51
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Krzhizhanovskaya VV, Závodszky G, Lees MH, Dongarra JJ, Sloot PMA, Brissos S, Teixeira J. On the Planarity of Validated Complexes of Model Organisms in Protein-Protein Interaction Networks. LECTURE NOTES IN COMPUTER SCIENCE 2020. [PMCID: PMC7302240 DOI: 10.1007/978-3-030-50371-0_48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Leveraging protein-protein interaction networks to identify groups of proteins and their common functionality is an important problem in bioinformatics. Systems-level analysis of protein-protein interactions is made possible through network science and modeling of high-throughput data. From these analyses, small protein complexes are traditionally represented graphically as complete graphs or dense clusters of nodes. However, there are certain graph theoretic properties that have not been extensively studied in PPI networks, especially as they pertain to cluster discovery, such as planarity. Planarity of graphs have been used to reflect the physical constraints of real-world systems outside of bioinformatics, in areas such as mapping and imaging. Here, we investigate the planarity property in network models of protein complexes. We hypothesize that complexes represented as PPI subgraphs will tend to be planar, reflecting the actual physical interface and limits of components in the complex. When testing the planarity of known complex subgraphs in S. cerevisiae and selected mammalian PPIs, we find that a majority of validated complexes possess this planar property. We discuss the biological motivation of planar versus nonplanar subgraphs, observing that planar subgraphs tend to have longer protein components. Functional classification of planar versus nonplanar complex subgraphs reveals differences in annotation of these groups relating to cellular component organization, structural molecule activity, catalytic activity, and nucleic acid binding. These results provide a new quantitative and biologically motivated measure of real protein complexes in the network model, important for the development of future complex-finding algorithms in PPIs. Accounting for this property paves the way to new means for discovering new protein complexes and uncovering the functionality of unknown or novel proteins.
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52
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Guevara T, Rodriguez-Banqueri A, Ksiazek M, Potempa J, Gomis-Rüth FX. Structure-based mechanism of cysteine-switch latency and of catalysis by pappalysin-family metallopeptidases. IUCRJ 2020; 7:18-29. [PMID: 31949901 PMCID: PMC6949598 DOI: 10.1107/s2052252519013848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/10/2019] [Indexed: 05/23/2023]
Abstract
Tannerella forsythia is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellular pappalysin family, as a zymogen that is proteolytically auto-activated extracellularly at the Ser54-Arg55 bond. Crystal structures of the catalytically impaired promirolysin point mutant E225A at 1.4 and 1.6 Å revealed that latency is exerted by an N-terminal 34-residue pro-segment that shields the front surface of the 274-residue catalytic domain, thus preventing substrate access. The catalytic domain conforms to the metzincin clan of metallopeptidases and contains a double calcium site, which acts as a calcium switch for activity. The pro-segment traverses the active-site cleft in the opposite direction to the substrate, which precludes its cleavage. It is anchored to the mature enzyme through residue Arg21, which intrudes into the specificity pocket in cleft sub-site S1'. Moreover, residue Cys23 within a conserved cysteine-glycine motif blocks the catalytic zinc ion by a cysteine-switch mechanism, first described for mammalian matrix metallopeptidases. In addition, a 1.5 Å structure was obtained for a complex of mature mirolysin and a tetradecapeptide, which filled the cleft from sub-site S1' to S6'. A citrate molecule in S1 completed a product-complex mimic that unveiled the mechanism of substrate binding and cleavage by mirolysin, the catalytic domain of which was already preformed in the zymogen. These results, including a preference for cleavage before basic residues, are likely to be valid for other unicellular pappalysins derived from archaea, bacteria, cyanobacteria, algae and fungi, including archetypal ulilysin from Methanosarcina acetivorans. They may further apply, at least in part, to the multi-domain orthologues of higher organisms.
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Affiliation(s)
- Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Arturo Rodriguez-Banqueri
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Miroslaw Ksiazek
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY 40202, USA
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, Kraków 30-387, Poland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY 40202, USA
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, Kraków 30-387, Poland
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
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53
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Guagnini F, Engilberge S, Ramberg KO, Pérez J, Crowley PB. Engineered assembly of a protein–cucurbituril biohybrid. Chem Commun (Camb) 2020; 56:360-363. [DOI: 10.1039/c9cc07198a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Additional Q7 binding sites drive protein aggregation in solution and statistical disorder in the crystalline biohybrid suggest new possibilities for protein-based materials.
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Affiliation(s)
| | | | - Kiefer O. Ramberg
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
| | - Javier Pérez
- Synchrotron SOLEIL
- L’Orme des Merisiers
- 91192 Gif-sur-Yvette Cedex
- France
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
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54
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Nithin C, Mukherjee S, Bahadur RP. A structure-based model for the prediction of protein-RNA binding affinity. RNA (NEW YORK, N.Y.) 2019; 25:1628-1645. [PMID: 31395671 PMCID: PMC6859855 DOI: 10.1261/rna.071779.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/05/2019] [Indexed: 05/28/2023]
Abstract
Protein-RNA recognition is highly affinity-driven and regulates a wide array of cellular functions. In this study, we have curated a binding affinity data set of 40 protein-RNA complexes, for which at least one unbound partner is available in the docking benchmark. The data set covers a wide affinity range of eight orders of magnitude as well as four different structural classes. On average, we find the complexes with single-stranded RNA have the highest affinity, whereas the complexes with the duplex RNA have the lowest. Nevertheless, free energy gain upon binding is the highest for the complexes with ribosomal proteins and the lowest for the complexes with tRNA with an average of -5.7 cal/mol/Å2 in the entire data set. We train regression models to predict the binding affinity from the structural and physicochemical parameters of protein-RNA interfaces. The best fit model with the lowest maximum error is provided with three interface parameters: relative hydrophobicity, conformational change upon binding and relative hydration pattern. This model has been used for predicting the binding affinity on a test data set, generated using mutated structures of yeast aspartyl-tRNA synthetase, for which experimentally determined ΔG values of 40 mutations are available. The predicted ΔGempirical values highly correlate with the experimental observations. The data set provided in this study should be useful for further development of the binding affinity prediction methods. Moreover, the model developed in this study enhances our understanding on the structural basis of protein-RNA binding affinity and provides a platform to engineer protein-RNA interfaces with desired affinity.
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Affiliation(s)
- Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sunandan Mukherjee
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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55
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Yang W, Sun X, Zhang C, Lai L. Discovery of novel helix binding sites at protein-protein interfaces. Comput Struct Biotechnol J 2019; 17:1396-1403. [PMID: 31768230 PMCID: PMC6872852 DOI: 10.1016/j.csbj.2019.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 01/09/2023] Open
Abstract
Protein-protein interactions (PPIs) play a key role in numerous biological processes. Many efforts have been undertaken to develop PPI modulators for therapeutic applications; however, to date, most of the peptide binders designed to target PPIs are derived from native binding helices or using the native helix binding site, which has limited the applications of protein-protein interface binding peptide design. Here, we developed a general computational algorithm, HPer (Helix Positioner), that locates single-helix binding sites at protein-protein interfaces based on the structure of protein targets. HPer performed well on known single-helix-mediated PPIs and recaptured the key interactions and hot-spot residues of native helical binders. We also screened non-helical-mediated PPIs in the PDBbind database and identified 17 PPIs that were suitable for helical peptide binding, and the helical binding sites in these PPIs were also predicted for designing novel peptide ligands. The L2 domain of EGFR, which was the top ranked, was selected as an example to show the protocol and results of designing novel helical peptide ligands on the searched binding site. The binding stability of the designed sequences were further investigated using molecular dynamics simulations.
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Affiliation(s)
- Wei Yang
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
| | - Xiangyu Sun
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changsheng Zhang
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Luhua Lai
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, AAIS, Peking University, Beijing 100084, China
- Center for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
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56
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A Model for the Homotypic Interaction between Na +,K +-ATPase β 1 Subunits Reveals the Role of Extracellular Residues 221-229 in Its Ig-Like Domain. Int J Mol Sci 2019; 20:ijms20184538. [PMID: 31540261 PMCID: PMC6770782 DOI: 10.3390/ijms20184538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 12/15/2022] Open
Abstract
The Na+, K+-ATPase transports Na+ and K+ across the membrane of all animal cells. In addition to its ion transporting function, the Na+, K+-ATPase acts as a homotypic epithelial cell adhesion molecule via its β1 subunit. The extracellular region of the Na+, K+-ATPase β1 subunit includes a single globular immunoglobulin-like domain. We performed Molecular Dynamics simulations of the ectodomain of the β1 subunit and a refined protein-protein docking prediction. Our results show that the β1 subunit Ig-like domain maintains an independent structure and dimerizes in an antiparallel fashion. Analysis of the putative interface identified segment Lys221-Tyr229. We generated triple mutations on YFP-β1 subunit fusion proteins to assess the contribution of these residues. CHO fibroblasts transfected with mutant β1 subunits showed a significantly decreased cell-cell adhesion. Association of β1 subunits in vitro was also reduced, as determined by pull-down assays. Altogether, we conclude that two Na+, K+-ATPase molecules recognize each other by a large interface spanning residues 221–229 and 198–207 on their β1 subunits.
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57
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Marchant A, Cisneros AF, Dubé AK, Gagnon-Arsenault I, Ascencio D, Jain H, Aubé S, Eberlein C, Evans-Yamamoto D, Yachie N, Landry CR. The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. eLife 2019; 8:46754. [PMID: 31454312 PMCID: PMC6711710 DOI: 10.7554/elife.46754] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/11/2019] [Indexed: 01/07/2023] Open
Abstract
Gene duplication is a driver of the evolution of new functions. The duplication of genes encoding homomeric proteins leads to the formation of homomers and heteromers of paralogs, creating new complexes after a single duplication event. The loss of these heteromers may be required for the two paralogs to evolve independent functions. Using yeast as a model, we find that heteromerization is frequent among duplicated homomers and correlates with functional similarity between paralogs. Using in silico evolution, we show that for homomers and heteromers sharing binding interfaces, mutations in one paralog can have structural pleiotropic effects on both interactions, resulting in highly correlated responses of the complexes to selection. Therefore, heteromerization could be preserved indirectly due to selection for the maintenance of homomers, thus slowing down functional divergence between paralogs. We suggest that paralogs can overcome the obstacle of structural pleiotropy by regulatory evolution at the transcriptional and post-translational levels.
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Affiliation(s)
- Axelle Marchant
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Angel F Cisneros
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
| | - Alexandre K Dubé
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Diana Ascencio
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Honey Jain
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, India
| | - Simon Aubé
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
| | - Chris Eberlein
- PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
| | - Daniel Evans-Yamamoto
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Yachie
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Christian R Landry
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Canada.,PROTEO, le réseau québécois de recherche sur la fonction, la structure et l'ingénierie des protéines, Université Laval, Québec, Canada.,Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada.,Département de biologie, Université Laval, Québec, Canada
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58
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Guin D, Gruebele M. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Chem Rev 2019; 119:10691-10717. [PMID: 31356058 DOI: 10.1021/acs.chemrev.8b00753] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In recent years, better instrumentation and greater computing power have enabled the imaging of elusive biomolecule dynamics in cells, driving many advances in understanding the chemical organization of biological systems. The focus of this Review is on interactions in the cell that affect both biomolecular stability and function and modulate them. The same protein or nucleic acid can behave differently depending on the time in the cell cycle, the location in a specific compartment, or the stresses acting on the cell. We describe in detail the crowding, sticking, and quinary structure in the cell and the current methods to quantify them both in vitro and in vivo. Finally, we discuss protein evolution in the cell in light of current biophysical evidence. We describe the factors that drive protein evolution and shape protein interaction networks. These interactions can significantly affect the free energy, ΔG, of marginally stable and low-population proteins and, due to epistasis, direct the evolutionary pathways in an organism. We finally conclude by providing an outlook on experiments to come and the possibility of collaborative evolutionary biology and biophysical efforts.
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Affiliation(s)
- Drishti Guin
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States.,Center for Biophysics and Quantitative Biology , University of Illinois , Urbana , Illinois 61801 , United States
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59
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Xu Z, Zhang Q, Shi J, Zhu W. Underestimated Noncovalent Interactions in Protein Data Bank. J Chem Inf Model 2019; 59:3389-3399. [PMID: 31294978 DOI: 10.1021/acs.jcim.9b00258] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Noncovalent interactions (NCIs) play essential roles in the structure and function of biomacromolecules. There are various NCIs, e.g., hydrogen bonds (HBs), cation-π and π-π interactions, and ionic bonds, among which HBs are the most widespread and well-studied. By utilizing the ratio of the observed HBs over pseudo HBs (1.0 Å longer than the HB distance criteria without angle constraints), we demonstrated that HBs in both protein-ligand and protein-protein interfaces are overlooked in structures deposited in PDB. After the QM/MM optimization of 12 protein-ligand complexes, we showed that the overlooked HBs could be recovered. With a systematic search in the PDB, we found that the HB number per residue (NHB/R) in proteins decreases as structural resolution becomes lower, implying that HBs are overlooked even today, regardless of the type of refinement approach used. Similarly, cation-π, π-π, and ionic interactions were found to be significantly lost, manifesting the universal underestimation of various NCIs. Considering the vital role of NCIs, it is important to recover the NCIs to facilitate drug design, to explore protein-protein interaction, and to study protein structure and function.
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Affiliation(s)
- Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Qian Zhang
- Department of Computer Science and Technology , East China Normal University , Shanghai 200241 , China
| | - Jiye Shi
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,Open Studio for Druggability Research of Marine Natural Products , Pilot National Laboratory for Marine Science and Technology (Qingdao) , Qingdao 266237 , China
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60
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Poddar S, Chakravarty D, Chakrabarti P. Structural changes in DNA-binding proteins on complexation. Nucleic Acids Res 2019. [PMID: 29534202 PMCID: PMC6283420 DOI: 10.1093/nar/gky170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Characterization and prediction of the DNA-biding regions in proteins are essential for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) and the bound (B) forms of proteins from the protein–DNA docking benchmark that contains 66 binary protein–DNA complexes along with their unbound counterparts. Proteins binding DNA undergo greater structural changes on complexation (in particular, those in the enzyme category) than those involved in protein–protein interactions (PPI). While interface atoms involved in PPI exhibit an increase in their solvent-accessible surface area (ASA) in the bound form in the majority of the cases compared to the unbound interface, protein–DNA interactions indicate increase and decrease in equal measure. In 25% structures, the U form has missing residues which are located in the interface in the B form. The missing atoms contribute more toward the buried surface area compared to other interface atoms. Lys, Gly and Arg are prominent in disordered segments that get ordered in the interface on complexation. In going from U to B, there may be an increase in coil and helical content at the expense of turns and strands. Consideration of flexibility cannot distinguish the interface residues from the surface residues in the U form.
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Affiliation(s)
- Sayan Poddar
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Devlina Chakravarty
- Bioinformatics Centre, Bose Institute, P1/12CIT Scheme VIIM, Kolkata 700054, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.,Bioinformatics Centre, Bose Institute, P1/12CIT Scheme VIIM, Kolkata 700054, India
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61
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Moroz OV, Blagova E, Reiser V, Saikia R, Dalal S, Jørgensen CI, Bhatia VK, Baunsgaard L, Andersen B, Svendsen A, Wilson KS. Novel Inhibitory Function of the Rhizomucor miehei Lipase Propeptide and Three-Dimensional Structures of Its Complexes with the Enzyme. ACS OMEGA 2019; 4:9964-9975. [PMID: 31460089 PMCID: PMC6648591 DOI: 10.1021/acsomega.9b00612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/13/2019] [Indexed: 06/10/2023]
Abstract
Many proteins are synthesized as precursors, with propeptides playing a variety of roles such as assisting in folding or preventing them from being active within the cell. While the precise role of the propeptide in fungal lipases is not completely understood, it was previously reported that mutations in the propeptide region of the Rhizomucor miehei lipase have an influence on the activity of the mature enzyme, stressing the importance of the amino acid composition of this region. We here report two structures of this enzyme in complex with its propeptide, which suggests that the latter plays a role in the correct maturation of the enzyme. Most importantly, we demonstrate that the propeptide shows inhibition of lipase activity in standard lipase assays and propose that an important role of the propeptide is to ensure that the enzyme is not active during its expression pathway in the original host.
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Affiliation(s)
- Olga V. Moroz
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Elena Blagova
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Verena Reiser
- Novozymes
A/S, Krogshøjvej
36, DK-2880 Bagsværd, Denmark
| | - Rakhi Saikia
- Novozymes
A/S, Plot No. 32, 47-50,
Genisys Building, Whitefield, EPIP Zone, Brookefield, Bengaluru, Karnataka 560066, India
| | - Sohel Dalal
- Novozymes
A/S, Plot No. 32, 47-50,
Genisys Building, Whitefield, EPIP Zone, Brookefield, Bengaluru, Karnataka 560066, India
| | | | | | | | | | - Allan Svendsen
- Novozymes
A/S, Krogshøjvej
36, DK-2880 Bagsværd, Denmark
| | - Keith S. Wilson
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
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62
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Picón-Pagès P, Bonet J, García-García J, Garcia-Buendia J, Gutierrez D, Valle J, Gómez-Casuso CE, Sidelkivska V, Alvarez A, Perálvarez-Marín A, Suades A, Fernàndez-Busquets X, Andreu D, Vicente R, Oliva B, Muñoz FJ. Human Albumin Impairs Amyloid β-peptide Fibrillation Through its C-terminus: From docking Modeling to Protection Against Neurotoxicity in Alzheimer's disease. Comput Struct Biotechnol J 2019; 17:963-971. [PMID: 31360335 PMCID: PMC6639691 DOI: 10.1016/j.csbj.2019.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/03/2019] [Accepted: 06/13/2019] [Indexed: 12/01/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative process characterized by the accumulation of extracellular deposits of amyloid β-peptide (Aβ), which induces neuronal death. Monomeric Aβ is not toxic but tends to aggregate into β-sheets that are neurotoxic. Therefore to prevent or delay AD onset and progression one of the main therapeutic approaches would be to impair Aβ assembly into oligomers and fibrils and to promote disaggregation of the preformed aggregate. Albumin is the most abundant protein in the cerebrospinal fluid and it was reported to bind Aβ impeding its aggregation. In a previous work we identified a 35-residue sequence of clusterin, a well-known protein that binds Aβ, that is highly similar to the C-terminus (CTerm) of albumin. In this work, the docking experiments show that the average binding free energy of the CTerm-Aβ1-42 simulations was significantly lower than that of the clusterin-Aβ1-42 binding, highlighting the possibility that the CTerm retains albumin's binding properties. To validate this observation, we performed in vitro structural analysis of soluble and aggregated 1 μM Aβ1-42 incubated with 5 μM CTerm, equimolar to the albumin concentration in the CSF. Reversed-phase chromatography and electron microscopy analysis demonstrated a reduction of Aβ1-42 aggregates when the CTerm was present. Furthermore, we treated a human neuroblastoma cell line with soluble and aggregated Aβ1-42 incubated with CTerm obtaining a significant protection against Aβ-induced neurotoxicity. These in silico and in vitro data suggest that the albumin CTerm is able to impair Aβ aggregation and to promote disassemble of Aβ aggregates protecting neurons.
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Key Words
- AD, Alzheimer's disease
- APP, amyloid precursor protein
- Albumin
- Alzheimer's disease
- Amyloid
- Aß, Amyloid-ß peptide
- CD, Circular dichroism
- CSF, cerebrospinal fluid
- CTerm, albumin C-terminus
- Docking
- HPLC, high performance liquid chromatography
- LC-MS, Liquid chromatography-mass spectrometry
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- NMR, nuclear magnetic resonance
- PBS, phosphate-buffered saline
- PDB, Protein Data Bank
- PPI, protein-protein interactions
- SDS, sodium dodecyl sulfate
- TEM, transmission electron microscopy
- TFA, trifluoroacetic acid
- UV, ultraviolet
- fAβ1–42, HiLyte Fluor488 labelled human Aβ1–42
- β-Sheet
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Affiliation(s)
- Pol Picón-Pagès
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaume Bonet
- Laboratory of Structural Bioinformatics (GRIB), Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Javier García-García
- Laboratory of Structural Bioinformatics (GRIB), Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Joan Garcia-Buendia
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniela Gutierrez
- Cell Signaling Laboratory, Centro UC de Envejecimiento y Regeneración (CARE), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javier Valle
- Laboratory of Proteomics and Protein Chemistry, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Carmen E.S. Gómez-Casuso
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Valeriya Sidelkivska
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Alejandra Alvarez
- Cell Signaling Laboratory, Centro UC de Envejecimiento y Regeneración (CARE), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alex Perálvarez-Marín
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Albert Suades
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, Facultat de Medicina, Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier Fernàndez-Busquets
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, ES-08028 Barcelona, Spain
- Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, ES-08036 Barcelona, Spain
| | - David Andreu
- Laboratory of Proteomics and Protein Chemistry, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Rubén Vicente
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Baldomero Oliva
- Laboratory of Structural Bioinformatics (GRIB), Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francisco J. Muñoz
- Laboratory of Molecular Physiology, Faculty of Health and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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63
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Drennan AC, Krishna S, Seeger MA, Andreas MP, Gardner JM, Sether EKR, Jaspersen SL, Rayment I. Structure and function of Spc42 coiled-coils in yeast centrosome assembly and duplication. Mol Biol Cell 2019; 30:1505-1522. [PMID: 30969903 PMCID: PMC6724696 DOI: 10.1091/mbc.e19-03-0167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/05/2019] [Indexed: 11/12/2022] Open
Abstract
Centrosomes and spindle pole bodies (SPBs) are membraneless organelles whose duplication and assembly is necessary for bipolar mitotic spindle formation. The structural organization and functional roles of major proteins in these organelles can provide critical insights into cell division control. Spc42, a phosphoregulated protein with an N-terminal dimeric coiled-coil (DCC), assembles into a hexameric array at the budding yeast SPB core, where it functions as a scaffold for SPB assembly. Here, we present in vitro and in vivo data to elucidate the structural arrangement and biological roles of Spc42 elements. Crystal structures reveal details of two additional coiled-coils in Spc42: a central trimeric coiled-coil and a C-terminal antiparallel DCC. Contributions of the three Spc42 coiled-coils and adjacent undetermined regions to the formation of an ∼145 Å hexameric lattice in an in vitro lipid monolayer assay and to SPB duplication and assembly in vivo reveal structural and functional redundancy in Spc42 assembly. We propose an updated model that incorporates the inherent symmetry of these Spc42 elements into a lattice, and thereby establishes the observed sixfold symmetry. The implications of this model for the organization of the central SPB core layer are discussed.
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Affiliation(s)
- Amanda C. Drennan
- Department of Biochemistry, University of Wisconsin–Madison, WI 53706
| | | | - Mark A. Seeger
- Department of Biochemistry, University of Wisconsin–Madison, WI 53706
| | | | | | | | - Sue L. Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Ivan Rayment
- Department of Biochemistry, University of Wisconsin–Madison, WI 53706
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64
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Geometric description of self-interaction potential in symmetric protein complexes. Sci Data 2019; 6:64. [PMID: 31101822 PMCID: PMC6525250 DOI: 10.1038/s41597-019-0058-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/29/2019] [Indexed: 01/23/2023] Open
Abstract
Proteins can self-associate with copies of themselves to form symmetric complexes called homomers. Homomers are widespread in all kingdoms of life and allow for unique geometric and functional properties, as reflected in viral capsids or allostery. Once a protein forms a homomer, however, its internal symmetry can compound the effect of point mutations and trigger uncontrolled self-assembly into high-order structures. We identified mutation hot spots for supramolecular assembly, which are predictable by geometry. Here, we present a dataset of descriptors that characterize these hot spot positions both geometrically and chemically, as well as computer scripts allowing the calculation and visualization of these properties for homomers of choice. Since the biological relevance of homomers is not readily available from their X-ray crystallographic structure, we also provide reliability estimates obtained by methods we recently developed. These data have implications in the study of disease-causing mutations, protein evolution and can be exploited in the design of biomaterials. Design Type(s) | protein interaction analysis objective • protein structure prediction objective • modeling and simulation objective | Measurement Type(s) | protein complex | Technology Type(s) | computational modeling technique | Factor Type(s) | Filtering • source | Sample Characteristic(s) | laboratory environment |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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65
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Ansammlungen gefalteter Proteine im Kontext von Evolution, Krankheiten und Proteinentwicklung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of Science Rehovot 7610001 Israel
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66
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Garcia‐Seisdedos H, Villegas JA, Levy ED. Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering. Angew Chem Int Ed Engl 2019; 58:5514-5531. [PMID: 30133878 PMCID: PMC6471489 DOI: 10.1002/anie.201806092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Indexed: 12/14/2022]
Abstract
Mutations and changes in a protein's environment are well known for their potential to induce misfolding and aggregation, including amyloid formation. Alternatively, such perturbations can trigger new interactions that lead to the polymerization of folded proteins. In contrast to aggregation, this process does not require misfolding and, to highlight this difference, we refer to it as agglomeration. This term encompasses the amorphous assembly of folded proteins as well as the polymerization in one, two, or three dimensions. We stress the remarkable potential of symmetric homo-oligomers to agglomerate even by single surface point mutations, and we review the double-edged nature of this potential: how aberrant assemblies resulting from agglomeration can lead to disease, but also how agglomeration can serve in cellular adaptation and be exploited for the rational design of novel biomaterials.
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Affiliation(s)
| | - José A. Villegas
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
| | - Emmanuel D. Levy
- Department of Structural BiologyWeizmann Institute of ScienceRehovot7610001Israel
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67
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Ni D, Lu S, Zhang J. Emerging roles of allosteric modulators in the regulation of protein-protein interactions (PPIs): A new paradigm for PPI drug discovery. Med Res Rev 2019; 39:2314-2342. [PMID: 30957264 DOI: 10.1002/med.21585] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/12/2019] [Accepted: 03/24/2019] [Indexed: 12/26/2022]
Abstract
Protein-protein interactions (PPIs) are closely implicated in various types of cellular activities and are thus pivotal to health and disease states. Given their fundamental roles in a wide range of biological processes, the modulation of PPIs has enormous potential in drug discovery. However, owing to the general properties of large, flat, and featureless interfaces of PPIs, previous attempts have demonstrated that the generation of therapeutic agents targeting PPI interfaces is challenging, rendering them almost "undruggable" for decades. To date, rapid progress in chemical and structural biology techniques has promoted the exploitation of allostery as a novel approach in drug discovery. By attaching to allosteric sites that are topologically and spatially distinct from PPI interfaces, allosteric modulators can achieve improved physiochemical properties. Thus, allosteric modulators may represent an alternative strategy to target intractable PPIs and have attracted intense pharmaceutical interest. In this review, we first briefly introduce the characteristics of PPIs and then present different approaches for investigating PPIs, as well as the latest methods for modulating PPIs. Importantly, we comprehensively review the recent progress in the development of allosteric modulators to inhibit or stabilize PPIs. Finally, we conclude with future perspectives on the discovery of allosteric PPI modulators, especially the application of computational methods to aid in allosteric PPI drug discovery.
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Affiliation(s)
- Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Center for Single-Cell Omics, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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68
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Rennie ML, Crowley PB. A Thermodynamic Model of Auto‐regulated Protein Assembly by a Supramolecular Scaffold. Chemphyschem 2019; 20:1011-1017. [DOI: 10.1002/cphc.201900153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Martin L. Rennie
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
- Present address: Institute of Molecular Cell and System BiologyUniversity of Glasgow University Avenue Glasgow UK
| | - Peter B. Crowley
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
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69
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Investigation of quaternary structure of aggregating 3-ketosteroid dehydrogenase from Sterolibacterium denitrificans: In the pursuit of consensus of various biophysical techniques. Biochim Biophys Acta Gen Subj 2019; 1863:1027-1039. [PMID: 30876874 DOI: 10.1016/j.bbagen.2019.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/15/2019] [Accepted: 03/10/2019] [Indexed: 11/22/2022]
Abstract
In this work we analyzed the quaternary structure of FAD-dependent 3-ketosteroid dehydrogenase (AcmB) from Sterolibacterium denitrificans, the protein that in solution forms massive aggregates (>600 kDa). Using size-excursion chromatography (SEC), dynamic light scattering (DLS), native-PAGE and atomic force microscopy (AFM) we studied the nature of enzyme aggregation. Partial protein de-aggregation was facilitated by the presence of non-ionic detergent such as Tween 20 or by a high degree of protein dilution but not by addition of a reducing agent or an increase of ionic strength. De-aggregating influence of Tween 20 had no impact on either enzyme's specific activity or FAD reconstitution to recombinant AcmB. The joint experimental (DLS, isoelectric focusing) and theoretical investigations demonstrated gradual shift of enzyme's isoelectric point upon aggregation from 8.6 for a monomeric form to even 5.0. The AFM imaging on mica or highly oriented pyrolytic graphite (HOPG) surface enabled observation of individual protein monomers deposited from a highly diluted solution (0.2 μg/ml). Such approach revealed that native AcmB can indeed be monomeric. AFM imaging supported by theoretical random sequential adsorption (RSA) kinetics allowed estimation of distribution enzyme forms in the bulk solution: 5%, monomer, 11.4% dimer and 12% trimer. Finally, based on results of AFM as well as analysis of the surface of AcmB homology models we have observed that aggregation is most probably initiated by hydrophobic forces and then assisted by electrostatic attraction between negatively charged aggregates and positively charged monomers.
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70
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El Khamlichi C, Reverchon-Assadi F, Hervouet-Coste N, Blot L, Reiter E, Morisset-Lopez S. Bioluminescence Resonance Energy Transfer as a Method to Study Protein-Protein Interactions: Application to G Protein Coupled Receptor Biology. Molecules 2019; 24:E537. [PMID: 30717191 PMCID: PMC6384791 DOI: 10.3390/molecules24030537] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/21/2019] [Accepted: 01/30/2019] [Indexed: 12/22/2022] Open
Abstract
The bioluminescence resonance energy transfer (BRET) approach involves resonance energy transfer between a light-emitting enzyme and fluorescent acceptors. The major advantage of this technique over biochemical methods is that protein-protein interactions (PPI) can be monitored without disrupting the natural environment, frequently altered by detergents and membrane preparations. Thus, it is considered as one of the most versatile technique for studying molecular interactions in living cells at "physiological" expression levels. BRET analysis has been applied to study many transmembrane receptor classes including G-protein coupled receptors (GPCR). It is well established that these receptors may function as dimeric/oligomeric forms and interact with multiple effectors to transduce the signal. Therefore, they are considered as attractive targets to identify PPI modulators. In this review, we present an overview of the different BRET systems developed up to now and their relevance to identify inhibitors/modulators of protein⁻protein interaction. Then, we introduce the different classes of agents that have been recently developed to target PPI, and provide some examples illustrating the use of BRET-based assays to identify and characterize innovative PPI modulators in the field of GPCRs biology. Finally, we discuss the main advantages and the limits of BRET approach to characterize PPI modulators.
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Affiliation(s)
- Chayma El Khamlichi
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, France.
- PRC, INRA, CNRS, Université François Rabelais-Tours, 37380 Nouzilly, France.
| | - Flora Reverchon-Assadi
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, France.
| | - Nadège Hervouet-Coste
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, France.
| | - Lauren Blot
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, France.
| | - Eric Reiter
- PRC, INRA, CNRS, Université François Rabelais-Tours, 37380 Nouzilly, France.
| | - Séverine Morisset-Lopez
- Centre de Biophysique Moléculaire, CNRS, UPR 4301, University of Orléans and INSERM, 45071 Orléans, France.
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71
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Alex JM, Corvaglia V, Hu X, Engilberge S, Huc I, Crowley PB. Crystal structure of a protein–aromatic foldamer composite: macromolecular chiral resolution. Chem Commun (Camb) 2019; 55:11087-11090. [DOI: 10.1039/c9cc05330a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A protein–foldamer crystal structure illustrates protein assembly by a sulfonated aromatic oligoamide, and chiral resolution of the foldamer helix handedness.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland
- Galway
- Ireland
| | - Valentina Corvaglia
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | - Xiaobo Hu
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | | | - Ivan Huc
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
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72
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Rennie ML, Fox GC, Pérez J, Crowley PB. Auto‐regulated Protein Assembly on a Supramolecular Scaffold. Angew Chem Int Ed Engl 2018; 57:13764-13769. [DOI: 10.1002/anie.201807490] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Martin L. Rennie
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
| | - Gavin C. Fox
- Synchrotron SOLEILL'Orme des Merisiers Saint-Aubin BP48 91192 Gif-sur-Yvette Cedex France
| | - Javier Pérez
- Synchrotron SOLEILL'Orme des Merisiers Saint-Aubin BP48 91192 Gif-sur-Yvette Cedex France
| | - Peter B. Crowley
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
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73
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Caetano-Anollés D, Caetano-Anollés K, Caetano-Anollés G. Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification. Sci Prog 2018; 101:360-383. [PMID: 30296968 PMCID: PMC10365222 DOI: 10.3184/003685018x15379391431599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The evolution of structure in biology is driven by accretion and diversification. Accretion brings together disparate parts to form bigger wholes. Diversification provides opportunities for growth and innovation. Here, we review patterns and processes that are responsible for a 'double tale' of accretion and diversification at various levels of complexity, from proteins and nucleic acids to high-rise building structures in cities. Parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organise into modules with tight linkage. In a second phase, variants of the modules evolve and become new parts for a new generative cycle of higher-level organisation. Evolutionary genomics and network biology support the 'double tale' of structural module creation and validate an evolutionary principle of maximum abundance that drives the gain and loss of modules.
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Affiliation(s)
- Derek Caetano-Anollés
- Department of Evolutionary Genetics of the Max-Planck Institute for Evolutionary Biology, Plön, Germany. Developmental Biology from the University of Illinois, Urbana-Champaign
| | - Kelsey Caetano-Anollés
- Division of Biomedical Informatics of Seoul National University College of Medicine, Republic of Korea. Animal Sciences from the University of Illinois, Urbana-Champaign
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences and Affiliate of the C.R. Woese Institute for Genomic Biology at the University of Illinois, Urbana-Champaign. University of La Plata in Argentina
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74
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Lazar T, Guharoy M, Schad E, Tompa P. Unique Physicochemical Patterns of Residues in Protein–Protein Interfaces. J Chem Inf Model 2018; 58:2164-2173. [DOI: 10.1021/acs.jcim.8b00270] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Tamas Lazar
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Mainak Guharoy
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok korutja 2, 1117 Budapest, Hungary
| | - Peter Tompa
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok korutja 2, 1117 Budapest, Hungary
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75
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Rennie ML, Fox GC, Pérez J, Crowley PB. Auto‐regulated Protein Assembly on a Supramolecular Scaffold. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Martin L. Rennie
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
| | - Gavin C. Fox
- Synchrotron SOLEILL'Orme des Merisiers Saint-Aubin BP48 91192 Gif-sur-Yvette Cedex France
| | - Javier Pérez
- Synchrotron SOLEILL'Orme des Merisiers Saint-Aubin BP48 91192 Gif-sur-Yvette Cedex France
| | - Peter B. Crowley
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
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76
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Lund BA, Thomassen AM, Nesheim BHB, Carlsen TJO, Isaksson J, Christopeit T, Leiros HKS. The biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity. FEBS J 2018; 285:4214-4228. [PMID: 30153368 DOI: 10.1111/febs.14643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 08/07/2018] [Accepted: 08/22/2018] [Indexed: 12/16/2022]
Abstract
Many class D β-lactamases form dimers in solution. The functional basis of the dimerization of OXA-48-like class D β-lactamases is not known, but in order to understand the structural requirements for dimerization of OXA-48, we have characterized the dimer interface. Size exclusion chromatography, small angle X-ray scattering (SAXS), and nuclear magnetic resonance (NMR) were used to confirm the oligomeric state of OXA-48 in solution. X-ray crystallographic structures were used to elucidate the key interactions of dimerization. In silico residue scanning combined with site-directed mutagenesis was used to probe hot spots of dimerization. The affinity of dimerization was quantified using microscale thermophoresis, and the overall thermostability was investigated using differential scanning calorimetry. OXA-48 was consistently found to be a dimer in solution regardless of the method used, and the biological assembly found from the SAXS envelope is consistent with the dimer identified from the crystal structures. The buried chloride that interacts with Arg206 and Arg206' at the dimer interface was found to enhance the thermal stability by > 4 °C and crystal structures and mutations (R189A, R189A/R206A) identified several additional important ionic interactions. The affinity for OXA-48 R206A dimerization was in the picomolar range, thus revealing very high dimer affinity. In summary, OXA-48 has a very stable dimer interface, facilitated by noncovalent and predominantly charged interactions, which is stronger than the dimer interfaces previously described for other class D β-lactamases. PDB CODES: The oxacillinase-48 (OXA-48) R206A structure has PDB ID: 5OFT and OXA-48 R189A has PDB ID: 6GOA.
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Affiliation(s)
- Bjarte Aarmo Lund
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Ane Molden Thomassen
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Birgit Helene Berg Nesheim
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Trine Josefine Olsen Carlsen
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tony Christopeit
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
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77
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Hong S, Wang Y, Park SY, Lee H. Progressive fuzzy cation-π assembly of biological catecholamines. SCIENCE ADVANCES 2018; 4:eaat7457. [PMID: 30202784 PMCID: PMC6128673 DOI: 10.1126/sciadv.aat7457] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/30/2018] [Indexed: 05/21/2023]
Abstract
Biological functions depend on biomolecular assembly processes. Assemblies of lipid bilayers, actins, microtubules, or chromosomes are indispensable for cellular functions. These hierarchical assembly processes are reasonably predictable by understanding chemical structures of the defined building blocks and their interactions. However, biopigment assembly is rather fuzzy and unpredictable because a series of covalently coupled intermediates from catecholamine oxidation pathways progressively form a higher-level hierarchy. This study reports a different yet unexplored type of assembly process named "cation-π progressive assembly." We demonstrated for the first time that the cation-π is the primary mechanism for intermolecular assembly in dopamine-melanin biopigment. We also found that the self-assembled products physically grow and chemically gain new functions "progressively" over time in which cation-π plays important roles. The progressive assembly explains how biological systems produce wide spectra of pigment colors and broad wavelength absorption through energy-efficient processes. Furthermore, we also demonstrate surface-independent wettability control using cation-π progressive assembly.
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Affiliation(s)
- Seonki Hong
- Department of Emerging Materials Science, Daegu Gyeongbuk Institute of Science and Technology, 333 Techno Jungang-daero, Hyeonpung-myeon, Dalseong-gun, Daegu 42988, Republic of Korea
- Corresponding author. (H.L.); (S.H.)
| | - Younseon Wang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sung Young Park
- Department of Chemical and Biological Engineering, Korea National University of Transportation, Chungju 380-702, Republic of Korea
| | - Haeshin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Corresponding author. (H.L.); (S.H.)
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78
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Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking. J Comput Aided Mol Des 2018; 32:769-779. [PMID: 30003468 DOI: 10.1007/s10822-018-0124-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 05/22/2018] [Indexed: 12/15/2022]
Abstract
Modulating protein interaction pathways may lead to the cure of many diseases. Known protein-protein inhibitors bind to large pockets on the protein-protein interface. Such large pockets are detected also in the protein-protein complexes without known inhibitors, making such complexes potentially druggable. The inhibitor-binding site is primary defined by the side chains that form the largest pocket in the protein-bound conformation. Low-resolution ligand docking shows that the success rate for the protein-bound conformation is close to the one for the ligand-bound conformation, and significantly higher than for the apo conformation. The conformational change on the protein interface upon binding to the other protein results in a pocket employed by the ligand when it binds to that interface. This proof-of-concept study suggests that rather than using computational pocket-opening procedures, one can opt for an experimentally determined structure of the target co-crystallized protein-protein complex as a starting point for drug design.
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79
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Yuenyao A, Petchyam N, Kamonsutthipaijit N, Chaiyen P, Pakotiprapha D. Crystal structure of the flavin reductase of Acinetobacter baumannii p-hydroxyphenylacetate 3-hydroxylase (HPAH) and identification of amino acid residues underlying its regulation by aromatic ligands. Arch Biochem Biophys 2018; 653:24-38. [PMID: 29940152 DOI: 10.1016/j.abb.2018.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/07/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022]
Abstract
The first step in the degradation of p-hydroxyphenylacetic acid (HPA) is catalyzed by the two-component enzyme p-hydroxyphenylacetate 3-hydroxylase (HPAH). The two components of Acinetobacter baumannii HPAH are known as C1 and C2, respectively. C1 is a flavin reductase that uses NADH to generate reduced flavin mononucleotide (FMNH-), which is used by C2 in the hydroxylation of HPA. Interestingly, although HPA is not directly involved in the reaction catalyzed by C1, the presence of HPA dramatically increases the FMN reduction rate. Amino acid sequence analysis revealed that C1 contains two domains: an N-terminal flavin reductase domain, and a C-terminal MarR domain. Although MarR proteins typically function as transcription regulators, the MarR domain of C1 was found to play an auto-inhibitory role. Here, we report a crystal structure of C1 and small-angle X-ray scattering (SAXS) studies that revealed that C1 undergoes a substantial conformational change in the presence of HPA, concomitant with the increase in the rate of flavin reduction. Amino acid residues that are important for HPA binding and regulation of C1 activity were identified by site-directed mutagenesis. Amino acid sequence similarity analysis revealed several as yet uncharacterized flavin reductases with N- or C-terminal fusions.
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Affiliation(s)
- Anan Yuenyao
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nopphon Petchyam
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | | | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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80
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Gaines JC, Acebes S, Virrueta A, Butler M, Regan L, O'Hern CS. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. Proteins 2018; 86:581-591. [PMID: 29427530 PMCID: PMC5912992 DOI: 10.1002/prot.25479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/23/2018] [Accepted: 02/06/2018] [Indexed: 12/26/2022]
Abstract
We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins.
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Affiliation(s)
- J C Gaines
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
| | - S Acebes
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - A Virrueta
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
| | - M Butler
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, 90007
| | - L Regan
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, 06520
- Department of Chemistry, Yale University, New Haven, Connecticut, 06520
| | - C S O'Hern
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520
- Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520
- Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520
- Department of Physics, Yale University, New Haven, Connecticut, 06520
- Department of Applied Physics, Yale University, New Haven, Connecticut, 06520
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81
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Bortot A, Zanzoni S, D'Onofrio M, Assfalg M. Specific Interaction Sites Determine Differential Adsorption of Protein Structural Isomers on Nanoparticle Surfaces. Chemistry 2018; 24:5911-5919. [PMID: 29446497 DOI: 10.1002/chem.201705994] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Indexed: 11/08/2022]
Abstract
In biological systems, nanoparticles (NPs) elicit bioactivity upon interaction with proteins. As a result of post-translational modification, proteins occur in a variety of alternative covalent forms, including structural isomers, which present unique molecular surfaces. We aimed at a detailed description of the recognition of protein isomeric species by NP surfaces. The transient adsorption of isomeric ubiquitin (Ub) dimers by NPs was investigated by solution NMR spectroscopy. Lys63- and Lys48-linked Ub2 were adsorbed by large anionic NPs with different affinities, whereas the binding strength was similar in the cases of smaller particles. After the incorporation of paramagnetic tags into NPs, the observed site-resolved paramagnetic footprints provided a high-resolution map of the different protein surfaces binding to NPs. The approach described could be extended to further protein isoforms and more specialized NP systems to allow better control of the interactions between NPs and protein targets.
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Affiliation(s)
- Andrea Bortot
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Serena Zanzoni
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
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82
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Škrbić T, Zamuner S, Hong R, Seno F, Laio A, Trovato A. Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes. Proteins 2018; 86:393-404. [DOI: 10.1002/prot.25454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/22/2017] [Accepted: 01/05/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Tatjana Škrbić
- Faculty of Physics; International School for Advanced Studies (SISSA/ISAS); Trieste Italy
- Department of Physics and Astronomy “Galileo Galilei”; University of Padova; Padova Italy
| | - Stefano Zamuner
- Department of Physics and Astronomy “Galileo Galilei”; University of Padova; Padova Italy
| | - Rolando Hong
- Faculty of Physics; International School for Advanced Studies (SISSA/ISAS); Trieste Italy
| | - Flavio Seno
- Department of Physics and Astronomy “Galileo Galilei”; University of Padova; Padova Italy
- Padova Section, National Institute of Nuclear Physics (INFN); Padova Italy
| | - Alessandro Laio
- Faculty of Physics; International School for Advanced Studies (SISSA/ISAS); Trieste Italy
| | - Antonio Trovato
- Department of Physics and Astronomy “Galileo Galilei”; University of Padova; Padova Italy
- Padova Section, National Institute of Nuclear Physics (INFN); Padova Italy
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83
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Lawrie J, Song X, Niu W, Guo J. A high throughput approach for the generation of orthogonally interacting protein pairs. Sci Rep 2018; 8:867. [PMID: 29343761 PMCID: PMC5772552 DOI: 10.1038/s41598-018-19281-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/27/2017] [Indexed: 11/17/2022] Open
Abstract
In contrast to the nearly error-free self-assembly of protein architectures in nature, artificial assembly of protein complexes with pre-defined structure and function in vitro is still challenging. To mimic nature's strategy to construct pre-defined three-dimensional protein architectures, highly specific protein-protein interacting pairs are needed. Here we report an effort to create an orthogonally interacting protein pair from its parental pair using a bacteria-based in vivo directed evolution strategy. This high throughput approach features a combination of a negative and a positive selection. The newly developed negative selection from this work was used to remove any protein mutants that retain effective interaction with their parents. The positive selection was used to identify mutant pairs that can engage in effective mutual interaction. By using the cohesin-dockerin protein pair that is responsible for the self-assembly of cellulosome as a model system, we demonstrated that a protein pair that is orthogonal to its parent pair could be readily generated using our strategy. This approach could open new avenues to a wide range of protein-based assembly, such as biocatalysis or nanomaterials, with pre-determined architecture and potentially novel functions and properties.
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Affiliation(s)
- Justin Lawrie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Xi Song
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
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84
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 485] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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85
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Dey S, Levy ED. Inferring and Using Protein Quaternary Structure Information from Crystallographic Data. Methods Mol Biol 2018; 1764:357-375. [PMID: 29605927 DOI: 10.1007/978-1-4939-7759-8_23] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A precise knowledge of the quaternary structure of proteins is essential to illuminate both their function and their evolution. The major part of our knowledge on quaternary structure is inferred from X-ray crystallography data, but this inference process is hard and error-prone. The difficulty lies in discriminating fortuitous protein contacts, which make up the lattice of protein crystals, from biological protein contacts that exist in the native cellular environment. Here, we review methods devised to discriminate between both types of contacts and describe resources for downloading protein quaternary structure information and identifying high-confidence quaternary structures. The use of high-confidence datasets of quaternary structures will be critical for the analysis of structural, functional, and evolutionary properties of proteins.
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Affiliation(s)
- Sucharita Dey
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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86
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Feng T, Chen F, Kang Y, Sun H, Liu H, Li D, Zhu F, Hou T. HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. J Cheminform 2017; 9:66. [PMID: 29282565 PMCID: PMC5745212 DOI: 10.1186/s13321-017-0254-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/14/2017] [Indexed: 01/09/2023] Open
Abstract
Deciphering the structural determinants of protein–protein interactions (PPIs) is essential to gain a deep understanding of many important biological functions in the living cells. Computational approaches for the structural modeling of PPIs, such as protein–protein docking, are quite needed to complement existing experimental techniques. The reliability of a protein–protein docking method is dependent on the ability of the scoring function to accurately distinguish the near-native binding structures from a huge number of decoys. In this study, we developed HawkRank, a novel scoring function designed for the sampling stage of protein–protein docking by summing the contributions from several energy terms, including van der Waals potentials, electrostatic potentials and desolvation potentials. First, based on the solvation free energies predicted by the Generalized Born model for ~ 800 proteins, a SASA (solvent accessible surface area)-based solvation model was developed, which can give the aqueous solvation free energies for proteins by summing the contributions of 21 atom types. Then, the van der Waals potentials and electrostatic potentials based on the Amber ff14SB force field were computed. Finally, the HawkRank scoring function was derived by determining the most optimal weights for five energy terms based on the training set. Here, MSR (modified success rate), a novel protein–protein scoring quality index, was used to assess the performance of HawkRank and three other popular protein–protein scoring functions, including ZRANK, FireDock and dDFIRE. The results show that HawkRank outperformed the other three scoring functions according to the total number of hits and MSR. HawkRank is available at http://cadd.zju.edu.cn/programs/hawkrank.
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Affiliation(s)
- Ting Feng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Fu Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China. .,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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87
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Peng X, Wang J, Peng W, Wu FX, Pan Y. Protein-protein interactions: detection, reliability assessment and applications. Brief Bioinform 2017; 18:798-819. [PMID: 27444371 DOI: 10.1093/bib/bbw066] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 01/06/2023] Open
Abstract
Protein-protein interactions (PPIs) participate in all important biological processes in living organisms, such as catalyzing metabolic reactions, DNA replication, DNA transcription, responding to stimuli and transporting molecules from one location to another. To reveal the function mechanisms in cells, it is important to identify PPIs that take place in the living organism. A large number of PPIs have been discovered by high-throughput experiments and computational methods. However, false-positive PPIs have been introduced too. Therefore, to obtain reliable PPIs, many computational methods have been proposed. Generally, these methods can be classified into two categories. One category includes the methods that are designed to determine new reliable PPIs. The other one is designed to assess the reliability of existing PPIs and filter out the unreliable ones. In this article, we review the two kinds of methods for detecting reliable PPIs, and then focus on evaluating the performance of some of these typical methods. Later on, we also enumerate several PPI network-based applications with taking a reliability assessment of the PPI data into consideration. Finally, we will discuss the challenges for obtaining reliable PPIs and future directions of the construction of reliable PPI networks. Our research will provide readers some guidance for choosing appropriate methods and features for obtaining reliable PPIs.
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88
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Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging. Nat Commun 2017; 8:1436. [PMID: 29127347 PMCID: PMC5681674 DOI: 10.1038/s41467-017-01668-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/05/2017] [Indexed: 12/13/2022] Open
Abstract
Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature resistance. The rod-shaped virus APBV1 (Aeropyrum pernix bacilliform virus 1) is among the most thermostable viruses known; it infects a hyperthermophile Aeropyrum pernix, which grows optimally at 90 °C. Here we report the structure of APBV1, determined by cryo-electron microscopy at near-atomic resolution. Tight packing of the major virion glycoprotein (VP1) is ensured by extended hydrophobic interfaces, and likely contributes to the extreme thermostability of the helical capsid. The double-stranded DNA is tightly packed in the capsid as a left-handed superhelix and held in place by the interactions with positively charged residues of VP1. The assembly is closed by specific capping structures at either end, which we propose to play a role in DNA packing and delivery. The rod-shaped virus APBV1 is among the most thermostable viruses known. Here, Ptchelkine et al. determine its structure at near-atomic resolution, show that the DNA is packed as left-handed superhelix and identify extended hydrophobic interfaces that likely contribute to the extreme thermostability of the capsid.
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89
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Ji L, Ma B, Meng Q, Li L, Liu K, Chen D. Detergent-resistant oligomeric Leptosphaeria rhodopsin is a promising bio-nanomaterial and an alternative to bacteriorhodopsin. Biochem Biophys Res Commun 2017; 493:352-357. [PMID: 28887035 DOI: 10.1016/j.bbrc.2017.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/05/2017] [Indexed: 01/10/2023]
Abstract
Bacteriorhodopsin has attracted remarkable attention as a photoactive bio-nanomaterial in the last decades. However, its instability in the presence of detergents has restricted the extent to which bacteriorhodopsin may be applied. In this study, we investigated the oligomerization of a eukaryotic light-driven H+-pump, Leptosphaeria rhodopsin, using circular dichroism spectroscopy and other biophysical and biochemical methods. Our findings revealed that Leptosphaeria rhodopsin assembled into oligomers in the cell membrane and also in 0.05% DDM detergent micelles. Moreover, unlike bacteriorhodopsin in purple membrane, Leptosphaeria rhodopsin retained its oligomeric structure in 1% Triton X-100 and demonstrated strong resistance to other common detergents. A maximal photocurrent density of ∼85 nA/cm2 was consistently generated, which was substantially larger than that of solubilized bacteriorhodopsin (∼10 nA/cm2). Therefore, oligomeric Leptosphaeria rhodopsin may be a promising bio-nanomaterial, and an alternative to bacteriorhodopsin, especially with the use of detergents.
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Affiliation(s)
- Liangliang Ji
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Meng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longjie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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90
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Ivanov SM, Cawley A, Huber RG, Bond PJ, Warwicker J. Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold. PLoS One 2017; 12:e0185928. [PMID: 29016650 PMCID: PMC5634604 DOI: 10.1371/journal.pone.0185928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/21/2017] [Indexed: 12/05/2022] Open
Abstract
An improved knowledge of protein-protein interactions is essential for better understanding of metabolic and signaling networks, and cellular function. Progress tends to be based on structure determination and predictions using known structures, along with computational methods based on evolutionary information or detailed atomistic descriptions. We hypothesized that for the case of interactions across a common interface, between proteins from a pair of paralogue families or within a family of paralogues, a relatively simple interface description could distinguish between binding and non-binding pairs. Using binding data for several systems, and large-scale comparative modeling based on known template complex structures, it is found that charge-charge interactions (for groups bearing net charge) are generally a better discriminant than buried non-polar surface. This is particularly the case for paralogue families that are less divergent, with more reliable comparative modeling. We suggest that electrostatic interactions are major determinants of specificity in such systems, an observation that could be used to predict binding partners.
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Affiliation(s)
- Stefan M. Ivanov
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Andrew Cawley
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jim Warwicker
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
- * E-mail:
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91
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Kyne C, Crowley PB. Short Arginine Motifs Drive Protein Stickiness in the Escherichia coli Cytoplasm. Biochemistry 2017; 56:5026-5032. [DOI: 10.1021/acs.biochem.7b00731] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ciara Kyne
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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92
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Bergendahl LT, Marsh JA. Functional determinants of protein assembly into homomeric complexes. Sci Rep 2017; 7:4932. [PMID: 28694495 PMCID: PMC5504011 DOI: 10.1038/s41598-017-05084-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 05/24/2017] [Indexed: 11/24/2022] Open
Abstract
Approximately half of proteins with experimentally determined structures can interact with other copies of themselves and assemble into homomeric complexes, the overwhelming majority of which (>96%) are symmetric. Although homomerisation is often assumed to a functionally beneficial result of evolutionary selection, there has been little systematic analysis of the relationship between homomer structure and function. Here, utilizing the large numbers of structures and functional annotations now available, we have investigated how proteins that assemble into different types of homomers are associated with different biological functions. We observe that homomers from different symmetry groups are significantly enriched in distinct functions, and can often provide simple physical and geometrical explanations for these associations in regards to substrate recognition or physical environment. One of the strongest associations is the tendency for metabolic enzymes to form dihedral complexes, which we suggest is closely related to allosteric regulation. We provide a physical explanation for why allostery is related to dihedral complexes: it allows for efficient propagation of conformational changes across isologous (i.e. symmetric) interfaces. Overall we demonstrate a clear relationship between protein function and homomer symmetry that has important implications for understanding protein evolution, as well as for predicting protein function and quaternary structure.
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Affiliation(s)
- L Therese Bergendahl
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK.
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
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93
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Vázquez-Iglesias L, Estefanell-Ucha B, Barcia-Castro L, Páez de la Cadena M, Álvarez-Chaver P, Ayude-Vázquez D, Rodríguez-Berrocal FJ. A simple electroelution method for rapid protein purification: isolation and antibody production of alpha toxin from Clostridium septicum. PeerJ 2017; 5:e3407. [PMID: 28652930 PMCID: PMC5483040 DOI: 10.7717/peerj.3407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/11/2017] [Indexed: 12/16/2022] Open
Abstract
Clostridium septicum produces a number of diseases in human and farm animals which, in most of the cases, are fatal without clinical intervention. Alpha toxin is an important agent and the unique lethal virulent factor produced by Clostridium septicum. This toxin is haemolytic, highly lethal and necrotizing activities but is being used as an antigen to develop animal vaccines. The aim of this study was to isolate the alpha toxin of Clostridium septicum and produce highly specific antibodies against it. In this work, we have developed a simple and efficient method for alpha toxin purification, based on electroelution that can be used as a time-saving method for purifying proteins. This technique avoids contamination by other proteins that could appear during other protein purification techniques such chromatography. The highly purified toxin was used to produce polyclonal antibodies. The specificity of the antibodies was tested by western blot and these antibodies can be applied to the quantitative determination of alpha toxin by slot blot.
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Affiliation(s)
- Lorena Vázquez-Iglesias
- Department of Biochemistry, Genetics and Immunology, Facultad de Biología, Universidad de Vigo, Vigo, Spain
| | - Borja Estefanell-Ucha
- Department of Biochemistry, Genetics and Immunology, Facultad de Biología, Universidad de Vigo, Vigo, Spain
| | - Leticia Barcia-Castro
- Department of Biochemistry, Genetics and Immunology, Facultad de Biología, Universidad de Vigo, Vigo, Spain
| | - María Páez de la Cadena
- Department of Biochemistry, Genetics and Immunology, Facultad de Biología, Universidad de Vigo, Vigo, Spain
| | - Paula Álvarez-Chaver
- Unidad de Proteómica, Servicio de Determinación Estructural, Proteómica y Genómica, CACTI, Universidad de Vigo, Spain
| | - Daniel Ayude-Vázquez
- Department of Biochemistry, Genetics and Immunology, Facultad de Biología, Universidad de Vigo, Vigo, Spain
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94
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Differential CLE peptide perception by plant receptors implicated from structural and functional analyses of TDIF-TDR interactions. PLoS One 2017; 12:e0175317. [PMID: 28384649 PMCID: PMC5383425 DOI: 10.1371/journal.pone.0175317] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/23/2017] [Indexed: 11/19/2022] Open
Abstract
Tracheary Element Differentiation Inhibitory Factor (TDIF) belongs to the family of post-translationally modified CLE (CLAVATA3/embryo surrounding region (ESR)-related) peptide hormones that control root growth and define the delicate balance between stem cell proliferation and differentiation in SAM (shoot apical meristem) or RAM (root apical meristem). In Arabidopsis, Tracheary Element Differentiation Inhibitory Factor Receptor (TDR) and its ligand TDIF signaling pathway is involved in the regulation of procambial cell proliferation and inhibiting its differentiation into xylem cells. Here we present the crystal structures of the extracellular domains (ECD) of TDR alone and in complex with its ligand TDIF resolved at 2.65 Ǻ and 2.75 Ǻ respectively. These structures provide insights about the ligand perception and specific interactions between the CLE peptides and their cognate receptors. Our in vitro biochemical studies indicate that the interactions between the ligands and the receptors at the C-terminal anchoring site provide conserved binding. While the binding interactions occurring at the N-terminal anchoring site dictate differential binding specificities between different ligands and receptors. Our studies will open different unknown avenues of TDR-TDIF signaling pathways that will enhance our knowledge in this field highlighting the receptor ligand interaction, receptor activation, signaling network, modes of action and will serve as a structure function relationship model between the ligand and the receptor for various similar leucine-rich repeat receptor-like kinases (LRR-RLKs).
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95
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Stanek KA, Patterson-West J, Randolph PS, Mura C. Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode. Acta Crystallogr D Struct Biol 2017; 73:294-315. [PMID: 28375142 PMCID: PMC5379935 DOI: 10.1107/s2059798317000031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/02/2017] [Indexed: 11/10/2022] Open
Abstract
The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus (Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore, Aae Hfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures of Aae Hfq were determined in space groups P1 and P6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.
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Affiliation(s)
- Kimberly A. Stanek
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Jennifer Patterson-West
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Peter S. Randolph
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
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96
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Marillet S, Lefranc MP, Boudinot P, Cazals F. Novel Structural Parameters of Ig-Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity. Front Immunol 2017; 8:34. [PMID: 28232828 PMCID: PMC5298999 DOI: 10.3389/fimmu.2017.00034] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/09/2017] [Indexed: 11/13/2022] Open
Abstract
Antibody–antigen complexes challenge our understanding, as analyses to date failed to unveil the key determinants of binding affinity and interaction specificity. We partially fill this gap based on novel quantitative analyses using two standardized databases, the IMGT/3Dstructure-DB and the structure affinity benchmark. First, we introduce a statistical analysis of interfaces which enables the classification of ligand types (protein, peptide, and chemical; cross-validated classification error of 9.6%) and yield binding affinity predictions of unprecedented accuracy (median absolute error of 0.878 kcal/mol). Second, we exploit the contributions made by CDRs in terms of position at the interface and atomic packing properties to show that in general, VH CDR3 and VL CDR3 make dominant contributions to the binding affinity, a fact also shown to be consistent with the enthalpy–entropy compensation associated with preconfiguration of CDR3. Our work suggests that the affinity prediction problem could be partially solved from databases of high resolution crystal structures of complexes with known affinity.
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Affiliation(s)
- Simon Marillet
- VIM, INRA and Université Paris-Saclay, Jouy-en-josas, France; Université Côte d'Azur and Inria, Sophia Antipolis, France
| | | | - Pierre Boudinot
- VIM, INRA and Université Paris-Saclay , Jouy-en-josas , France
| | - Frédéric Cazals
- Université Côte d'Azur and Inria , Sophia Antipolis , France
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97
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Kyne C, Jordon K, Filoti DI, Laue TM, Crowley PB. Protein charge determination and implications for interactions in cell extracts. Protein Sci 2017; 26:258-267. [PMID: 27813264 PMCID: PMC5275725 DOI: 10.1002/pro.3077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/24/2016] [Accepted: 10/27/2016] [Indexed: 01/30/2023]
Abstract
Decades of dilute-solution studies have revealed the influence of charged residues on protein stability, solubility and stickiness. Similar characterizations are now required in physiological solutions to understand the effect of charge on protein behavior under native conditions. Toward this end, we used free boundary and native gel electrophoresis to explore the charge of cytochrome c in buffer and in Escherichia coli extracts. We find that the charge of cytochrome c was ∼2-fold lower than predicted from primary structure analysis. Cytochrome c charge was tuned by sulfate binding and was rendered anionic in E. coli extracts due to interactions with macroanions. Mutants in which three or four cationic residues were replaced with glutamate were charge-neutral and "inert" in extracts. A comparison of the interaction propensities of cytochrome c and the mutants emphasizes the role of negative charge in stabilizing physiological environments. Charge-charge repulsion and preferential hydration appear to prevent aggregation. The implications for molecular organization in vivo are discussed.
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Affiliation(s)
- Ciara Kyne
- School of ChemistryNational University of IrelandGalway, University RoadGalwayIreland
| | - Kiara Jordon
- Spin Analytical468 Portland StreetBerwickMaine03901
| | - Dana I. Filoti
- Centre to Advance Macromolecular Interaction Sciences University of New HampshireDurhamNew Hampshire03824
| | - Thomas M. Laue
- Spin Analytical468 Portland StreetBerwickMaine03901
- Centre to Advance Macromolecular Interaction Sciences University of New HampshireDurhamNew Hampshire03824
| | - Peter B. Crowley
- School of ChemistryNational University of IrelandGalway, University RoadGalwayIreland
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98
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Holinski A, Heyn K, Merkl R, Sterner R. Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex. Proteins 2017; 85:312-321. [PMID: 27936490 DOI: 10.1002/prot.25225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 01/20/2023]
Abstract
It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH. Initial fluorescence titration experiments showed that HisH from Zymomonas mobilis (zmHisH) binds with high affinity to the reconstructed HisF from the last universal common ancestor (LUCA-HisF) but not to HisF from Pyrobaculum arsenaticum (paHisF), which differ by 103 residues. Subsequent titration experiments with a reconstructed evolutionary intermediate linking LUCA-HisF and paHisF and inspection of the subunit interface of a contemporary ImGPS allowed us to narrow down the differences crucial for zmHisH binding to nine amino acids of HisF. Homology modeling and in silico mutagenesis studies suggested that at most two of these nine HisF residues are crucial for zmHisH binding. These computational results were verified by experimental site-directed mutagenesis, which finally enabled us to pinpoint a single amino acid residue in HisF that is decisive for high-affinity binding of zmHisH. Our work shows that the identification of protein interface hotspots can be very efficient when reconstructed proteins with different binding properties are included in the analysis. Proteins 2017; 85:312-321. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexandra Holinski
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Kristina Heyn
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, D-93040, Germany
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99
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Fadda E, Nixon MG. The transient manifold structure of the p53 extreme C-terminal domain: insight into disorder, recognition, and binding promiscuity by molecular dynamics simulations. Phys Chem Chem Phys 2017; 19:21287-21296. [DOI: 10.1039/c7cp02485a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The extreme C-terminus of the p53 tumour suppressor (p53-CTD) is a 30 residue long intrinsically disordered region, responsible for regulating the p53 DNA binding activity. Extensive conformational sampling through MD simulations of a p53-CTD derived peptide in solution highlights its propensity to form short and stable secondary structure motifs, specifically localized within the sequence.
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Affiliation(s)
- E. Fadda
- Department of Chemistry
- Maynooth University, and Hamilton Institute
- Maynooth University
- Maynooth
- Ireland
| | - M. G. Nixon
- Department of Chemistry
- Maynooth University, and Hamilton Institute
- Maynooth University
- Maynooth
- Ireland
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100
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Dai W, Wu A, Ma L, Li YX, Jiang T, Li YY. A novel index of protein-protein interface propensity improves interface residue recognition. BMC SYSTEMS BIOLOGY 2016; 10:112. [PMID: 28155660 PMCID: PMC5259823 DOI: 10.1186/s12918-016-0351-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Background Protein-protein interface holds important information of protein-protein interactions which play key roles in most biological processes. In the past few years, a lot of efforts have been made to improve interface residue recognition by characterizing protein-protein interfaces and extracting relevant features. However, most previous studies were carried out in a qualitative level, and there are also some inconsistencies between them. Results In the present work, to improve interface residue recognition, we built a novel quantitative residue protein-protein interface propensity index (QIPI) and gained a comprehensive picture of protein-protein interface through analyzing protein-protein interfaces on our comprehensive protein-protein interfaces dataset (Astral2.05-40-4506). Furthermore, in order to assess the effect of QIPI in improving the protein-protein interface prediction, we developed an interface residue recognition method SPR (Single domain based Patch Recognition) based on the QIPI. The evaluation results proved that our novel QIPI is able to improve the interface residue recognition. Conclusions Through a comprehensive quantitative analysis of protein-protein interface, we constructed a novel quantitative protein-protein interface propensity index (QIPI), which could be easily applied to improve the interface residue recognition and helpful in understanding the protein-protein interface. Availability QIPI and SPR are available to non-commercial users at our website: http://www.scbit.org/QIPI/. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0351-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wentao Dai
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 2012035, People's Republic of China.,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Liangxiao Ma
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 2012035, People's Republic of China
| | - Yi-Xue Li
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 2012035, People's Republic of China.,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.,Shanghai Engineering Research Center of Pharmaceutical Translation, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China
| | - Taijiao Jiang
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China. .,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 2012035, People's Republic of China. .,Shanghai Industrial Technology Institute, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China. .,Shanghai Engineering Research Center of Pharmaceutical Translation, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.
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