1
|
Vincenzi M, Mercurio FA, Leone M. NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview. Curr Med Chem 2021; 28:2729-2782. [PMID: 32614739 DOI: 10.2174/0929867327666200702131032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. OBJECTIVE This review provides a toolkit to investigate peptide conformational properties by NMR. METHODS Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. RESULTS The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. CONCLUSION NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.
Collapse
Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| |
Collapse
|
2
|
Nardelli F, Ghitti M, Quilici G, Gori A, Luo Q, Berardi A, Sacchi A, Monieri M, Bergamaschi G, Bermel W, Chen F, Corti A, Curnis F, Musco G. A stapled chromogranin A-derived peptide is a potent dual ligand for integrins αvβ6 and αvβ8. Chem Commun (Camb) 2020; 55:14777-14780. [PMID: 31755501 DOI: 10.1039/c9cc08518a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Combining 2D STD-NMR, computation, biochemical assays and click-chemistry, we have identified a chromogranin-A derived compound (5) that has high affinity and bi-selectivity for αvβ6 and αvβ8 integrins and is stable in microsomal preparations. 5 is suitable for nanoparticle functionalization and delivery to cancer cells, holding promise for diagnostic and/or therapeutic applications.
Collapse
Affiliation(s)
- Francesca Nardelli
- IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
| | - Michela Ghitti
- IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
| | - Giacomo Quilici
- IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
| | - Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milan, Italy
| | - Qingqiong Luo
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Andrea Berardi
- IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
| | - Angelina Sacchi
- IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
| | - Matteo Monieri
- IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
| | - Greta Bergamaschi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milan, Italy
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, Rheinstetten, 76287, Germany
| | - Fuxiang Chen
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Angelo Corti
- IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy. and Vita Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
| | - Flavio Curnis
- IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
| | - Giovanna Musco
- IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy.
| |
Collapse
|
3
|
Production of the recombinant antimicrobial peptide UBI 18-35 in Escherichia coli. Protein Expr Purif 2018; 143:38-44. [DOI: 10.1016/j.pep.2017.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 11/21/2022]
|
4
|
Lin Z, Zhao Q, Xing L, Zhou B, Wang X. Aggregating tags for column-free protein purification. Biotechnol J 2015; 10:1877-86. [PMID: 26556016 DOI: 10.1002/biot.201500299] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 08/27/2015] [Accepted: 10/14/2015] [Indexed: 12/30/2022]
Abstract
Protein purification remains a central need for biotechnology. In recent years, a class of aggregating tags has emerged, which offers a quick, cost-effective and column-free alternative for producing recombinant proteins (and also peptides) with yield and purity comparable to that of the popular His-tag. These column-free tags induce the formation of aggregates (during or after expression) when fused to a target protein or peptide, and upon separation from soluble impurities, the target protein or peptide is subsequently released via a cleavage site. In this review, we categorize these tags as follows: (i) tags that induce inactive protein aggregates in vivo; (ii) tags that induce active protein aggregates in vivo; and (iii) tags that induce soluble expression in vivo, but aggregates in vitro. The respective advantages and disadvantages of these tags are discussed, and compared to the three conventional tags (His-tag, maltose-binding protein [MBP] tag, and intein-mediated purification with a chitin-binding tag [IMPACT-CN]). While this new class of aggregating tags is promising, more systematic tests are required to further the use. It is conceivable, however, that the combination of these tags and the more traditional columns may significantly reduce the costs for resins and columns, particularly for the industrial scale.
Collapse
Affiliation(s)
- Zhanglin Lin
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes, Tsinghua University, Beijing, China.
| | - Qing Zhao
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes, Tsinghua University, Beijing, China
| | - Lei Xing
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes, Tsinghua University, Beijing, China
| | - Bihong Zhou
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes, Tsinghua University, Beijing, China
| | - Xu Wang
- Department of Chemical Engineering, National Engineering Laboratory for Industrial Enzymes, Tsinghua University, Beijing, China
| |
Collapse
|
5
|
Sorge JL, Wagstaff JL, Rowe ML, Williamson RA, Howard MJ. Q2DSTD NMR deciphers epitope-mapping variability for peptide recognition of integrin αvβ6. Org Biomol Chem 2015; 13:8001-7. [PMID: 26119198 PMCID: PMC4541471 DOI: 10.1039/c5ob01237f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Integrin αvβ6 is a cell surface arginine-glycine-aspartic acid (RGD)-specific heterodimeric glycoprotein that is only expressed on epithelia during processes of tissue remodelling, including cancer. The specificity and molecular nature of interactions toward this integrin are poorly understood and new insights into such processes are important to cell biologists and pharmaceutical drug discovery. This study demonstrates the application of quantitative two-dimensional saturation transfer (Q2DSTD) NMR to obtain precise details of peptide interactions with integrin αvβ6 and their correlation to specificity for the integrin. This approach highlights subtle but significant differences in ligand contact by three related 21-mer peptides: FMDV2, an αvβ6 specific peptide and DBD1 and LAP2T1 peptides that bind many αv integrins in addition to αvβ6. FMDV2 and DBD1 differ only by the cyclisation of DBD1; a process that removes αvβ6 specificity. Q2DSTD NMR demonstrates these peptides experience significantly different interactions with the integrin; FMDV contacts primarily through four residues: 6Leu, 10Leu, 12Val and 13Leu, whereas DBD1 and LAP2T1 have more widespread contacts across their sequences. Q2DSTD NMR combined two-dimensional STD with quantitation by considering the relaxation of the ligand (CRL) to provide precise ligand contact information. This study also examines the role of CRL in the Q2DSTD process and how quantitation modifies STD data and unravels epitope-mapping variability to provide precise results that differentiate interactions at the atomic level for each peptide.
Collapse
Affiliation(s)
- Jessica L Sorge
- School of Biosciences, University of Kent, Canterbury, Kent, UK.
| | | | | | | | | |
Collapse
|
6
|
Quinn CM, Lu M, Suiter CL, Hou G, Zhang H, Polenova T. Magic angle spinning NMR of viruses. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:21-40. [PMID: 25919197 PMCID: PMC4413014 DOI: 10.1016/j.pnmrs.2015.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/27/2015] [Accepted: 02/08/2015] [Indexed: 05/02/2023]
Abstract
Viruses, relatively simple pathogens, are able to replicate in many living organisms and to adapt to various environments. Conventional atomic-resolution structural biology techniques, X-ray crystallography and solution NMR spectroscopy provided abundant information on the structures of individual proteins and nucleic acids comprising viruses; however, viral assemblies are not amenable to analysis by these techniques because of their large size, insolubility, and inherent lack of long-range order. In this article, we review the recent advances in magic angle spinning NMR spectroscopy that enabled atomic-resolution analysis of structure and dynamics of large viral systems and give examples of several exciting case studies.
Collapse
Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Christopher L Suiter
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Huilan Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| |
Collapse
|
7
|
Wagstaff JL, Rowe ML, Hsieh SJ, DiCara D, Marshall JF, Williamson RA, Howard MJ. NMR relaxation and structural elucidation of peptides in the presence and absence of trifluoroethanol illuminates the critical molecular nature of integrin αvβ6 ligand specificity. RSC Adv 2012; 2:11019-11028. [PMID: 27182435 PMCID: PMC4864471 DOI: 10.1039/c2ra21655h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Integrin αvβ6 is an important emerging target for both imaging and therapy of cancer that requires specific ligands based on Arg-Gly-Asp (RGD) peptides. There remains little correlation between integrin-RGD ligand specificity despite studies suggesting an RGD-turn-helix ligand motif is required. Here, we describe the application of 15N NMR relaxation analyses and structure determination of αvβ6 peptide ligands in the presence and absence of trifluoroethanol (TFE) to identify their critical molecular nature that influences specificity, interaction and function. Two linear peptides; one known to demonstrate αvβ6 specificity (FMDV2) and the other based on a natural RGD ligand (LAP2), were compared to two additional peptides based on FMDV2 but cyclised in different positions using a disulphide bond (DBD1 and DBD2). The cyclic adaptation in DBD1 produces a significant alteration in backbone dynamic properties when compared to FMDV2; a potential driver for the loss in αvβ6 specificity by DBD1. The importance of ligand dynamics are highlighted through a comprehensive reduced spectral density and ModelFree analysis of peptide 15N NMR relaxation data and suggest αvβ6 specificity requires the formation of a structurally rigid helix preceded by a RGD motif exhibiting slow internal motion. Additional observations include the effect of TFE/water viscosity on global NMR dynamics and the advantages of using spectral density NMR relaxation data to estimate correlation times and motional time regimes for peptides in solution.
Collapse
Affiliation(s)
- Jane L. Wagstaff
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Michelle L. Rowe
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Shu-Ju Hsieh
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Danielle DiCara
- Queen Mary University of London, Barts and The London School of Medicine and Dentistry, Institute of Cancer and CRUK Clinical Centre, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
| | - John F. Marshall
- Queen Mary University of London, Barts and The London School of Medicine and Dentistry, Institute of Cancer and CRUK Clinical Centre, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Richard A. Williamson
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Mark J. Howard
- Protein Science Group, School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| |
Collapse
|