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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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Bello-Perez M, Falco A, Novoa B, Perez L, Coll J. Hydroxycholesterol binds and enhances the anti-viral activities of zebrafish monomeric c-reactive protein isoforms. PLoS One 2019; 14:e0201509. [PMID: 30653529 PMCID: PMC6336239 DOI: 10.1371/journal.pone.0201509] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/28/2018] [Indexed: 01/26/2023] Open
Abstract
C-reactive proteins (CRPs) are among the faster acute-phase inflammation-responses proteins encoded by one gene (hcrp) in humans and seven genes (crp1-7) in zebrafish (Danio rerio) with importance in bacterial and viral infections. In this study, we described novel preferential bindings of 25-hydroxycholesterol (25HOCh) to CRP1-7 compared with other lipids and explored the antiviral effects of both 25HOCh and CRP1-7 against spring viremia carp virus (SVCV) infection in zebrafish. Both in silico and in vitro results confirmed the antiviral effect of 25HOCh and CRP1-7 interactions, thereby showing that the crosstalk between them differed among the zebrafish isoforms. The presence of oxidized cholesterols in human atherosclerotic plaques amplifies the importance that similar interactions may occur for vascular and/or neurodegenerative diseases during viral infections. In this context, the zebrafish model offers a genetic tool to further investigate these interactions.
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Affiliation(s)
- Melissa Bello-Perez
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández (IBMC-UMH), Elche, Spain
| | - Alberto Falco
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández (IBMC-UMH), Elche, Spain
| | - Beatriz Novoa
- Institute of Marine Research (IIM), CSIC, Vigo, Spain
| | - Luis Perez
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández (IBMC-UMH), Elche, Spain
| | - Julio Coll
- Department of Biotechnology, Instituto Nacional Investigaciones y Tecnologías Agrarias y Alimentarias, INIA, Madrid, Spain
- * E-mail:
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Caprio V, Badimon L, Di Napoli M, Fang WH, Ferris GR, Guo B, Iemma RS, Liu D, Zeinolabediny Y, Slevin M. pCRP-mCRP Dissociation Mechanisms as Potential Targets for the Development of Small-Molecule Anti-Inflammatory Chemotherapeutics. Front Immunol 2018; 9:1089. [PMID: 29892284 PMCID: PMC5985513 DOI: 10.3389/fimmu.2018.01089] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/01/2018] [Indexed: 12/29/2022] Open
Abstract
Circulating C-reactive protein (CRP) is a key acute-phase protein and one of the main clinical biomarkers for inflammation and infection. CRP is an important upstream mediator of inflammation and is associated with the onset of a number of important disease states including cardiovascular disease and neurodegenerative disorders such as Alzheimer’s disease. This pentraxin exerts pro-inflammatory properties via dissociation of the pentamer (pCRP) to a monomeric form (mCRP). This dissociation is induced by binding of pCRP to cell surface phosphocholine residues exposed by the action of phospholipase A2 (PLA2). Given the association of CRP with the onset of a range of serious disease states this CRP dissociation process is a tempting drug target for the development of novel small-molecule therapeutics. This review will discuss potential targets for chemotherapeutic intervention elucidated during studies of CRP-mediated inflammation and provide an up-to-date summary of the development of small molecules, not only targeted directly at inhibiting conversion of pCRP to mCRP, but also those developed for activity against PLA2, given the key role of this enzyme in the activation of CRP.
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Affiliation(s)
- Vittorio Caprio
- Faculty of Science and Engineering, School of Healthcare Science, Manchester Metropolitan University, Manchester, United Kingdom
| | - Lina Badimon
- Hospital de la Santa Creu I Sant Pau, IIB Sant Pau, Barcelona, Spain
| | - Mario Di Napoli
- Neurological Service, Ospedale San Camillo de Lellis, Rieti, Italy
| | - Wen-Hui Fang
- Faculty of Science and Engineering, School of Healthcare Science, Manchester Metropolitan University, Manchester, United Kingdom
| | - Glenn R Ferris
- Faculty of Science and Engineering, School of Healthcare Science, Manchester Metropolitan University, Manchester, United Kingdom
| | - Baoqiang Guo
- Faculty of Science and Engineering, School of Healthcare Science, Manchester Metropolitan University, Manchester, United Kingdom.,Institute of Dementia and Neurological Aging, Weifang Medical University, Weifang, China
| | - Rocco S Iemma
- Faculty of Science and Engineering, School of Healthcare Science, Manchester Metropolitan University, Manchester, United Kingdom
| | - Donghui Liu
- Faculty of Science and Engineering, School of Healthcare Science, Manchester Metropolitan University, Manchester, United Kingdom.,University of Medicine and Pharmacy, Targu Mures, Romania
| | - Yasmin Zeinolabediny
- Faculty of Science and Engineering, School of Healthcare Science, Manchester Metropolitan University, Manchester, United Kingdom.,University of Medicine and Pharmacy, Targu Mures, Romania
| | - Mark Slevin
- Faculty of Science and Engineering, School of Healthcare Science, Manchester Metropolitan University, Manchester, United Kingdom.,Hospital de la Santa Creu I Sant Pau, IIB Sant Pau, Barcelona, Spain.,Institute of Dementia and Neurological Aging, Weifang Medical University, Weifang, China.,University of Medicine and Pharmacy, Targu Mures, Romania
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