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Wang G, Yu G, Gao D, Jiang G, Wang H, Yuwen T, Zhang X, Li C, Yang D, He L, Liu M. Protein Conformational Exchanges Modulated by the Environment of Outer Membrane Vesicles. J Phys Chem Lett 2023; 14:2772-2777. [PMID: 36897994 DOI: 10.1021/acs.jpclett.3c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Protein function, in many cases, is strongly coupled to the dynamics and conformational equilibria of the protein. The environment surrounding proteins is critical for their dynamics and can dramatically affect the conformational equilibria and subsequently the activities of proteins. However, it is unclear how protein conformational equilibria are modulated by their crowded native environments. Here we reveal that outer membrane vesicle (OMV) environments modulate the conformational exchanges of Im7 protein at its local frustrated sites and shift the conformation toward its ground state. Further experiments show both macromolecular crowding and quinary interactions with the periplasmic components stabilize the ground state of Im7. Our study highlights the key role that the OMV environment plays in the protein conformational equilibria and subsequently the conformation-related protein functions. Furthermore, the long-lasting nuclear magnetic resonance measurement time of proteins within OMVs indicates that they could serve as a promising system for investigating protein structures and dynamics in situ via nuclear magnetic spectroscopy.
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Affiliation(s)
- Guan Wang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gangjin Yu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dawei Gao
- State Key Laboratory of Metastable Materials Science and Technology, Nano-biotechnology Key Lab of Hebei Province, Applying Chemistry Key Lab of Hebei Province, Heavy Metal Deep-Remediation in Water and Resource Reuse Key Lab of Hebei, Yanshan University, Qinhuangdao 066004, China
| | - Guosheng Jiang
- Department of Immunology, Binzhou Medical University, Yantai, Shandong 264000, China
- School of Life Science and Technology, Weifang Medical University, Weifang, Shandong 261053, China
| | - Huan Wang
- School of Life Science and Technology, Weifang Medical University, Weifang, Shandong 261053, China
| | - Tairan Yuwen
- Department of Pharmaceutical Analysis and State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daiwen Yang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Hubei 430074, China
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Shushan A, Kosloff M. Structural design principles for specific ultra-high affinity interactions between colicins/pyocins and immunity proteins. Sci Rep 2021; 11:3789. [PMID: 33589691 PMCID: PMC7884437 DOI: 10.1038/s41598-021-83265-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/28/2021] [Indexed: 12/13/2022] Open
Abstract
The interactions of the antibiotic proteins colicins/pyocins with immunity proteins is a seminal model system for studying protein–protein interactions and specificity. Yet, a precise and quantitative determination of which structural elements and residues determine their binding affinity and specificity is still lacking. Here, we used comparative structure-based energy calculations to map residues that substantially contribute to interactions across native and engineered complexes of colicins/pyocins and immunity proteins. We show that the immunity protein α1–α2 motif is a unique structurally-dissimilar element that restricts interaction specificity towards all colicins/pyocins, in both engineered and native complexes. This motif combines with a diverse and extensive array of electrostatic/polar interactions that enable the exquisite specificity that characterizes these interactions while achieving ultra-high affinity. Surprisingly, the divergence of these contributing colicin residues is reciprocal to residue conservation in immunity proteins. The structurally-dissimilar immunity protein α1–α2 motif is recognized by divergent colicins similarly, while the conserved immunity protein α3 helix interacts with diverse colicin residues. Electrostatics thus plays a key role in setting interaction specificity across all colicins and immunity proteins. Our analysis and resulting residue-level maps illuminate the molecular basis for these protein–protein interactions, with implications for drug development and rational engineering of these interfaces.
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Affiliation(s)
- Avital Shushan
- The Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838, Haifa, Israel
| | - Mickey Kosloff
- The Department of Human Biology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., Mt. Carmel, 3498838, Haifa, Israel.
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Following evolutionary paths to protein-protein interactions with high affinity and selectivity. Nat Struct Mol Biol 2009; 16:1049-55. [PMID: 19749752 DOI: 10.1038/nsmb.1670] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 08/04/2009] [Indexed: 11/08/2022]
Abstract
How do intricate multi-residue features such as protein-protein interfaces evolve? To address this question, we evolved a new colicin-immunity binding interaction. We started with Im9, which inhibits its cognate DNase ColE9 at 10(-14) M affinity, and evolved it toward ColE7, which it inhibits promiscuously (Kd > 10(-8) M). Iterative rounds of random mutagenesis and selection toward higher affinity for ColE7, and selectivity (against ColE9 inhibition), led to an approximately 10(5)-fold increase in affinity and a 10(8)-fold increase in selectivity. Analysis of intermediates along the evolved variants revealed that changes in the binding configuration of the Im protein uncovered a latent set of interactions, thus providing the key to the rapid divergence of new Im7 variants. Overall, protein-protein interfaces seem to share the evolvability features of enzymes, that is, the exploitation of promiscuous interactions and alternative binding configurations via 'generalist' intermediates, and the key role of compensatory stabilizing mutations in facilitating the divergence of new functions.
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Bernath K, Magdassi S, Tawfik DS. Directed Evolution of Protein Inhibitors of DNA-nucleases by in Vitro Compartmentalization (IVC) and Nano-droplet Delivery. J Mol Biol 2005; 345:1015-26. [PMID: 15644201 DOI: 10.1016/j.jmb.2004.11.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 11/07/2004] [Accepted: 11/09/2004] [Indexed: 11/18/2022]
Abstract
In vitro compartmentalization (IVC) uses water-in-oil emulsions to create artificial cell-like compartments in which genes can be individually transcribed and translated. Here, we present a new application of IVC for the selection of DNA-nuclease inhibitors. We developed a nano-droplets delivery system that allows the transport of various solutes, including metal ions, into the emulsion droplets. This transport mechanism was used to regulate the activity of colicin nucleases that were co-compartmentalized with the genes, so that the nucleases were activated by nickel or cobalt ions only after the potential inhibitor genes have been translated. Thus, genes encoding nuclease inhibitors survived the digestion and were subsequently amplified and isolated. Selection is therefore directly for inhibition, and not for binding of the nuclease. The stringency of selection can be easily modulated to give high enrichments (100-500-fold) and recoveries. We demonstrated its utility by selecting libraries of the gene encoding the cognate inhibitor of colicin E9 (immunity protein 9, or Im9) for inhibition of another colicin (ColE7). The in vitro evolved inhibitors show significant inhibition of ColE7 both in vitro and in vivo. These Im9 variants carry mutations into residues that determine the selectivity of the natural counterpart (Im7) while completely retaining the residues that are conserved throughout the family of immunity protein inhibitors. The in vitro evolution process confirms earlier hypotheses regarding the "dual recognition" binding mechanism and the way in which new colicin-immunity pairs diverged from existing ones.
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Affiliation(s)
- Kalia Bernath
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Graille M, Mora L, Buckingham RH, van Tilbeurgh H, de Zamaroczy M. Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein. EMBO J 2004; 23:1474-82. [PMID: 15014439 PMCID: PMC391069 DOI: 10.1038/sj.emboj.7600162] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2004] [Accepted: 02/13/2004] [Indexed: 11/09/2022] Open
Abstract
Colicins are toxins secreted by Escherichia coli in order to kill their competitors. Colicin D is a 75 kDa protein that consists of a translocation domain, a receptor-binding domain and a cytotoxic domain, which specifically cleaves the anticodon loop of all four tRNA(Arg) isoacceptors, thereby inactivating protein synthesis and leading to cell death. Here we report the 2.0 A resolution crystal structure of the complex between the toxic domain and its immunity protein ImmD. Neither component shows structural homology to known RNases or their inhibitors. In contrast to other characterized colicin nuclease-Imm complexes, the colicin D active site pocket is completely blocked by ImmD, which, by bringing a negatively charged cluster in opposition to a positively charged cluster on the surface of colicin D, appears to mimic the tRNA substrate backbone. Site-directed mutations affecting either the catalytic domain or the ImmD protein have led to the identification of the residues vital for catalytic activity and for the tight colicin D/ImmD interaction that inhibits colicin D toxicity and tRNase catalytic activity.
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Affiliation(s)
| | | | | | - Herman van Tilbeurgh
- LEBS, CNRS, UPR 9063, Gif sur Yvette, France
- IBBMC, CNRS, UMR 8619, Université Paris 11, Orsay, France
| | - Miklos de Zamaroczy
- IBPC, CNRS, UPR 9073, Paris, France
- IBPC, CNRS, UPR 9073, 13 rue Pierre et Marie Curie, 75005 Paris, France. Tel.: +33 1 5841 51 54; Fax: +33 1 5841 50 20; E-mail:
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Chen SY, Kao CF, Chen CM, Shih CM, Hsu MJ, Chao CH, Wang SH, You LR, Lee YHW. Mechanisms for inhibition of hepatitis B virus gene expression and replication by hepatitis C virus core protein. J Biol Chem 2003; 278:591-607. [PMID: 12401801 DOI: 10.1074/jbc.m204241200] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We have demonstrated previously that the core protein of hepatitis C virus (HCV) exhibits suppression activity on gene expression and replication of hepatitis B virus (HBV). Here we further elucidated the suppression mechanism of HCV core protein. We demonstrated that HCV core protein retained the inhibitory effect on HBV gene expression and replication when expressed as part of the full length of HCV polyprotein. Based on the substitution mutational analysis, our results suggested that mutation introduced into the bipartite nuclear localization signal of the HCV core protein resulted in the cytoplasmic localization of core protein but did not affect its suppression ability on HBV gene expression. Mutational studies also indicated that almost all dibasic residue mutations within the N-terminal 101-amino acid segment of the HCV core protein (except Arg(39)-Arg(40)) impaired the suppression activity on HBV replication but not HBV gene expression. The integrity of Arg residues at positions 101, 113, 114, and 115 was found to be essential for both suppressive effects, whereas the Arg residue at position 104 was important only in the suppression of HBV gene expression. Moreover, our results indicated that the suppression on HBV gene expression was mediated through the direct interaction of HCV core protein with the trans-activator HBx protein, whereas the suppression of HBV replication involved the complex formation between HBV polymerase (pol) and the HCV core protein, resulting in the structural incompetence for the HBV pol to bind the package signal and consequently abolished the formation of the HBV virion. Altogether, this study suggests that these two suppression effects on HBV elicited by the HCV core protein likely depend on different structural context but not on nuclear localization of the core protein, and the two effects can be decoupled as revealed by its differential targets (HBx or HBV pol) on these two processes of the HBV life cycle.
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Affiliation(s)
- Shiow-Yi Chen
- Institute of Biochemistry and Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
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