed: 12/13/2022]
Abstract
A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full complement of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come.
Collapse
Affiliation(s)
- Kelly N Chuh
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Anna R Batt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
3
|
Calce E, De Luca S. Microwave heating in peptide side chain modification via cysteine alkylation. Amino Acids 2016; 48:2267-71. [PMID: 27351201 DOI: 10.1007/s00726-016-2284-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022]
Abstract
Microwave irradiation has been successfully applied to a selective synthetic procedure for introducing molecular substituents on peptides, providing a noticeable reduction of the reaction time and also an increased crude peptide purity for some compounds.
Collapse
Affiliation(s)
- Enrica Calce
- Institute of Biostructures and Bioimaging, National Research Council, 80134, Naples, Italy
| | - Stefania De Luca
- Institute of Biostructures and Bioimaging, National Research Council, 80134, Naples, Italy.
| |
Collapse
|
4
|
Bosmans RPG, Hendriksen WE, Verheijden M, Eelkema R, Jonkheijm P, van Esch JH, Brunsveld L. Supramolecular Protein Immobilization on Lipid Bilayers. Chemistry 2015; 21:18466-73. [DOI: 10.1002/chem.201502461] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 01/08/2023]
|
5
|
Iversen L, Tu HL, Lin WC, Christensen SM, Abel SM, Iwig J, Wu HJ, Gureasko J, Rhodes C, Petit RS, Hansen SD, Thill P, Yu CH, Stamou D, Chakraborty AK, Kuriyan J, Groves JT. Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics. Science 2014; 345:50-4. [PMID: 24994643 DOI: 10.1126/science.1250373] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average.
Collapse
Affiliation(s)
- Lars Iversen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hsiung-Lin Tu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wan-Chen Lin
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sune M Christensen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Steven M Abel
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Jeff Iwig
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hung-Jen Wu
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jodi Gureasko
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher Rhodes
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rebecca S Petit
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Scott D Hansen
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Peter Thill
- Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Cheng-Han Yu
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Dimitrios Stamou
- Department of Chemistry and Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. Department of Chemistry, MIT, Cambridge, MA 02139, USA. Department of Biological Engineering, MIT, Cambridge, MA 02139, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA. Department of Physics, MIT, Cambridge, MA 02139, USA. Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - John Kuriyan
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay T Groves
- Howard Hughes Medical Institute, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA. Mechanobiology Institute, National University of Singapore, Singapore. Physical Biosciences and Materials Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Berkeley Education Alliance for Research in Singapore, 1 Create Way, CREATE tower level 11, University Town, Singapore 138602.
| |
Collapse
|
6
|
Calce E, Leone M, Monfregola L, De Luca S. Lipidated peptides via post-synthetic thioalkylation promoted by molecular sieves. Amino Acids 2014; 46:1899-905. [DOI: 10.1007/s00726-014-1742-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/03/2014] [Indexed: 11/29/2022]
|
7
|
Abstract
One of the main reasons of the high diversity and complexity of the human proteome compared to the human genome is the extensive work performed by the posttranslational machinery to incorporate numerous different functionalities on proteins. The covalent attachment of chemical moieties in proteins after translation is known as posttranslational modification (PTM) and has a crucial role in controlling protein localization and activity. Relevant modifications include phosphorylation, carboxymethylation, glycosylation, acetylation, or lipidation. Despite their essential role on protein function, the synthesis of fully posttranslationally modified proteins has been challenging. However, important advances on chemical biology have enabled the synthesis of fully posttranslationally modified peptides and proteins. As a result of this, peptides bearing, i.e., phosphorylated amino acids, C-terminal methylations, lipid modifications, or nonnatural tags have become accessible. These peptides, as well as the corresponding proteins obtained using ligation techniques, have been invaluable tools in biochemical and biophysical studies. As an example of these advances, this chapter describes the methods developed for the synthesis of lipidated peptides from the Ras and Rab families.
Collapse
Affiliation(s)
- Federica Rosi
- Abt. Chemische Biologie, Max-Planck-Institut für Molekulare Physiologie, Dortmund, Germany
| | | |
Collapse
|
8
|
Mandal SM, Barbosa AEAD, Franco OL. Lipopeptides in microbial infection control: scope and reality for industry. Biotechnol Adv 2013; 31:338-45. [PMID: 23318669 DOI: 10.1016/j.biotechadv.2013.01.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 01/04/2013] [Accepted: 01/04/2013] [Indexed: 01/12/2023]
Abstract
Lipopeptides are compounds that are formed by cyclic or short linear peptides linked with a lipid tail or other lipophilic molecules. Recently, several lipopeptides were characterized, showing surfactant, antimicrobial and cytotoxic activities. The properties of lipopeptides may lead to applications in diverse industrial fields including the pharmaceutical industry as conventional antibiotics; the cosmetic industry for dermatological product development due to surfactant and anti-wrinkle properties; in food production acting as emulsifiers in various foodstuffs; and also in the field of biotechnology as biosurfactants. Some lipopeptides have reached a commercial antibiotic status, such as daptomycin, caspofungin, micafungin, and anidulafungin. This will be the focus of this review. Moreover, the review presented here will focus on the biotechnological utilization of lipopeptides in different fields as well as the functional-structure relation, connecting recent aspects of synthesis and structure diversity.
Collapse
Affiliation(s)
- Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, W B, India
| | | | | |
Collapse
|
9
|
Abstract
After having successfully synthesized a peptide, it has to be released from the solid support, unless it is being used for on-resin display. The linker and, in some cases, the cleavage mixture determine the C-terminal functionality of the released peptide. In most cases, the peptide is released with concomitant removal of side-chain protecting groups. However, some combinations of linkers and side-chain protecting groups enable a two-stage procedure, either using orthogonal chemistry or graduated labilities. Herein, we describe protocols for the release of peptides from the most commonly used linker types providing a variety of different C-terminal functionalities, including acids, amides, amines, and aldehydes. Moreover, suggestions for determination of peptide purity and for storage conditions are provided.
Collapse
Affiliation(s)
- Søren L Pedersen
- IGM, Faculty of Life Sciences, University of Copenhagen, Gubra, Hørsholm, Denmark
| | | |
Collapse
|
10
|
Abstract
This chapter provides an introduction to and overview of peptide chemistry with a focus on solid-phase peptide synthesis. The background, the most common reagents, and some mechanisms are presented. This chapter also points to the different chapters and puts them into perspective.
Collapse
Affiliation(s)
- Knud J Jensen
- Department of Chemistry, Faculty of Sciences, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
11
|
Damodaran VB, Fee CJ. Synthesis and Evaluation of α-(β-Alanine)-ω-carboxy PEG Derivative as a Novel Cleavable Heterobifunctional PEG Tether for Solid-Phase Polymeric Drug Delivery. INT J POLYM MATER PO 2011. [DOI: 10.1080/00914037.2010.531811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
12
|
Small molecule inhibition of protein depalmitoylation as a new approach towards downregulation of oncogenic Ras signalling. Bioorg Med Chem 2011; 19:1376-80. [DOI: 10.1016/j.bmc.2010.11.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 11/08/2010] [Accepted: 11/08/2010] [Indexed: 01/18/2023]
|
13
|
Peptide and glycopeptide dendrimers and analogous dendrimeric structures and their biomedical applications. Amino Acids 2010; 40:301-70. [DOI: 10.1007/s00726-010-0707-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/15/2010] [Indexed: 02/08/2023]
|
14
|
Alexander M, Gerauer M, Pechlivanis M, Popkirova B, Dvorsky R, Brunsveld L, Waldmann H, Kuhlmann J. Mapping the isoprenoid binding pocket of PDEdelta by a semisynthetic, photoactivatable N-Ras lipoprotein. Chembiochem 2009; 10:98-108. [PMID: 18846587 DOI: 10.1002/cbic.200800275] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Biologically functional Ras isoforms undergo post-translational modifications starting with farnesylation of the most C-terminal cysteine. Combined with further processing steps, this isoprenylation allows for the anchoring of these proteins in endomembranes, where signal transduction events take place. The specific localization is subject to dynamic regulation and assumed to modulate the activity of Ras proteins by governing their spatiotemporal distribution. The delta subunit of phosphodiesterase (PDEdelta) has attracted attention as a solubilization factor of isoprenylated Ras. In this study, we demonstrate that critical residues in the putative isoprenoid pocket of PDEdelta can be mapped by coupling with a semisynthetic N-Ras lipoprotein in which the native farnesyl group of the processed protein was replaced by a photoactivatable geranyl benzophenone moiety. The crosslinked product included parts of beta-sheet 9 of PDEdelta, which contains the highly conserved amino acids V145 and L147. Modeling of the PDEdelta-geranyl benzophenone (GerBP) complex supports the conclusion that the photolabeled sequence is embedded in the putative isoprenoid pocket of PDEdelta.
Collapse
Affiliation(s)
- Michael Alexander
- Department of Structural Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Strasse 11, Dortmund, Germany
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Brunsveld L, Waldmann H, Huster D. Membrane binding of lipidated Ras peptides and proteins--the structural point of view. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:273-88. [PMID: 18771652 DOI: 10.1016/j.bbamem.2008.08.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 08/01/2008] [Accepted: 08/06/2008] [Indexed: 10/21/2022]
Abstract
Biological membranes are interesting interfaces, at which important biological processes occur. In addition to integral membrane proteins, a number of proteins bind to the membrane surface and associate with it. Posttranslational lipid modification is one important mechanism, by which soluble molecules develop a propensity towards the membrane and reversibly bind to it. Membrane binding by insertion of hydrophobic lipid moieties is relevant for up to 10% of all cellular proteins. A particular interesting lipid-modified protein is the small GTPase Ras, which plays a key role in cellular signal transduction. Until recently, the structural basis for membrane binding of Ras was not well-defined. However, with the advent of new synthesis techniques and the advancement of several biophysical methods, a number of structural and dynamical features about membrane binding of Ras proteins have been revealed. This review will summarize the chemical biology of Ras and discuss in more detail the biophysical and structural features of the membrane bound C-terminus of the protein.
Collapse
Affiliation(s)
- Luc Brunsveld
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | | |
Collapse
|
16
|
Gorfe AA, Babakhani A, McCammon JA. H-ras protein in a bilayer: interaction and structure perturbation. J Am Chem Soc 2007; 129:12280-6. [PMID: 17880077 PMCID: PMC2530826 DOI: 10.1021/ja073949v] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ras GTPases become functionally active when anchored to membranes by inserting their lipid modified side chains. Their role in cell division, development, and cancer has made them targets of extensive research efforts, yet the mechanism of membrane insertion and the structure of the resulting complex remain elusive. Recently, the structure of the full-length H-ras protein in a DMPC bilayer has been computationally characterized. Here, the atomic interactions between the H-ras membrane anchor and the DMPC bilayer are investigated in detail. We find that the palmitoylated cysteines and Met182 have dual contributions to membrane affinity: hydrogen bonding by their amides and van der Waals interaction by their hydrophobic side chains. The polar side chains help maintain the orientation of the anchor. Although the overall structure of the bilayer is similar to that of a pure DMPC, there are localized perturbations. These perturbations depend on the insertion depth and backbone localization of the anchor, which in turn is modulated by the catalytic domain and the linker. The pattern of anchor amide-DMPC phosphate/carbonyl hydrogen bonds and the flexibility of Palm184 are important in discriminating between different modes of ras-DMPC interactions. The results provide structural arguments in support of the proposed participation of ras in the organization of membrane nanoclusters.
Collapse
Affiliation(s)
- Alemayehu A. Gorfe
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093-0365
- Correspondence: Tel. 858-822-0255; Fax. 858-534-4974;
| | - Arneh Babakhani
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093-0365
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093-0365
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, 92093-0365
- Department of Pharmacology, University of California at San Diego, La Jolla, CA, 92093-0365
| |
Collapse
|