1
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Nguyen T, Narayanareddy BRJ, Gross SP, Miles CE. Competition between physical search and a weak-to-strong transition rate-limits kinesin binding times. PLoS Comput Biol 2024; 20:e1012158. [PMID: 38768214 PMCID: PMC11142708 DOI: 10.1371/journal.pcbi.1012158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/31/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024] Open
Abstract
The self-organization of cells relies on the profound complexity of protein-protein interactions. Challenges in directly observing these events have hindered progress toward understanding their diverse behaviors. One notable example is the interaction between molecular motors and cytoskeletal systems that combine to perform a variety of cellular functions. In this work, we leverage theory and experiments to identify and quantify the rate-limiting mechanism of the initial association between a cargo-bound kinesin motor and a microtubule track. Recent advances in optical tweezers provide binding times for several lengths of kinesin motors trapped at varying distances from a microtubule, empowering the investigation of competing models. We first explore a diffusion-limited model of binding. Through Brownian dynamics simulations and simulation-based inference, we find this simple diffusion model fails to explain the experimental binding times, but an extended model that accounts for the ADP state of the molecular motor agrees closely with the data, even under the scrutiny of penalizing for additional model complexity. We provide quantification of both kinetic rates and biophysical parameters underlying the proposed binding process. Our model suggests that a typical binding event is limited by ADP state rather than physical search. Lastly, we predict how these association rates can be modulated in distinct ways through variation of environmental concentrations and physical properties.
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Affiliation(s)
- Trini Nguyen
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | | | - Steven P. Gross
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Department of Physics, University of California, Irvine, Irvine, California, United States of America
| | - Christopher E. Miles
- Department of Mathematics, University of California, Irvine, Irvine, California, United States of America
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2
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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3
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Yu TG, Lee J, Yoon J, Choi JM, Kim DG, Heo WD, Song JJ, Kim HS. Engineering of a Fluorescent Protein for a Sensing of an Intrinsically Disordered Protein through Transition in the Chromophore State. JACS AU 2023; 3:3055-3065. [PMID: 38034956 PMCID: PMC10685427 DOI: 10.1021/jacsau.3c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023]
Abstract
Intrinsically disordered proteins (IDPs) not only play important roles in biological processes but are also linked with the pathogenesis of various human diseases. Specific and reliable sensing of IDPs is crucial for exploring their roles but remains elusive due to structural plasticity. Here, we present the development of a new type of fluorescent protein for the ratiometric sensing and tracking of an IDP. A β-strand of green fluorescent protein (GFP) was truncated, and the resulting GFP was further engineered to undergo the transition in the absorption maximum upon binding of a target motif within amyloid-β (Aβ) as a model IDP through rational design and directed evolution. Spectroscopic and structural analyses of the engineered truncated GFP demonstrated that a shift in the absorption maximum is driven by the change in the chromophore state from an anionic (460 nm) state into a neutral (390 nm) state as the Aβ binds, allowing a ratiometric detection of Aβ. The utility of the developed GFP was shown by the efficient and specific detection of an Aβ and the tracking of its conformational change and localization in astrocytes.
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Affiliation(s)
- Tae-Geun Yu
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jinsu Lee
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jungmin Yoon
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jung Min Choi
- School
of Food Biotechnology and Nutrition, Kyungsung
University, Busan 48434, Korea
| | - Dong-Gun Kim
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Won Do Heo
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ji-Joon Song
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hak-Sung Kim
- Departement
of Biological Sciences, Korea Advanced Institute
of Science and Technology (KAIST), Daejeon 34141, Korea
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4
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Nguyen T, Narayanareddy BJ, Gross SP, Miles CE. ADP release can explain spatially-dependent kinesin binding times. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.563482. [PMID: 37986962 PMCID: PMC10659338 DOI: 10.1101/2023.11.08.563482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The self-organization of cells relies on the profound complexity of protein-protein interactions. Challenges in directly observing these events have hindered progress toward understanding their diverse behaviors. One notable example is the interaction between molecular motors and cytoskeletal systems that combine to perform a variety of cellular functions. In this work, we leverage theory and experiments to identify and quantify the rate-limiting mechanism of the initial association between a cargo-bound kinesin motor and a microtubule track. Recent advances in optical tweezers provide binding times for several lengths of kinesin motors trapped at varying distances from a microtubule, empowering the investigation of competing models. We first explore a diffusion-limited model of binding. Through Brownian dynamics simulations and simulation-based inference, we find this simple diffusion model fails to explain the experimental binding times, but an extended model that accounts for the ADP state of the molecular motor agrees closely with the data, even under the scrutiny of penalizing for additional model complexity. We provide quantification of both kinetic rates and biophysical parameters underlying the proposed binding process. Our model suggests that most but not every motor binding event is limited by their ADP state. Lastly, we predict how these association rates can be modulated in distinct ways through variation of environmental concentrations and spatial distances.
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Affiliation(s)
- Trini Nguyen
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697
| | | | - Steven P. Gross
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697
| | - Christopher E. Miles
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697
- Center for Multiscale Cell Fate, University of California, Irvine, Irvine, CA 92697
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5
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Niazi SK. A Critical Analysis of the FDA's Omics-Driven Pharmacodynamic Biomarkers to Establish Biosimilarity. Pharmaceuticals (Basel) 2023; 16:1556. [PMID: 38004421 PMCID: PMC10675618 DOI: 10.3390/ph16111556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 11/26/2023] Open
Abstract
Demonstrating biosimilarity entails comprehensive analytical assessment, clinical pharmacology profiling, and efficacy testing in patients for at least one medical indication, as required by the U.S. Biologics Price Competition and Innovation Act (BPCIA). The efficacy testing can be waived if the drug has known pharmacodynamic (PD) markers, leaving most therapeutic proteins out of this concession. To overcome this, the FDA suggests that biosimilar developers discover PD biomarkers using omics technologies such as proteomics, glycomics, transcriptomics, genomics, epigenomics, and metabolomics. This approach is redundant since the mode-action-action biomarkers of approved therapeutic proteins are already available, as compiled in this paper for the first time. Other potential biomarkers are receptor binding and pharmacokinetic profiling, which can be made more relevant to ensure biosimilarity without requiring biosimilar developers to conduct extensive research, for which they are rarely qualified.
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Affiliation(s)
- Sarfaraz K Niazi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL 60612, USA
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6
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Parres-Gold J, Levine M, Emert B, Stuart A, Elowitz MB. Principles of Computation by Competitive Protein Dimerization Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564854. [PMID: 37961250 PMCID: PMC10634983 DOI: 10.1101/2023.10.30.564854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Many biological signaling pathways employ proteins that competitively dimerize in diverse combinations. These dimerization networks can perform biochemical computations, in which the concentrations of monomers (inputs) determine the concentrations of dimers (outputs). Despite their prevalence, little is known about the range of input-output computations that dimerization networks can perform (their "expressivity") and how it depends on network size and connectivity. Using a systematic computational approach, we demonstrate that even small dimerization networks (3-6 monomers) are expressive, performing diverse multi-input computations. Further, dimerization networks are versatile, performing different computations when their protein components are expressed at different levels, such as in different cell types. Remarkably, individual networks with random interaction affinities, when large enough (≥8 proteins), can perform nearly all (~90%) potential one-input network computations merely by tuning their monomer expression levels. Thus, even the simple process of competitive dimerization provides a powerful architecture for multi-input, cell-type-specific signal processing.
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Affiliation(s)
- Jacob Parres-Gold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Matthew Levine
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin Emert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrew Stuart
- Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B. Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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7
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Prabantu VM, Tandon H, Sandhya S, Sowdhamini R, Srinivasan N. The alteration of structural network upon transient association between proteins studied using graph theory. Proteins 2023. [PMID: 37902388 DOI: 10.1002/prot.26606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/31/2023] [Accepted: 09/14/2023] [Indexed: 10/31/2023]
Abstract
Proteins such as enzymes perform their function by predominant non-covalent bond interactions between transiently interacting units. There is an impact on the overall structural topology of the protein, albeit transient nature of such interactions, that enable proteins to deactivate or activate. This aspect of the alteration of the structural topology is studied by employing protein structural networks, which are node-edge representative models of protein structure, reported as a robust tool for capturing interactions between residues. Several methods have been optimized to collect meaningful, functionally relevant information by studying alteration of structural networks. In this article, different methods of comparing protein structural networks are employed, along with spectral decomposition of graphs to study the subtle impact of protein-protein interactions. A detailed analysis of the structural network of interacting partners is performed across a dataset of around 900 pairs of bound complexes and corresponding unbound protein structures. The variation in network parameters at, around, and far away from the interface are analyzed. Finally, we present interesting case studies, where an allosteric mechanism of structural impact is understood from communication-path detection methods. The results of this analysis are beneficial in understanding protein stability, for future engineering, and docking studies.
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Affiliation(s)
| | - Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Sankaran Sandhya
- Faculty of Life and Health Sciences, Department of Biotechnology, Ramaiah University of Applied Sciences, Bangalore, India
| | - Ramanathan Sowdhamini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- National Centre for Biological Sciences (TIFR), Bangalore, India
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
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8
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Vallina Estrada E, Zhang N, Wennerström H, Danielsson J, Oliveberg M. Diffusive intracellular interactions: On the role of protein net charge and functional adaptation. Curr Opin Struct Biol 2023; 81:102625. [PMID: 37331204 DOI: 10.1016/j.sbi.2023.102625] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
A striking feature of nucleic acids and lipid membranes is that they all carry net negative charge and so is true for the majority of intracellular proteins. It is suggested that the role of this negative charge is to assure a basal intermolecular repulsion that keeps the cytosolic content suitably 'fluid' for function. We focus in this review on the experimental, theoretical and genetic findings which serve to underpin this idea and the new questions they raise. Unlike the situation in test tubes, any functional protein-protein interaction in the cytosol is subject to competition from the densely crowded background, i.e. surrounding stickiness. At the nonspecific limit of this stickiness is the 'random' protein-protein association, maintaining profuse populations of transient and constantly interconverting complexes at physiological protein concentrations. The phenomenon is readily quantified in studies of the protein rotational diffusion, showing that the more net negatively charged a protein is the less it is retarded by clustering. It is further evident that this dynamic protein-protein interplay is under evolutionary control and finely tuned across organisms to maintain optimal physicochemical conditions for the cellular processes. The emerging picture is then that specific cellular function relies on close competition between numerous weak and strong interactions, and where all parts of the protein surfaces are involved. The outstanding challenge is now to decipher the very basics of this many-body system: how the detailed patterns of charged, polar and hydrophobic side chains not only control protein-protein interactions at close- and long-range but also the collective properties of the cellular interior as a whole.
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Affiliation(s)
- Eloy Vallina Estrada
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Nannan Zhang
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Håkan Wennerström
- Division of Physical Chemistry, Department of Chemistry, Lund University, Box 124, 22100 Lund, Sweden
| | - Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.
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9
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Devkota SR, Aryal P, Pokhrel R, Jiao W, Perry A, Panjikar S, Payne RJ, Wilce MCJ, Bhusal RP, Stone MJ. Engineering broad-spectrum inhibitors of inflammatory chemokines from subclass A3 tick evasins. Nat Commun 2023; 14:4204. [PMID: 37452046 PMCID: PMC10349104 DOI: 10.1038/s41467-023-39879-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
Chemokines are key regulators of leukocyte trafficking and attractive targets for anti-inflammatory therapy. Evasins are chemokine-binding proteins from tick saliva, whose application as anti-inflammatory therapeutics will require manipulation of their chemokine target selectivity. Here we describe subclass A3 evasins, which are unique to the tick genus Amblyomma and distinguished from "classical" class A1 evasins by an additional disulfide bond near the chemokine recognition interface. The A3 evasin EVA-AAM1001 (EVA-A) bound to CC chemokines and inhibited their receptor activation. Unlike A1 evasins, EVA-A was not highly dependent on N- and C-terminal regions to differentiate chemokine targets. Structures of chemokine-bound EVA-A revealed a deep hydrophobic pocket, unique to A3 evasins, that interacts with the residue immediately following the CC motif of the chemokine. Mutations to this pocket altered the chemokine selectivity of EVA-A. Thus, class A3 evasins provide a suitable platform for engineering proteins with applications in research, diagnosis or anti-inflammatory therapy.
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Affiliation(s)
- Shankar Raj Devkota
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Pramod Aryal
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Rina Pokhrel
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, 1142, New Zealand
| | - Andrew Perry
- Monash Bioinformatics Platform, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Santosh Panjikar
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
- Australian Synchrotron, ANSTO, Clayton, VIC, 3168, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Ram Prasad Bhusal
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
| | - Martin J Stone
- Monash Biomedicine Discovery Institute, and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
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10
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Ghose DA, Przydzial KE, Mahoney EM, Keating AE, Laub MT. Marginal specificity in protein interactions constrains evolution of a paralogous family. Proc Natl Acad Sci U S A 2023; 120:e2221163120. [PMID: 37098061 PMCID: PMC10160972 DOI: 10.1073/pnas.2221163120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/24/2023] [Indexed: 04/26/2023] Open
Abstract
The evolution of novel functions in biology relies heavily on gene duplication and divergence, creating large paralogous protein families. Selective pressure to avoid detrimental cross-talk often results in paralogs that exhibit exquisite specificity for their interaction partners. But how robust or sensitive is this specificity to mutation? Here, using deep mutational scanning, we demonstrate that a paralogous family of bacterial signaling proteins exhibits marginal specificity, such that many individual substitutions give rise to substantial cross-talk between normally insulated pathways. Our results indicate that sequence space is locally crowded despite overall sparseness, and we provide evidence that this crowding has constrained the evolution of bacterial signaling proteins. These findings underscore how evolution selects for "good enough" rather than optimized phenotypes, leading to restrictions on the subsequent evolution of paralogs.
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Affiliation(s)
- Dia A. Ghose
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Kaitlyn E. Przydzial
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Emily M. Mahoney
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Koch Center for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
- HHMI, Massachusetts Institute of Technology, Cambridge, MA02139
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11
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Gupta MN, Uversky VN. Moonlighting enzymes: when cellular context defines specificity. Cell Mol Life Sci 2023; 80:130. [PMID: 37093283 PMCID: PMC11073002 DOI: 10.1007/s00018-023-04781-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 04/15/2023] [Indexed: 04/25/2023]
Abstract
It is not often realized that the absolute protein specificity is an exception rather than a rule. Two major kinds of protein multi-specificities are promiscuity and moonlighting. This review discusses the idea of enzyme specificity and then focusses on moonlighting. Some important examples of protein moonlighting, such as crystallins, ceruloplasmin, metallothioniens, macrophage migration inhibitory factor, and enzymes of carbohydrate metabolism are discussed. How protein plasticity and intrinsic disorder enable the removing the distinction between enzymes and other biologically active proteins are outlined. Finally, information on important roles of moonlighting in human diseases is updated.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612-4799, USA.
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12
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Yifrach E, Rudowitz M, Cruz-Zaragoza LD, Tirosh A, Gazi Z, Peleg Y, Kunze M, Eisenstein M, Schliebs W, Schuldiner M, Erdmann R, Zalckvar E. Determining the targeting specificity of the selective peroxisomal targeting factor Pex9. Biol Chem 2023; 404:121-133. [PMID: 36279206 DOI: 10.1515/hsz-2022-0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022]
Abstract
Accurate and regulated protein targeting is crucial for cellular function and proteostasis. In the yeast Saccharomyces cerevisiae, peroxisomal matrix proteins, which harboring a Peroxisomal Targeting Signal 1 (PTS1), can utilize two paralog targeting factors, Pex5 and Pex9, to target correctly. While both proteins are similar and recognize PTS1 signals, Pex9 targets only a subset of Pex5 cargo proteins. However, what defines this substrate selectivity remains uncovered. Here, we used unbiased screens alongside directed experiments to identify the properties underlying Pex9 targeting specificity. We find that the specificity of Pex9 is largely determined by the hydrophobic nature of the amino acid preceding the PTS1 tripeptide of its cargos. This is explained by structural modeling of the PTS1-binding cavities of the two factors showing differences in their surface hydrophobicity. Our work outlines the mechanism by which targeting specificity is achieved, enabling dynamic rewiring of the peroxisomal proteome in changing metabolic needs.
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Affiliation(s)
- Eden Yifrach
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Markus Rudowitz
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Luis Daniel Cruz-Zaragoza
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Asa Tirosh
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Gazi
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Peleg
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain research, Medical University of Vienna, Spitalgasse 4, A-1090 Vienna, Austria
| | - Miriam Eisenstein
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ralf Erdmann
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Einat Zalckvar
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
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13
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SH2 Domains: Folding, Binding and Therapeutical Approaches. Int J Mol Sci 2022; 23:ijms232415944. [PMID: 36555586 PMCID: PMC9783222 DOI: 10.3390/ijms232415944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
SH2 (Src Homology 2) domains are among the best characterized and most studied protein-protein interaction (PPIs) modules able to bind and recognize sequences presenting a phosphorylated tyrosine. This post-translational modification is a key regulator of a plethora of physiological and molecular pathways in the eukaryotic cell, so SH2 domains possess a fundamental role in cell signaling. Consequently, several pathologies arise from the dysregulation of such SH2-domains mediated PPIs. In this review, we recapitulate the current knowledge about the structural, folding stability, and binding properties of SH2 domains and their roles in molecular pathways and pathogenesis. Moreover, we focus attention on the different strategies employed to modulate/inhibit SH2 domains binding. Altogether, the information gathered points to evidence that pharmacological interest in SH2 domains is highly strategic to developing new therapeutics. Moreover, a deeper understanding of the molecular determinants of the thermodynamic stability as well as of the binding properties of SH2 domains appears to be fundamental in order to improve the possibility of preventing their dysregulated interactions.
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14
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Wong A, Bi C, Chi W, Hu N, Gehring C. Amino acid motifs for the identification of novel protein interactants. Comput Struct Biotechnol J 2022; 21:326-334. [PMID: 36582434 PMCID: PMC9791077 DOI: 10.1016/j.csbj.2022.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Biological systems consist of multiple components of different physical and chemical properties that require complex and dynamic regulatory loops to function efficiently. The discovery of ever more novel interacting sites in complex proteins suggests that we are only beginning to understand how cellular and biological functions are integrated and tuned at the molecular and systems levels. Here we review recently discovered interacting sites which have been identified through rationally designed amino acid motifs diagnostic for specific molecular functions, including enzymatic activities and ligand-binding properties. We specifically discuss the nature of the latter using as examples, novel hormone recognition and gas sensing sites that occur in moonlighting protein complexes. Drawing evidence from the current literature, we discuss the potential implications at the cellular, tissue, and/or organismal levels of such non-catalytic interacting sites and provide several promising avenues for the expansion of amino acid motif searches to discover hitherto unknown protein interactants and interaction networks. We believe this knowledge will unearth unexpected functions in both new and well-characterized proteins, thus filling existing conceptual gaps or opening new avenues for applications either as drug targets or tools in pharmacology, cell biology and bio-catalysis. Beyond this, motif searches may also support the design of novel, effective and sustainable approaches to crop improvements and the development of new therapeutics.
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Affiliation(s)
- Aloysius Wong
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chuyun Bi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China,Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province 325060, China,Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Wei Chi
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Ningxin Hu
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province 325060, China
| | - Chris Gehring
- Department of Chemistry, Biology & Biotechnology, University of Perugia, Perugia 06121, Italy,Corresponding author.
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15
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Macquet J, Mounichetty S, Raffaele S. Genetic co-option into plant-filamentous pathogen interactions. TRENDS IN PLANT SCIENCE 2022; 27:1144-1158. [PMID: 35909010 DOI: 10.1016/j.tplants.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/16/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Plants are engaged in a coevolutionary arms race with their pathogens that drives rapid diversification and specialization of genes involved in resistance and virulence. However, some major innovations in plant-pathogen interactions, such as molecular decoys, trans-kingdom RNA interference, two-speed genomes, and receptor networks, evolved through the expansion of the functional landscape of genes. This is a typical outcome of genetic co-option, the evolutionary process by which available genes are recruited into new biological functions. Co-option into plant-pathogen interactions emerges generally from (i) cis-regulatory variation, (ii) horizontal gene transfer (HGT), (iii) mutations altering molecular promiscuity, and (iv) rewiring of gene networks and protein complexes. Understanding these molecular mechanisms is key for the functional and predictive biology of plant-pathogen interactions.
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Affiliation(s)
- Joris Macquet
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Shantala Mounichetty
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France.
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16
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Lázár T, Tantos A, Tompa P, Schad E. Intrinsic protein disorder uncouples affinity from binding specificity. Protein Sci 2022; 31:e4455. [PMID: 36305763 PMCID: PMC9601785 DOI: 10.1002/pro.4455] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins often function by molecular recognition, in which they undergo induced folding. Based on prior generalizations, the idea prevails in the IDP field that due to the entropic penalty of induced folding, the major functional advantage associated with this binding mode is "uncoupling" specificity from binding strength. Nevertheless, both weaker binding and high specificity of IDPs/IDRs rest on limited experimental observations, making these assumptions more speculations than evidence-supported facts. The issue is also complicated by the rather vague concept of specificity that lacks an exact measure, such as the Kd for binding strength. We addressed these issues by creating and analyzing a comprehensive dataset of well-characterized ID/globular protein complexes, for which both the atomic structure of the complex and free energy (ΔG, Kd ) of interaction is known. Through this analysis, we provide evidence that the affinity distributions of IDP/globular and globular/globular complexes show different trends, whereas specificity does not connote to weaker binding strength of IDPs/IDRs. Furthermore, protein disorder extends the spectrum in the direction of very weak interactions, which may have important regulatory consequences and suggest that, in a biological sense, strict correlation of specificity and binding strength are uncoupled by structural disorder.
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Affiliation(s)
- Tamas Lázár
- VIB‐VUB Center for Structural BiologyFlanders Institute for Biotechnology (VIB)BrusselsBelgium,Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
| | - Agnes Tantos
- Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
| | - Peter Tompa
- VIB‐VUB Center for Structural BiologyFlanders Institute for Biotechnology (VIB)BrusselsBelgium,Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium,Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
| | - Eva Schad
- Institute of EnzymologyResearch Centre for Natural SciencesBudapestHungary
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17
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Abstract
Membrane fusion of sperm and eggs is pivotal in sexual reproduction. Tmem95 knockout mice produce sperm that can bind to, but do not fuse with, eggs. How TMEM95 facilitates membrane fusion was unknown. We show here that human TMEM95 binds eggs. Our crystal structure of TMEM95 suggests a region where this binding may occur. We develop monoclonal antibodies against TMEM95 that impair sperm-egg fusion but do not block sperm-egg binding. Thus, we propose that there is a receptor-mediated interaction of sperm TMEM95 with eggs, and that this interaction may have a direct role in membrane fusion. Our work suggests avenues for the identification of the TMEM95 egg receptor and the development of infertility treatments and contraceptives for humans. Tmem95 encodes a sperm acrosomal membrane protein, whose knockout has a male-specific sterility phenotype in mice. Tmem95 knockout murine sperm can bind to, but do not fuse with, eggs. How TMEM95 plays a role in membrane fusion of sperm and eggs has remained elusive. Here, we utilize a sperm penetration assay as a model system to investigate the function of human TMEM95. We show that human TMEM95 binds to hamster egg membranes, providing evidence for a TMEM95 receptor on eggs. Using X-ray crystallography, we reveal an evolutionarily conserved, positively charged region of TMEM95 as a putative receptor-binding surface. Amino acid substitutions within this region of TMEM95 ablate egg-binding activity. We identify monoclonal antibodies against TMEM95 that reduce the number of human sperm fused with hamster eggs in sperm penetration assays. Strikingly, these antibodies do not block binding of sperm to eggs. Taken together, these results provide strong evidence for a specific, receptor-mediated interaction of sperm TMEM95 with eggs and suggest that this interaction may have a role in facilitating membrane fusion during fertilization.
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18
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Moreno MJ, Loura LMS, Martins J, Salvador A, Velazquez-Campoy A. Analysis of the Equilibrium Distribution of Ligands in Heterogeneous Media–Approaches and Pitfalls. Int J Mol Sci 2022; 23:ijms23179757. [PMID: 36077155 PMCID: PMC9478965 DOI: 10.3390/ijms23179757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
The equilibrium distribution of small molecules (ligands) between binding agents in heterogeneous media is an important property that determines their activity. Heterogeneous systems containing proteins and lipid membranes are particularly relevant due to their prevalence in biological systems, and their importance to ligand distribution, which, in turn, is crucial to ligand’s availability and biological activity. In this work, we review several approaches and formalisms for the analysis of the equilibrium distribution of ligands in the presence of proteins, lipid membranes, or both. Special attention is given to common pitfalls in the analysis, with the establishment of the validity limits for the distinct approaches. Due to its widespread use, special attention is given to the characterization of ligand binding through the analysis of Stern–Volmer plots of protein fluorescence quenching. Systems of increasing complexity are considered, from proteins with single to multiple binding sites, from ligands interacting with proteins only to biomembranes containing lipid bilayers and membrane proteins. A new formalism is proposed, in which ligand binding is treated as a partition process, while considering the saturation of protein binding sites. This formalism is particularly useful for the characterization of interaction with membrane proteins.
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Affiliation(s)
- Maria João Moreno
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal
- Correspondence:
| | - Luís M. S. Loura
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Jorge Martins
- Centro de Ciências do Mar (CCMAR/CIMAR, LA) and DCBB-FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Armindo Salvador
- Coimbra Chemistry Center—Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
- CNC—Center for Neuroscience and Cell Biology, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Adrian Velazquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain
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19
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Narasimhan M, Simon R. Spatial range, temporal span, and promiscuity of CLE-RLK signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:906087. [PMID: 36092449 PMCID: PMC9459042 DOI: 10.3389/fpls.2022.906087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) signaling through receptor-like kinases (RLKs) regulates developmental transitions and responses to biotic and abiotic inputs by communicating the physiological state of cells and tissues. CLE peptides have varying signaling ranges, which can be defined as the distance between the source, i.e., the cells or tissue that secrete the peptide, and their destination, i.e., cells or tissue where the RLKs that bind the peptide and/or respond are expressed. Case-by-case analysis substantiates that CLE signaling is predominantly autocrine or paracrine, and rarely endocrine. Furthermore, upon CLE reception, the ensuing signaling responses extend from cellular to tissue, organ and whole organism level as the downstream signal gets amplified. CLE-RLK-mediated effects on tissue proliferation and differentiation, or on subsequent primordia and organ development have been widely studied. However, studying how CLE-RLK regulates different stages of proliferation and differentiation at cellular level can offer additional insights into these processes. Notably, CLE-RLK signaling also mediates diverse non-developmental effects, which are less often observed; however, this could be due to biased experimental approaches. In general, CLEs and RLKs, owing to the sequence or structural similarity, are prone to promiscuous interactions at least under experimental conditions in which they are studied. Importantly, there are regulatory mechanisms that suppress CLE-RLK cross-talk in vivo, thereby eliminating the pressure for co-evolving binding specificity. Alternatively, promiscuity in signaling may also offer evolutionary advantages and enable different CLEs to work in combination to activate or switch off different RLK signaling pathways.
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Affiliation(s)
- Madhumitha Narasimhan
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Rüdiger Simon
- Institute for Developmental Genetics and Cluster of Excellence in Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany
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20
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Vince MJK, Holub JM. Synthesis of Scyllatoxin-Based BH3 Domain Mimetics with Diverse Patterns of Native Disulfide Bonds. Curr Protoc 2022; 2:e526. [PMID: 35994574 DOI: 10.1002/cpz1.526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This article outlines the design and development of scyllatoxin (ScTx)-based BH3 domain mimetics with diverse patterns of native disulfide bonds. More specifically, this method summarizes the total chemical synthesis of ScTx-based peptides that contain zero, one, two, or three disulfide linkages, including techniques to generate variants with any combination of native disulfides. Each peptide reported herein is generated on solid-phase support using microwave-assisted coupling procedures, and all reaction parameters related to the peptide synthesis are described in detail. The various disulfide patterns of the ScTx-based constructs are established during peptide synthesis and are ultimately verified by mass analysis of trypsin-digested fragments. The BH3 domain mimetics developed herein were generated by transposing residues from the helical BH3 domain of the pro-apoptotic BCL2 protein Bax to the α-helix of wild-type ScTx. Interestingly, we found that the relative binding affinities of ScTx-Bax peptides for the anti-apoptotic BCL2 protein Bcl-2 (proper) were heavily influenced by the number and position of disulfide linkages within the ScTx-Bax sequence. As a consequence, we were able to utilize ScTx-Bax BH3 domain mimetics with varied patterns of disulfide bonds to survey how structural rigidity within the helical Bax BH3 domain affects binding to promiscuous anti-apoptotic BCL2 proteins. More broadly, the ability to generate ScTx-based molecules that contain any combination of native disulfide bonds expands the utility of such constructs as tools to study the molecular nature of protein-protein interactions. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Synthesis and characterization of ScTx-based Bax BH3 domain mimetics Basic Protocol 2: Oxidation of ScTx-Bax BH3 domain mimetics containing one, two, or three disulfide linkages Support Protocol: Mapping of disulfide linkages in oxidized ScTx-Bax BH3 domain mimetics.
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Affiliation(s)
- Matthew J K Vince
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio
- Institut für Bioanalytische Chemie, Fakultät für Chemie und Mineralogie, Universität Leipzig, Leipzig, Germany
- Biotechnologisch-Biomedizinisches Zentrum, Universität Leipzig, Leipzig, Germany
| | - Justin M Holub
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio
- Edison Biotechnology Institute, Ohio University, Athens, Ohio
- Molecular and Cellular Biology Program, Ohio University, Athens, Ohio
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21
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Colman DR, Labesse G, Swapna G, Stefanakis J, Montelione GT, Boyd ES, Royer CA. Structural evolution of the ancient enzyme, dissimilatory sulfite reductase. Proteins 2022; 90:1331-1345. [PMID: 35122336 PMCID: PMC9018543 DOI: 10.1002/prot.26315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/29/2022] [Indexed: 07/21/2023]
Abstract
Dissimilatory sulfite reductase is an ancient enzyme that has linked the global sulfur and carbon biogeochemical cycles since at least 3.47 Gya. While much has been learned about the phylogenetic distribution and diversity of DsrAB across environmental gradients, far less is known about the structural changes that occurred to maintain DsrAB function as the enzyme accompanied diversification of sulfate/sulfite reducing organisms (SRO) into new environments. Analyses of available crystal structures of DsrAB from Archaeoglobus fulgidus and Desulfovibrio vulgaris, representing early and late evolving lineages, respectively, show that certain features of DsrAB are structurally conserved, including active siro-heme binding motifs. Whether such structural features are conserved among DsrAB recovered from varied environments, including hot spring environments that host representatives of the earliest evolving SRO lineage (e.g., MV2-Eury), is not known. To begin to overcome these gaps in our understanding of the evolution of DsrAB, structural models from MV2.Eury were generated and evolutionary sequence co-variance analyses were conducted on a curated DsrAB database. Phylogenetically diverse DsrAB harbor many conserved functional residues including those that ligate active siro-heme(s). However, evolutionary co-variance analysis of monomeric DsrAB subunits revealed several False Positive Evolutionary Couplings (FPEC) that correspond to residues that have co-evolved despite being too spatially distant in the monomeric structure to allow for direct contact. One set of FPECs corresponds to residues that form a structural path between the two active siro-heme moieties across the interface between heterodimers, suggesting the potential for allostery or electron transfer within the enzyme complex. Other FPECs correspond to structural loops and gaps that may have been selected to stabilize enzyme function in different environments. These structural bioinformatics results suggest that DsrAB has maintained allosteric communication pathways between subunits as SRO diversified into new environments. The observations outlined here provide a framework for future biochemical and structural analyses of DsrAB to examine potential allosteric control of this enzyme.
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Affiliation(s)
- Daniel R. Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - Gilles Labesse
- Centre de Biochimie Structurale, CNRS UMR 5048, Montpellier, France 34090
| | - G.V.T. Swapna
- Dept of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854 USA
| | | | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
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22
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Melanker O, Goloubinoff P, Schreiber G. In vitro evolution of uracil glycosylase towards DnaKJ and GroEL binding evolves different misfolded states. J Mol Biol 2022; 434:167627. [PMID: 35597550 DOI: 10.1016/j.jmb.2022.167627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
Natural evolution is driven by random mutations that improve fitness. In vitro evolution mimics this process, however, on a short time-scale and is driven by the given bait. Here, we used directed in vitro evolution of a random mutant library of Uracil glycosylase (eUNG) displayed on yeast surface to select for binding to chaperones GroEL, DnaK+DnaJ+ATP (DnaKJ) or E.coli cell extract (CE), using binding to the eUNG inhibitor Ugi as probe for native fold. The CE selected population was further divided to Ugi binders (+U) or non-binders (-U). The aim here was to evaluate the sequence space and physical state of the evolved protein binding the different baits. We found that GroEL, DnaKJ and CE-U select and enrich for mutations causing eUNG to misfold, with the three being enriched in mutations in buried and conserved positions, with a tendency to increase positive charge. Still, each selection had its own trajectory, with GroEL and CE-U selecting mutants highly sensitive to protease cleavage while DnaKJ selected partially structured misfolded species with a tendency to refold, making them less sensitive to proteases. More general, our results show that GroEL has a higher tendency to purge promiscuous misfolded protein mutants from the system, while DnaKJ binds misfolding-prone mutant species that are, upon chaperone release, more likely to natively refold. CE-U shares some of the properties of GroEL- and DnaKJ-selected populations, while harboring also unique properties that can be explained by the presence of additional chaperones in CE, such as Trigger factor, HtpG and ClpB.
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Affiliation(s)
- Oran Melanker
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Lausanne University, 1015 Lausanne, Switzerland
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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23
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Chakrabarti P, Chakravarty D. Intrinsically disordered proteins/regions and insight into their biomolecular interactions. Biophys Chem 2022; 283:106769. [DOI: 10.1016/j.bpc.2022.106769] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
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24
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Engineering the T cell receptor for fun and profit: Uncovering complex biology, interrogating the immune system, and targeting disease. Curr Opin Struct Biol 2022; 74:102358. [PMID: 35344834 DOI: 10.1016/j.sbi.2022.102358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/13/2022] [Accepted: 02/21/2022] [Indexed: 11/21/2022]
Abstract
T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptide antigens bound and presented by major histocompatibility complex (MHC) proteins. Due to the TCR's central role in immunity and tight connection with human health, there has been significant interest in modulating TCR properties through protein engineering methods. Complicating these efforts is the complexity and vast diversity of TCR-peptide/MHC interfaces, the interdependency between TCR affinity, specificity, and cross-reactivity, and the sophisticated relationships between TCR binding properties and T cell function, many aspects of which are not well understood. Here we review TCR engineering, starting with a brief historical overview followed by discussions of more recent developments, including new efforts and opportunities to engineer TCR affinity, modulate specificity, and develop novel TCR-based constructs.
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25
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Kalita J, Kapinos LE, Zheng T, Rencurel C, Zilman A, Lim RYH. Karyopherin enrichment and compensation fortifies the nuclear pore complex against nucleocytoplasmic leakage. J Cell Biol 2022; 221:212986. [PMID: 35089308 PMCID: PMC8932525 DOI: 10.1083/jcb.202108107] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022] Open
Abstract
Nuclear pore complexes (NPCs) discriminate nonspecific macromolecules from importin and exportin receptors, collectively termed “karyopherins” (Kaps), that mediate nucleocytoplasmic transport. This selective barrier function is attributed to the behavior of intrinsically disordered phenylalanine-glycine nucleoporins (FG Nups) that guard the NPC channel. However, NPCs in vivo are typically enriched with different Kaps, and how they impact the NPC barrier remains unknown. Here, we show that two major Kaps, importinβ1/karyopherinβ1 (Kapβ1) and exportin 1/chromosomal maintenance 1 (CRM1), are required to fortify NPC barrier function in vivo. Their enrichment at the NPC is sustained by promiscuous binding interactions with the FG Nups, which enable CRM1 to compensate for the loss of Kapβ1 as a means to maintain NPC barrier function. However, such a compensatory mechanism is constrained by the cellular abundances and different binding kinetics for each respective Kap, as evidenced for importin-5. Consequently, we find that NPC malfunction and nucleocytoplasmic leakage result from poor Kap enrichment.
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Affiliation(s)
- Joanna Kalita
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Tiantian Zheng
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Chantal Rencurel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
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26
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Structure-guided engineering of tick evasins for targeting chemokines in inflammatory diseases. Proc Natl Acad Sci U S A 2022; 119:2122105119. [PMID: 35217625 PMCID: PMC8892493 DOI: 10.1073/pnas.2122105119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 12/13/2022] Open
Abstract
Inflammatory diseases collectively account for numerous deaths and morbidity worldwide. New treatment approaches are needed. A central feature of inflammatory diseases is the recruitment of leukocytes to the affected tissues, which is stimulated by secreted proteins called chemokines. Effective suppression of leukocyte recruitment could be achieved by simultaneously targeting multiple chemokines, a natural molecular strategy used by tick salivary proteins called evasins. Here, we describe the structural and molecular features of a tick evasin that control its ability to bind and block a limited set of chemokines. By modifying these features, we demonstrate that evasins can be engineered to alter the array of chemokines that they target. Thus, this study establishes a structure-based paradigm for the development of antiinflammatory therapeutics. As natural chemokine inhibitors, evasin proteins produced in tick saliva are potential therapeutic agents for numerous inflammatory diseases. Engineering evasins to block the desired chemokines and avoid off-target side effects requires structural understanding of their target selectivity. Structures of the class A evasin EVA-P974 bound to human CC chemokine ligands 7 and 17 (CCL7 and CCL17) and to a CCL8-CCL7 chimera reveal that the specificity of class A evasins for chemokines of the CC subfamily is defined by conserved, rigid backbone–backbone interactions, whereas the preference for a subset of CC chemokines is controlled by side-chain interactions at four hotspots in flexible structural elements. Hotspot mutations alter target preference, enabling inhibition of selected chemokines. The structure of an engineered EVA-P974 bound to CCL2 reveals an underlying molecular mechanism of EVA-P974 target preference. These results provide a structure-based framework for engineering evasins as targeted antiinflammatory therapeutics.
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27
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Structural and evolutionary analysis unveil functional adaptations in the promiscuous behavior of serum albumins. Biochimie 2022; 197:113-120. [DOI: 10.1016/j.biochi.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022]
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Linciano S, Wong EL, Mazzocato Y, Chinellato M, Scaravetti T, Caregnato A, Cacco V, Romanyuk Z, Angelini A. Guidelines, Strategies, and Principles for the Directed Evolution of Cross-Reactive Antibodies Using Yeast Surface Display Technology. Methods Mol Biol 2022; 2491:251-262. [PMID: 35482195 DOI: 10.1007/978-1-0716-2285-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The ability of cross-reactive antibodies to bind multiple related or unrelated targets derived from different species provides not only superior therapeutic efficacy but also a better assessment of treatment toxicity, thereby facilitating the transition from preclinical models to human clinical studies. This chapter provides some guidelines for the directed evolution of cross-reactive antibodies using yeast surface display technology. Cross-reactive antibodies are initially isolated from a naïve library by combining highly avid magnetic bead separations followed by multiple cycles of flow cytometry sorting. Once initial cross-reactive clones are identified, sequential rounds of mutagenesis and two-pressure selection strategies are applied to engineer cross-reactive antibodies with improved affinity and yet retained or superior cross-reactivity.
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Affiliation(s)
- Sara Linciano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ee Lin Wong
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ylenia Mazzocato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Monica Chinellato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
- Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Tiziano Scaravetti
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alberto Caregnato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Veronica Cacco
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Zhanna Romanyuk
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy.
- European Centre for Living Technology (ECLT), Ca' Bottacin, Venice, Italy.
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29
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Pérez de la Lastra JM, Baca-González V, González-Acosta S, Asensio-Calavia P, Otazo-Pérez A, Morales-delaNuez A. Antibodies targeting enzyme inhibition as potential tools for research and drug development. Biomol Concepts 2021; 12:215-232. [PMID: 35104929 DOI: 10.1515/bmc-2021-0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/31/2021] [Indexed: 12/29/2022] Open
Abstract
Antibodies have transformed biomedical research and are now being used for different experimental applications. Generally, the interaction of enzymes with their specific antibodies can lead to a reduction in their enzymatic activity. The effect of the antibody is dependent on its narrow i.e. the regions of the enzyme to which it is directed. The mechanism of this inhibition is rarely a direct combination of the antibodies with the catalytic site, but is rather due to steric hindrance, barring the substrate access to the active site. In several systems, however, the interaction with the antibody induces conformational changes on the enzyme that can either inhibit or enhance its catalytic activity. The extent of enzyme inhibition or enhancement is, therefore, a reflection of the nature and distribution of the various antigenic determinants on the enzyme molecule. Currently, the mode of action of many enzymes has been elucidated at the molecular level. We here review the molecular mechanisms and recent trends by which antibodies inhibit the catalytic activity of enzymes and provide examples of how specific antibodies can be useful for the neutralization of biologically active molecules.
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Affiliation(s)
- José Manuel Pérez de la Lastra
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain
| | - Victoria Baca-González
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain.,Escuela Doctorado y Estudios de Posgrado. Universidad de La Laguna (ULL). C/ Pedro Zerolo, s/n. 38200. San Cristóbal de La Laguna. S/C de Tenerife, Spain
| | - Sergio González-Acosta
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain
| | - Patricia Asensio-Calavia
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain.,Escuela Doctorado y Estudios de Posgrado. Universidad de La Laguna (ULL). C/ Pedro Zerolo, s/n. 38200. San Cristóbal de La Laguna. S/C de Tenerife, Spain
| | - Andrea Otazo-Pérez
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain.,Escuela Doctorado y Estudios de Posgrado. Universidad de La Laguna (ULL). C/ Pedro Zerolo, s/n. 38200. San Cristóbal de La Laguna. S/C de Tenerife, Spain
| | - Antonio Morales-delaNuez
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain
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30
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Hwang T, Parker SS, Hill SM, Ilunga MW, Grant RA, Mouneimne G, Keating AE. A distributed residue network permits conformational binding specificity in a conserved family of actin remodelers. eLife 2021; 10:e70601. [PMID: 34854809 PMCID: PMC8639148 DOI: 10.7554/elife.70601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Metazoan proteomes contain many paralogous proteins that have evolved distinct functions. The Ena/VASP family of actin regulators consists of three members that share an EVH1 interaction domain with a 100 % conserved binding site. A proteome-wide screen revealed photoreceptor cilium actin regulator (PCARE) as a high-affinity ligand for ENAH EVH1. Here, we report the surprising observation that PCARE is ~100-fold specific for ENAH over paralogs VASP and EVL and can selectively bind ENAH and inhibit ENAH-dependent adhesion in cells. Specificity arises from a mechanism whereby PCARE stabilizes a conformation of the ENAH EVH1 domain that is inaccessible to family members VASP and EVL. Structure-based modeling rapidly identified seven residues distributed throughout EVL that are sufficient to differentiate binding by ENAH vs. EVL. By exploiting the ENAH-specific conformation, we rationally designed the tightest and most selective ENAH binder to date. Our work uncovers a conformational mechanism of interaction specificity that distinguishes highly similar paralogs and establishes tools for dissecting specific Ena/VASP functions in processes including cancer cell invasion.
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Affiliation(s)
- Theresa Hwang
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Sara S Parker
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of ArizonaTucsonUnited States
| | - Samantha M Hill
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of ArizonaTucsonUnited States
| | - Meucci W Ilunga
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ghassan Mouneimne
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of ArizonaTucsonUnited States
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering and Koch Institue for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
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31
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Kröger P, Shanmugaratnam S, Scheib U, Höcker B. Fine-tuning spermidine binding modes in the putrescine binding protein PotF. J Biol Chem 2021; 297:101419. [PMID: 34801550 PMCID: PMC8666671 DOI: 10.1016/j.jbc.2021.101419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/09/2022] Open
Abstract
A profound understanding of the molecular interactions between receptors and ligands is important throughout diverse research, such as protein design, drug discovery, or neuroscience. What determines specificity and how do proteins discriminate against similar ligands? In this study, we analyzed factors that determine binding in two homologs belonging to the well-known superfamily of periplasmic binding proteins, PotF and PotD. Building on a previously designed construct, modes of polyamine binding were swapped. This change of specificity was approached by analyzing local differences in the binding pocket as well as overall conformational changes in the protein. Throughout the study, protein variants were generated and characterized structurally and thermodynamically, leading to a specificity swap and improvement in affinity. This dataset not only enriches our knowledge applicable to rational protein design but also our results can further lay groundwork for engineering of specific biosensors as well as help to explain the adaptability of pathogenic bacteria.
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Affiliation(s)
- Pascal Kröger
- Department for Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Sooruban Shanmugaratnam
- Department for Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ulrike Scheib
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Birte Höcker
- Department for Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany.
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32
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Gaspar VP, Ibrahim S, Zahedi RP, Borchers CH. Utility, promise, and limitations of liquid chromatography-mass spectrometry-based therapeutic drug monitoring in precision medicine. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4788. [PMID: 34738286 PMCID: PMC8597589 DOI: 10.1002/jms.4788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 05/03/2023]
Abstract
Therapeutic drug monitoring (TDM) is typically referred to as the measurement of the concentration of drugs in patient blood. Although in the past, TDM was restricted to drugs with a narrow therapeutic range in order to avoid drug toxicity, TDM has recently become a major tool for precision medicine being applied to many more drugs. Through compensating for interindividual differences in a drug's pharmacokinetics, improved dosing of individual patients based on TDM ensures maximum drug effectiveness while minimizing side effects. This is especially relevant for individuals that present a particularly high intervariability in pharmacokinetics, such as newborns, or for critically/severely ill patients. In this article, we will review the applications for and limitations of TDM, discuss for which patients TDM is most beneficial and why, examine which techniques are being used for TDM, and demonstrate how mass spectrometry is increasingly becoming a reliable and convenient alternative for the TDM of different classes of drugs. We will also highlight the advances, challenges, and limitations of the existing repertoire of TDM methods and discuss future opportunities for TDM-based precision medicine.
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Affiliation(s)
- Vanessa P. Gaspar
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
| | - Sahar Ibrahim
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Division of Experimental MedicineMcGill UniversityMontrealQuebecCanada
- Clinical Pathology DepartmentMenoufia UniversityShibin el KomEgypt
| | - René P. Zahedi
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscowRussia
| | - Christoph H. Borchers
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscowRussia
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33
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Adegawa S, Yamaguchi N, Sato R. The base and root of domain II loops of Cry toxins contribute to binding to Bombyx mori ABC transporter C2. FEBS J 2021; 289:965-984. [PMID: 34618400 DOI: 10.1111/febs.16224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/28/2021] [Accepted: 10/06/2021] [Indexed: 01/17/2023]
Abstract
Little information is available regarding the region of Cry toxins involved in binding to their major receptors, the ATP-binding cassette (ABC) transporters. We analyzed which Cry1Aa amino acid residues contribute to binding to Bombyx mori ABC transporter C2 (BmABCC2). Several two oxidized double-cysteine substitution mutant toxins were made. In these, two amino acids at distant positions on toxin loop α8 and loop 2 or loop 2 and loop 3 were substituted with cysteine residues and crosslinked. These mutants exhibited a marked reduction in binding affinity to BmABCC2, suggesting that the binding site comprises complex cavities formed by loops α8, 2, and 3. Loop swapping between Cry1Aa and other BmABCC2-incompatible toxins indicated that loop 2 acts as a binding affinity-generating part of Cry1Aa toxin. Using single amino acid substitution mutants, the results of surface plasmon resonance (SPR) analysis and response assays with BmABCC2-expressing Sf9 cells indicated that Y366, R367, R368, and L447 in the Cry1Aa root and base region of loops 2 and 3 play important roles in binding. Furthermore, SPR analyses of these mutants suggested that a two-state binding model fits best the data obtained. Moreover, complex cavities and the above-mentioned amino acid residues contribute to the generation of multiple binding points and high-affinity binding. Finally, we found that the binding site of B. mori cadherin-like protein consists of complex cavities comprising loops 1, 2, and 3, partially overlapping that of BmABCC2, suggesting that the loop region of Cry1Aa toxin acts as a promiscuous binding site.
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Affiliation(s)
- Satomi Adegawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan.,Japan Society for the Promotion of Science Research Fellowship for Young Scientists, Chiyoda, Japan
| | - Naomi Yamaguchi
- Tokyo University of Agriculture and Technology, Koganei, Japan
| | - Ryoichi Sato
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan
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34
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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35
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Khazaee M, Christie E, Cheng W, Michalsen M, Field J, Ng C. Perfluoroalkyl Acid Binding with Peroxisome Proliferator-Activated Receptors α, γ, and δ, and Fatty Acid Binding Proteins by Equilibrium Dialysis with a Comparison of Methods. TOXICS 2021; 9:45. [PMID: 33652875 PMCID: PMC7996760 DOI: 10.3390/toxics9030045] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/13/2021] [Accepted: 02/19/2021] [Indexed: 01/09/2023]
Abstract
The biological impacts of per- and polyfluorinated alkyl substances (PFAS) are linked to their protein interactions. Existing research has largely focused on serum albumin and liver fatty acid binding protein, and binding affinities determined with a variety of methods show high variability. Moreover, few data exist for short-chain PFAS, though their prevalence in the environment is increasing. We used molecular dynamics (MD) to screen PFAS binding to liver and intestinal fatty acid binding proteins (L- and I-FABPs) and peroxisome proliferator activated nuclear receptors (PPAR-α, -δ and -γ) with six perfluoroalkyl carboxylates (PFCAs) and three perfluoroalkyl sulfonates (PFSAs). Equilibrium dissociation constants, KDs, were experimentally determined via equilibrium dialysis (EqD) with liquid chromatography tandem mass spectrometry for protein-PFAS pairs. A comparison was made between KDs derived from EqD, both here and in literature, and other in vitro approaches (e.g., fluorescence) from literature. EqD indicated strong binding between PPAR-δ and perfluorobutanoate (0.044 ± 0.013 µM) and perfluorohexane sulfonate (0.035 ± 0.0020 µM), and between PPAR-α and perfluorohexanoate (0.097 ± 0.070 µM). Unlike binding affinities for L-FABP, which increase with chain length, KDs for PPARs showed little chain length dependence by either MD simulation or EqD. Compared with other in vitro approaches, EqD-based KDs consistently indicated higher affinity across different proteins. This is the first study to report PPARs binding with short-chain PFAS with KDs in the sub-micromolar range.
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Affiliation(s)
- Manoochehr Khazaee
- Department of Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; (M.K.); (W.C.)
| | - Emerson Christie
- Department of Molecular and Environmental Toxicology, Oregon State University, Corvallis, OR 97330, USA; (E.C.); (J.F.)
| | - Weixiao Cheng
- Department of Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; (M.K.); (W.C.)
| | - Mandy Michalsen
- U.S. Army Engineer Research Development Center—Environmental Lab, Vicksburg, MS 39180, USA;
| | - Jennifer Field
- Department of Molecular and Environmental Toxicology, Oregon State University, Corvallis, OR 97330, USA; (E.C.); (J.F.)
| | - Carla Ng
- Department of Civil & Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; (M.K.); (W.C.)
- Secondary Appointment, Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
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36
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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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37
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Bertolini M, Fenzl K, Kats I, Wruck F, Tippmann F, Schmitt J, Auburger JJ, Tans S, Bukau B, Kramer G. Interactions between nascent proteins translated by adjacent ribosomes drive homomer assembly. Science 2021; 371:57-64. [PMID: 33384371 DOI: 10.1126/science.abc7151] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/27/2020] [Indexed: 12/13/2022]
Abstract
Accurate assembly of newly synthesized proteins into functional oligomers is crucial for cell activity. In this study, we investigated whether direct interaction of two nascent proteins, emerging from nearby ribosomes (co-co assembly), constitutes a general mechanism for oligomer formation. We used proteome-wide screening to detect nascent chain-connected ribosome pairs and identified hundreds of homomer subunits that co-co assemble in human cells. Interactions are mediated by five major domain classes, among which N-terminal coiled coils are the most prevalent. We were able to reconstitute co-co assembly of nuclear lamin in Escherichia coli, demonstrating that dimer formation is independent of dedicated assembly machineries. Co-co assembly may thus represent an efficient way to limit protein aggregation risks posed by diffusion-driven assembly routes and ensure isoform-specific homomer formation.
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Affiliation(s)
- Matilde Bertolini
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Kai Fenzl
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Ilia Kats
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Florian Wruck
- AMOLF, Science Park 104, 1098 XG Amsterdam, Netherlands
| | - Frank Tippmann
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Jaro Schmitt
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Josef Johannes Auburger
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Sander Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, Netherlands.,Department of Bionanoscience, Delft University of Technology and Kavli Institute of Nanoscience Delft, 2629HZ Delft, Netherlands
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.
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38
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Perez-Borrajero C, Heinkel F, Gsponer J, McIntosh LP. Conformational Plasticity and DNA-Binding Specificity of the Eukaryotic Transcription Factor Pax5. Biochemistry 2021; 60:104-117. [PMID: 33398994 DOI: 10.1021/acs.biochem.0c00737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The eukaryotic transcription factor Pax5 has a DNA-binding Paired domain composed of two independent helical bundle subdomains joined by a flexible linker. Previously, we showed distinct biophysical properties of the N-terminal (NTD) and C-terminal (CTD) subdomains, with implications for how these two regions cooperate to distinguish nonspecific and cognate DNA sites [Perez-Borrajero, C., et al. (2016) J. Mol. Biol. 428, 2372-2391]. In this study, we combined experimental methods and molecular dynamics (MD) simulations to dissect the mechanisms underlying the functional differences between the Pax5 subdomains. Both subdomains showed a similar dependence of DNA-binding affinity on ionic strength. However, due to a greater contribution of non-ionic interactions, the NTD bound its cognate DNA half-site with an affinity approximately 10-fold higher than that of the CTD with its half-site. These interactions involve base-mediated contacts as evidenced by nuclear magnetic resonance spectroscopy-monitored chemical shift perturbations. Isothermal titration calorimetry revealed that favorable enthalpic and compensating unfavorable entropic changes were substantially larger for DNA binding by the NTD than by the CTD. Complementary MD simulations indicated that the DNA recognition helix H3 of the NTD is particularly flexible in the absence of DNA and undergoes the largest changes in conformational dynamics upon binding. Overall, these data suggest that the differences observed for the subdomains of Pax5 are due to the coupling of DNA binding with dampening of motions in the NTD required for specific base contacts. Thus, the conformational plasticity of the Pax5 Paired domain underpins the differing roles of its subdomains in association with nonspecific versus cognate DNA sites.
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Affiliation(s)
- Cecilia Perez-Borrajero
- Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Florian Heinkel
- Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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39
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Kröger P, Shanmugaratnam S, Ferruz N, Schweimer K, Höcker B. A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF. Structure 2021; 29:433-443.e4. [PMID: 33406388 DOI: 10.1016/j.str.2020.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/28/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022]
Abstract
Periplasmic binding proteins (PBPs) are ubiquitous receptors in gram-negative bacteria. They sense solutes and play key roles in nutrient uptake. Escherichia coli's putrescine receptor PotF has been reported to bind putrescine and spermidine. We reveal that several similar biogenic polyamines are recognized by PotF. Using isothermal titration calorimetry paired with X-ray crystallography of the different complexes, we unveil PotF's binding modes in detail. The binding site for PBPs is located between two lobes that undergo a large conformational change upon ligand recognition. Hence, analyzing the influence of ligands on complex formation is crucial. Therefore, we solved crystal structures of an open and closed apo state and used them as a basis for molecular dynamics simulations. In addition, we accessed structural behavior in solution for all complexes by 1H-15N HSQC NMR spectroscopy. This combined analysis provides a robust framework for understanding ligand binding for future developments in drug design and protein engineering.
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Affiliation(s)
- Pascal Kröger
- Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Sooruban Shanmugaratnam
- Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Kristian Schweimer
- Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany; Northern Bavarian NMR Center, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany.
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40
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Abstract
Over the past decades, peptide-based drugs have gained increasing interest in a wide range of treatment applications, primarily because of high potency and selectivity, as well as good efficacy, tolerability, and safety often achieved with peptides. Attempts to target postsynaptic density protein of 95 (PSD-95) PSD-95/Discs large/Zonula occludens-1 (PDZ) domains, which mediate the formation of a ternary complex with the N-methyl-D-aspartate (NMDA) receptor and neuronal nitric oxide synthase (nNOS) responsible for excitotoxicity in ischemic stroke, by high-affinity small molecules have failed in the past. In this chapter, we focus on the discovery of peptide-based drugs targeting PSD-95, using AVLX-144 as an example, from the synthesis, over binding assays to its target, to further in vitro experiments based on the development of AVLX-144, a potential stroke treatment, which is planned to enter clinical trials in 2020.
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Affiliation(s)
- Dominik J Essig
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk A/S, Research Chemistry 3, Måløv, Denmark
| | - Javier R Balboa
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk A/S, Research Chemistry 3, Måløv, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark.
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41
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Shin G, Lim SI. Site-specific proximity ligation provides molecular insights into biologically relevant interfaces of protein-protein interaction. Biochem Biophys Res Commun 2020; 533:932-937. [PMID: 33008597 DOI: 10.1016/j.bbrc.2020.09.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 11/30/2022]
Abstract
Dynamic protein-protein interactions (PPIs) are fundamental to spatiotemporal control of protein functions in biological systems. Dissecting binding interfaces in aqueous solution (i.e., biological interfaces) is of great importance for identifying molecular determinants that contribute to the affinity and specificity of PPIs. Herein, we describe a biochemical method, termed site-specific proximity ligation (SPL), that enables the identification and reconstruction of native binding interfaces distinct from those present in crystal structures and models from computational prediction. SPL involves the strategic incorporation of an aryl azide-containing unnatural amino acid (AZF) into residues of interest in a particular protein that forms a multiprotein complex. Depending on the interfacial role of a targeted residue, a photo-inducible highly reactive incorporated AZF moiety may react with neighboring functional groups to covalently capture an otherwise non-covalent or weak interaction with a specific partner protein, thereby revealing the landscape of biological interfaces. Using a heterotrimeric nuclear pore protein as a model, we show that the biological interfaces of the complex mapped by SPL provide new insight into dynamic molecular recognition that is missed by, or even in conflict with, static models.
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Affiliation(s)
- Goeun Shin
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea.
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42
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Tandon H, de Brevern AG, Srinivasan N. Transient association between proteins elicits alteration of dynamics at sites far away from interfaces. Structure 2020; 29:371-384.e3. [PMID: 33306961 DOI: 10.1016/j.str.2020.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
Proteins are known to undergo structural changes upon binding to partner proteins. However, the prevalence, extent, location, and function of change in protein dynamics due to transient protein-protein interactions is not well documented. Here, we have analyzed a dataset of 58 protein-protein complexes of known three-dimensional structure and structures of their corresponding unbound forms to evaluate dynamics changes induced by binding. Fifty-five percent of cases showed significant dynamics change away from the interfaces. This change is not always accompanied by an observed structural change. Binding of protein partner is found to alter inter-residue communication within the tertiary structure in about 90% of cases. Also, residue motions accessible to proteins in unbound form were not always maintained in the bound form. Further analyses revealed functional roles for the distant site where dynamics change was observed. Overall, the results presented here strongly suggest that alteration of protein dynamics due to binding of a partner protein commonly occurs.
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Affiliation(s)
- Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, 75739 Paris, France; Univ Paris, UMR_S 1134, 75739 Paris, France; Institut National de la Transfusion Sanguine (INTS), 75739 Paris, France; Laboratoire d'Excellence GR-Ex, 75739 Paris, France
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43
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Hertle R, Nazet J, Semmelmann F, Schlee S, Funke F, Merkl R, Sterner R. Reprogramming the Specificity of a Protein Interface by Computational and Data-Driven Design. Structure 2020; 29:292-304.e3. [PMID: 33296666 DOI: 10.1016/j.str.2020.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/21/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
The formation of specific protein complexes in a cell is a non-trivial problem given the co-existence of thousands of different polypeptide chains. A particularly difficult case are two glutamine amidotransferase complexes (anthranilate synthase [AS] and aminodeoxychorismate synthase [ADCS]), which are composed of homologous pairs of synthase and glutaminase subunits. We have attempted to identify discriminating interface residues of the glutaminase subunit TrpG from AS, which are responsible for its specific interaction with the synthase subunit TrpEx and prevent binding to the closely related synthase subunit PabB from ADCS. For this purpose, TrpG-specific interface residues were grafted into the glutaminase subunit PabA from ADCS by two different approaches, namely a computational and a data-driven one. Both approaches resulted in PabA variants that bound TrpEx with higher affinity than PabB. Hence, we have accomplished a reprogramming of protein-protein interaction specificity that provides insights into the evolutionary adaptation of protein interfaces.
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Affiliation(s)
- Regina Hertle
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Julian Nazet
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Florian Semmelmann
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Franziska Funke
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany.
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93040 Regensburg, Germany.
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44
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Naderi S, Roshan R, Ghaderi H, Behdani M, Mahmoudi S, Habibi-Anbouhi M, Shokrgozar MA, Kazemi-Lomedasht F. Selection and characterization of specific nanobody against neuropilin-1 for inhibition of angiogenesis. Mol Immunol 2020; 128:56-63. [DOI: 10.1016/j.molimm.2020.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 07/08/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
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45
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Pechmann S. Programmed Trade-offs in Protein Folding Networks. Structure 2020; 28:1361-1375.e4. [PMID: 33053320 DOI: 10.1016/j.str.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/25/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
Molecular chaperones as specialized protein quality control enzymes form the core of cellular protein homeostasis. How chaperones selectively interact with their substrate proteins thus allocate their overall limited capacity remains poorly understood. Here, I present an integrated analysis of sequence and structural determinants that define interactions of protein domains as the basic protein folding unit with the Saccharomyces cerevisiae Hsp70 Ssb. Structural homologs of single-domain proteins that differentially interact with Ssb for de novo folding were found to systematically differ in complexity of their folding landscapes, selective use of nonoptimal codons, and presence of short discriminative sequences, thus highlighting pervasive trade-offs in chaperone-assisted protein folding landscapes. However, short discriminative sequences were found to contribute by far the strongest signal toward explaining Ssb interactions. This observation suggested that some chaperone interactions may be directly programmed in the amino acid sequences rather than responding to folding challenges, possibly for regulatory advantages.
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Affiliation(s)
- Sebastian Pechmann
- Département de biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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46
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Abstract
A key functional event in eukaryotic gene activation is the formation of dynamic protein-protein interaction networks between transcriptional activators and transcriptional coactivators. Seemingly incongruent with the tight regulation of transcription, many biochemical and biophysical studies suggest that activators use nonspecific hydrophobic and/or electrostatic interactions to bind to coactivators, with few if any specific contacts. Here a mechanistic dissection of a set of representative dynamic activator•coactivator complexes, comprised of the ETV/PEA3 family of activators and the coactivator Med25, reveals a different molecular recognition model. The data demonstrate that small sequence variations within an activator family significantly redistribute the conformational ensemble of the complex while not affecting overall affinity, and distal residues within the activator-not often considered as contributing to binding-play a key role in mediating conformational redistribution. The ETV/PEA3•Med25 ensembles are directed by specific contacts between the disordered activator and the Med25 interface, which is facilitated by structural shifts of the coactivator binding surface. Taken together, these data highlight the critical role coactivator plasticity plays in recognition of disordered activators and indicate that molecular recognition models of disordered proteins must consider the ability of the binding partners to mediate specificity.
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47
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Lite TLV, Grant RA, Nocedal I, Littlehale ML, Guo MS, Laub MT. Uncovering the basis of protein-protein interaction specificity with a combinatorially complete library. eLife 2020; 9:e60924. [PMID: 33107822 PMCID: PMC7669267 DOI: 10.7554/elife.60924] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/26/2020] [Indexed: 12/27/2022] Open
Abstract
Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence degeneracy, and epistasis. Using bacterial toxin-antitoxin systems as a model, we screened a combinatorially complete library of antitoxin variants at three key positions against two toxins. This library enabled us to measure the effect of individual substitutions on specificity in hundreds of genetic backgrounds. These distributions allow inferences about the general nature of interface residues in promoting specificity. We find that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, a wild-type antitoxin appears optimized for specificity as no substitutions improve discrimination between cognate and non-cognate partners. By comparing crystal structures of paralogous complexes, we provide a rationale for our observations. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition.
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Affiliation(s)
- Thuy-Lan V Lite
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Robert A Grant
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Isabel Nocedal
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Megan L Littlehale
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Monica S Guo
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
| | - Michael T Laub
- Department of Biology Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute Massachusetts Institute of TechnologyCambridgeUnited States
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48
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Blay V, Otero-Muras I, Annis DA. Solving the Competitive Binding Equilibria between Many Ligands: Application to High-Throughput Screening and Affinity Optimization. Anal Chem 2020; 92:12630-12638. [PMID: 32812419 DOI: 10.1021/acs.analchem.0c02715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Modern small-molecule drug discovery relies on the selective targeting of biological macromolecules by low-molecular weight compounds. Therefore, the binding affinities of candidate drugs to their targets are key for pharmacological activity and clinical use. For drug discovery methods where multiple drug candidates can simultaneously bind to the same target, a competition is established, and the resulting equilibrium depends on the dissociation constants and concentration of all the species present. Such coupling between all equilibrium-governing parameters complicates analysis and development of improved mixture-based, high-throughput drug discovery techniques. In this work, we present an iterative computational algorithm to solve coupled equilibria between an arbitrary number of ligands and a biomolecular target that is efficient and robust. The algorithm does not require the estimation of initial values to rapidly converge to the solution of interest. We explored binding equilibria under ligand/receptor conditions used in mixture-based library screening by affinity selection-mass spectrometry (AS-MS). Our studies support a facile method for affinity-ranking hits. The ranking method involves varying the receptor-to-ligand concentration ratio in a pool of candidate ligands in two sequential AS-MS analyses. The ranking is based on the relative change in bound ligand concentration. The method proposed does not require a known reference ligand and produces a ranking that is insensitive to variations in the concentration of individual compounds, thereby enabling the use of unpurified compounds generated by mixture-based combinatorial synthesis techniques.
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Affiliation(s)
- Vincent Blay
- Division of Biomaterials and Bioengineering, University of California San Francisco, San Francisco, California 94143, United States
| | - Irene Otero-Muras
- BioProcess Engineering Group, IIM-CSIC, Spanish National Research Council, Vigo 36208, Spain
| | - David Allen Annis
- Aileron Therapeutics, Inc., 490 Arsenal Way, Watertown, Massachusetts 02472, United States
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49
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Arslan M, Karadag D, Kalyoncu S. Conformational changes in a Vernier zone region: Implications for antibody dual specificity. Proteins 2020; 88:1447-1457. [PMID: 32526069 DOI: 10.1002/prot.25964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/23/2020] [Accepted: 06/06/2020] [Indexed: 11/07/2022]
Abstract
Understanding the determinants of antibody specificity is one of the challenging tasks in antibody development. Monospecific antibodies are still dominant in approved antibody therapeutics but there is a significant body of work to show that multispecific antibodies can increase the overall therapeutic effect. Dual-specific or "Two-in-One" antibodies can bind to two different antigens separately with the same antigen-binding site as opposed to bispecifics, which simultaneously bind to two different antigens through separate antigen-binding units. These nonstandard dual-specific antibodies were recently shown to be promising for new antibody-based therapeutics. Here, we physicochemically and structurally analyzed six different antibodies of which two are monospecific and four are dual-specific antibodies derived from monospecific templates to gain insight about dual-specificity determinants. These dual-specific antibodies can target both human epidermal growth factor receptor 2 and vascular endothelial growth factor at different binding affinities. We showed that a particular region of clustered Vernier zone residues might play key roles in gaining dual specificity. While there are minimal intramolecular interactions between a certain Vernier zone region, namely LV4 and LCDR1 of monospecific template, there is a significant structural change and consequently close contact formation between LV4-LCDR1 loops of derived dual-specific antibodies. Although Vernier zone residues were previously shown to be important for humanization applications, they are mostly underestimated in the literature. Here, we also aim to resurrect Vernier zone residues for antibody engineering efforts.
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Affiliation(s)
- Merve Arslan
- Izmir Biomedicine and Genome Center, Izmir, Turkey.,Izmir Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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50
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Blundell TL, Gupta MN, Hasnain SE. Intrinsic disorder in proteins: Relevance to protein assemblies, drug design and host-pathogen interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 156:34-42. [PMID: 32628954 DOI: 10.1016/j.pbiomolbio.2020.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
Intrinsic disorder in proteins resulting in considerable variation in structure can lead to multiple functions including multi-specificity and diverse pathologies. Protein interfaces can involve disordered regions that assemble through a concerted-fold-and-bind mechanism. The binding involves both enthalpic and entropic gains by exploiting 'hot spots' on the partner and displacing water molecules placed in thermodynamically unfavorable situations. The examples of Rad51-BRCA2 and Artemis-DNA-PKCs/LigIV complexes illustrate this in the context of drug design. This overview tracks the seamless involvement of protein disorder in multi-specificity of biocatalysts, protein assembly formations and host-pathogen interactions, where intrinsic disorder can in Mycobacteria, compensate for genome reduction by carrying out multiple functions and in some RNA viruses facilitate adaption to the host. These present challenging opportunities for designing new drugs and interventions.
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Affiliation(s)
- Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
| | - Munishwar N Gupta
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Seyed E Hasnain
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Prof C.R. Rao Road, Hyderabad, India.
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