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Kimura Y, Kawai-Noma S, Saito K, Umeno D. Directed Evolution of the Stringency of the LuxR Vibrio fischeri Quorum Sensor without OFF-State Selection. ACS Synth Biol 2020; 9:567-575. [PMID: 31999435 DOI: 10.1021/acssynbio.9b00444] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Stringency (low leak) is one of the most important specifications required for genetic circuits and induction systems, but it is challenging to evolve without sacrificing the maximum output level. This problem also comes from the absence of truly tunable negative selection methods. This paper reports that stringently switching variants can sometimes emerge with surprising frequency upon mutations. We randomly mutated the previously generated leaky variants of LuxR, the quorum-sensing transcription activator from Vibrio fischeri, to restore the stringency. We found as much as 10-20% of the entire population exhibited significantly improved signal-to-noise ratios compared with their parents. This indicated that these mutants arose by the loss of folding capability by accumulating destabilizing mutations, not by introducing rare adaptive mutations, thereby becoming AHL-dependent folders. Only four rounds of mutagenesis and ON-state selection resulted in the domination of the entire population by the improved variants with low leak, without direct selection pressure for stringency. With this surprising frequency, conversion into the "ligand-addicted folders" should be one of the prevailing modes of evolving stringency both in the laboratory and in nature, and the workflow described here provides a rapid and versatile method of improving the signal-to-noise ratio of various genetic switches.
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Affiliation(s)
- Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
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2
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Farías-Rico JA, Ruud Selin F, Myronidi I, Frühauf M, von Heijne G. Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome. Proc Natl Acad Sci U S A 2018; 115:E9280-E9287. [PMID: 30224455 PMCID: PMC6176590 DOI: 10.1073/pnas.1812756115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
During the last five decades, studies of protein folding in dilute buffer solutions have produced a rich picture of this complex process. In the cell, however, proteins can start to fold while still attached to the ribosome (cotranslational folding) and it is not yet clear how the ribosome affects the folding of protein domains of different sizes, thermodynamic stabilities, and net charges. Here, by using arrest peptides as force sensors and on-ribosome pulse proteolysis, we provide a comprehensive picture of how the distance from the peptidyl transferase center in the ribosome at which proteins fold correlates with protein size. Moreover, an analysis of a large collection of mutants of the Escherichia coli ribosomal protein S6 shows that the force exerted on the nascent chain by protein folding varies linearly with the thermodynamic stability of the folded state, and that the ribosome environment disfavors folding of domains of high net-negative charge.
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Affiliation(s)
| | - Frida Ruud Selin
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ioanna Myronidi
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marie Frühauf
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
- Science for Life Laboratory, Stockholm University, SE-171 21 Solna, Sweden
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3
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Kabir A, Honda RP, Kamatari YO, Endo S, Fukuoka M, Kuwata K. Effects of ligand binding on the stability of aldo-keto reductases: Implications for stabilizer or destabilizer chaperones. Protein Sci 2016; 25:2132-2141. [PMID: 27595938 PMCID: PMC5119574 DOI: 10.1002/pro.3036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/30/2016] [Indexed: 01/26/2023]
Abstract
Ligands such as enzyme inhibitors stabilize the native conformation of a protein upon binding to the native state, but some compounds destabilize the native conformation upon binding to the non-native state. The former ligands are termed "stabilizer chaperones" and the latter ones "destabilizer chaperones." Because the stabilization effects are essential for the medical chaperone (MC) hypothesis, here we have formulated a thermodynamic system consisting of a ligand and a protein in its native- and non-native state. Using the differential scanning fluorimetry and the circular dichroism varying the urea concentration and temperature, we found that when the coenzyme NADP+ was absent, inhibitors such as isolithocholic acid stabilized the aldo-keto reductase AKR1A1 upon binding, which showed actually the three-state folding, but destabilized AKR1B10. In contrast, in the presence of NADP+ , they destabilized AKR1A1 and stabilized AKR1B10. To explain these phenomena, we decomposed the free energy of stabilization (ΔΔG) into its enthalpy (ΔΔH) and entropy (ΔΔS) components. Then we found that in a relatively unstable protein showing the three-state folding, native conformation was stabilized by the negative ΔΔH in association with the negative ΔΔS, suggesting that the stabilizer chaperon decreases the conformational fluctuation of the target protein or increase its hydration. However, in other cases, ΔΔG was essentially determined by the delicate balance between ΔΔH and ΔΔS. The proposed thermodynamic formalism is applicable to the system including multiple ligands with allosteric interactions. These findings would promote the development of screening strategies for MCs to regulate the target conformations.
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Affiliation(s)
- Aurangazeb Kabir
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
| | - Ryo P. Honda
- Department of Molecular Pathobiochemistry, Graduate School of MedicineGifu UniversityGifu501‐1193Japan
| | | | - Satoshi Endo
- Laboratory of BiochemistryGifu Pharmaceutical UniversityGifu501‐1196Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information SciencesGifu UniversityGifu501‐1193Japan
- Department of Gene and Development, Graduate School of MedicineGifu UniversityGifu501‐1193Japan
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4
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Rodríguez Plaza JG, Villalón Rojas A, Herrera S, Garza-Ramos G, Torres Larios A, Amero C, Zarraga Granados G, Gutiérrez Aguilar M, Lara Ortiz MT, Polanco Gonzalez C, Uribe Carvajal S, Coria R, Peña Díaz A, Bredesen DE, Castro-Obregon S, del Rio G. Moonlighting peptides with emerging function. PLoS One 2012; 7:e40125. [PMID: 22808104 PMCID: PMC3396687 DOI: 10.1371/journal.pone.0040125] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 06/01/2012] [Indexed: 12/20/2022] Open
Abstract
Hunter-killer peptides combine two activities in a single polypeptide that work in an independent fashion like many other multi-functional, multi-domain proteins. We hypothesize that emergent functions may result from the combination of two or more activities in a single protein domain and that could be a mechanism selected in nature to form moonlighting proteins. We designed moonlighting peptides using the two mechanisms proposed to be involved in the evolution of such molecules (i.e., to mutate non-functional residues and the use of natively unfolded peptides). We observed that our moonlighting peptides exhibited two activities that together rendered a new function that induces cell death in yeast. Thus, we propose that moonlighting in proteins promotes emergent properties providing a further level of complexity in living organisms so far unappreciated.
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Affiliation(s)
- Jonathan G. Rodríguez Plaza
- Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - Amanda Villalón Rojas
- Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - Sur Herrera
- Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - Georgina Garza-Ramos
- Biochemistry Department, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | - Alfredo Torres Larios
- Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - Carlos Amero
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca Morelos, México
| | - Gabriela Zarraga Granados
- Department of Developmental Genetics and Molecular Physiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos, México
| | - Manuel Gutiérrez Aguilar
- Molecular Genetics Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - María Teresa Lara Ortiz
- Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - Carlos Polanco Gonzalez
- Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - Salvador Uribe Carvajal
- Molecular Genetics Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - Roberto Coria
- Molecular Genetics Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - Antonio Peña Díaz
- Molecular Genetics Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
| | - Dale E. Bredesen
- Buck Institute for Age Research, Novato, California, United States of America
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Susana Castro-Obregon
- Department of Developmental Genetics and Molecular Physiology, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos, México
| | - Gabriel del Rio
- Biochemistry and Structural Biology Department, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F., México
- * E-mail:
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5
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Binolfi A, Fernández CO, Sica MP, Delfino JM, Santos J. Recognition between a short unstructured peptide and a partially folded fragment leads to the thioredoxin fold sharing native-like dynamics. Proteins 2012; 80:1448-64. [DOI: 10.1002/prot.24043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 12/27/2011] [Accepted: 01/11/2012] [Indexed: 11/09/2022]
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6
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Kiefhaber T, Bachmann A, Jensen KS. Dynamics and mechanisms of coupled protein folding and binding reactions. Curr Opin Struct Biol 2011; 22:21-9. [PMID: 22129832 DOI: 10.1016/j.sbi.2011.09.010] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 09/27/2011] [Indexed: 11/28/2022]
Abstract
Protein folding coupled to binding of a specific ligand is frequently observed in biological processes. In recent years numerous studies have addressed the structural properties of the unfolded proteins in the absence of their ligands. Surprisingly few time-resolved investigations on coupled folding and binding reactions have been published up to date and the dynamics and kinetic mechanisms of these processes are still only poorly understood. Especially, it is still unsolved for most systems which conformation of the protein is recognized by the ligand (conformational selection vs. folding-after-binding) and whether the ligand influences the folding kinetics. Here we review experimental methods, kinetic models and time-resolved experimental studies of coupled folding and binding reactions.
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Affiliation(s)
- Thomas Kiefhaber
- Munich Center for Integrated Protein Science at the Chemistry Department, TU München, Lichtenbergstrasse 4, D-85747 Garching, Germany.
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7
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Zhuang Z, Jewett AI, Kuttimalai S, Bellesia G, Gnanakaran S, Shea JE. Assisted peptide folding by surface pattern recognition. Biophys J 2011; 100:1306-15. [PMID: 21354404 DOI: 10.1016/j.bpj.2010.12.3735] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 12/09/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022] Open
Abstract
Natively disordered proteins belong to a unique class of biomolecules whose function is related to their flexibility and their ability to adopt desired conformations upon binding to substrates. In some cases these proteins can bind multiple partners, which can lead to distinct structures and promiscuity in functions. In other words, the capacity to recognize molecular patterns on the substrate is often essential for the folding and function of intrinsically disordered proteins. Biomolecular pattern recognition is extremely relevant both in vivo (e.g., for oligomerization, immune response, induced folding, substrate binding, and molecular switches) and in vitro (e.g., for biosensing, catalysis, chromatography, and implantation). Here, we use a minimalist computational model system to investigate how polar/nonpolar patterns on a surface can induce the folding of an otherwise unstructured peptide. We show that a model peptide that exists in the bulk as a molten globular state consisting of many interconverting structures can fold into either a helix-coil-helix or an extended helix structure in the presence of a complementary designed patterned surface at low hydrophobicity (3.7%) or a uniform surface at high hydrophobicity (50%). However, we find that a carefully chosen surface pattern can bind to and catalyze the folding of a natively unfolded protein much more readily or effectively than a surface with a noncomplementary or uniform distribution of hydrophobic residues.
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Affiliation(s)
- Zhuoyun Zhuang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
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8
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Shang GG, Zhang JH, Lü YG, Yun J. Bioinformatics-led design of single-chain antibody molecules targeting DNA sequences for retinoblastoma. Int J Ophthalmol 2011; 4:8-13. [PMID: 22553599 DOI: 10.3980/j.issn.2222-3959.2011.01.02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 01/20/2011] [Indexed: 02/01/2023] Open
Abstract
AIM To analyze the relationship between the structure and function of single-chain Fv antibody (scFv) with bioinformatics methods, so as to provide theoretical basis for retinoblastoma targeted therapy. METHODS Single-chain antibodies are reconstructed for cancer-targeted therapy to provide good penetration into tumor tissue and to improve their pharmacokinetics in vivo, offering a clinically valuable application. The relationship needs to be analyzed that there may be some variations between the structure and function of the fusion proteins, and the relationship between the structure and function of protein molecules was obtained through analyzing relevant literature at home and abroad as well as modeling analysis. RESULTS Through our analysis of the interaction region between the antibody and the antigen, and of the binding sites for molecular conformation, it is clear that existing antibodies need to be modified at the DNA sequence level, enhancing the biological activity of the antibodies. Based on the view that bio-molecular computer models are closely integrated with biological experiments, a bio-molecular structure-activity relationship model can be established in terms of molecular conformation, physical and chemical properties and the biological activity of single-chain antibodies. Two enlightenments are obtained from our analysis. On the one hand, the structure-activity relationship is clear for new immune molecules at the gene expression level. On the other hand, a single-chain antibody molecule can be designed and optimized for the cancer-oriented treatment. CONCLUSION In this article, we provide the theoretical and experimental basis for the development of single-chain antibodies appropriate for retinoblastoma therapy.
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Affiliation(s)
- Guo-Gang Shang
- Department of Radiotherapy, Zhengzhou People's Hospital, Zhengzhou 450052, Henan Province, China
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9
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Wands AM, Wang N, Lum JK, Hsieh J, Fierke CA, Mapp AK. Transient-state kinetic analysis of transcriptional activator·DNA complexes interacting with a key coactivator. J Biol Chem 2011; 286:16238-45. [PMID: 21317429 DOI: 10.1074/jbc.m110.207589] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Several lines of evidence suggest that the prototypical amphipathic transcriptional activators Gal4, Gcn4, and VP16 interact with the key coactivator Med15 (Gal11) during transcription initiation despite little sequence homology. Recent cross-linking data further reveal that at least two of the activators utilize the same binding surface within Med15 for transcriptional activation. To determine whether these three activators use a shared binding mechanism for Med15 recruitment, we characterized the thermodynamics and kinetics of Med15·activator·DNA complex formation by fluorescence titration and stopped-flow techniques. Combination of each activator·DNA complex with Med15 produced biphasic time courses. This is consistent with a minimum two-step binding mechanism composed of a bimolecular association step limited by diffusion, followed by a conformational change in the Med15·activator·DNA complex. Furthermore, the equilibrium constant for the conformational change (K(2)) correlates with the ability of an activator to stimulate transcription. VP16, the most potent of the activators, has the largest K(2) value, whereas Gcn4, the least potent, has the smallest value. This correlation is consistent with a model in which transcriptional activation is regulated at least in part by the rearrangement of the Med15·activator·DNA ternary complex. These results are the first detailed kinetic characterization of the transcriptional activation machinery and provide a framework for the future design of potent transcriptional activators.
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Affiliation(s)
- Amberlyn M Wands
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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10
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OHGANE K, DODO K, HASHIMOTO Y. Structural Development Study of a Novel Pharmacological Chaperone for Folding-defective Rhodopsin Mutants Responsible for Retinitis Pigmentosa. YAKUGAKU ZASSHI 2011; 131:325-34. [DOI: 10.1248/yakushi.131.325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kenji OHGANE
- Institute of Molecular and Cellular Biosciences, The University of Tokyo
| | | | - Yuichi HASHIMOTO
- Institute of Molecular and Cellular Biosciences, The University of Tokyo
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11
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Cogliati C, Ragona L, D'Onofrio M, Günther U, Whittaker S, Ludwig C, Tomaselli S, Assfalg M, Molinari H. Site-Specific Investigation of the Steady-State Kinetics and Dynamics of the Multistep Binding of Bile Acid Molecules to a Lipid Carrier Protein. Chemistry 2010; 16:11300-10. [DOI: 10.1002/chem.201000498] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Zhou HX. From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions. Biophys J 2010; 98:L15-7. [PMID: 20303846 DOI: 10.1016/j.bpj.2009.11.029] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 11/19/2009] [Accepted: 11/23/2009] [Indexed: 11/16/2022] Open
Abstract
In receptor-ligand binding, a question that generated considerable interest is whether the mechanism is induced fit or conformational selection. This question is addressed here by a solvable model, in which a receptor undergoes transitions between active and inactive forms. The inactive form is favored while unbound but the active form is favored while a ligand is loosely bound. As the active-inactive transition rates increase, the binding mechanism gradually shifts from conformational selection to induced fit. The timescale of conformational transitions thus plays a crucial role in controlling binding mechanisms.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA.
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13
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Aguado-Llera D, Goormaghtigh E, de Geest N, Quan XJ, Prieto A, Hassan BA, Gómez J, Neira JL. The basic helix-loop-helix region of human neurogenin 1 is a monomeric natively unfolded protein which forms a "fuzzy" complex upon DNA binding. Biochemistry 2010; 49:1577-89. [PMID: 20102160 DOI: 10.1021/bi901616z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Neuronal specification is regulated by the activity of transcription factors containing the basic helix-loop-helix motif (bHLH); these regulating proteins include, among others, the neurogenin (Ngn) family, related to the atonal family of genes. Neurogenin 1 (NGN1) is a 237-residue protein that contains a bHLH domain and is involved in neuronal differentiation. In this work, we synthesized the bHLH region of NGN1 (bHLHN) comprising residues 90-150 of the full-length NGN1. The domain is a monomeric natively unfolded protein with a pH-dependent premolten globule conformation, as shown by several spectroscopic techniques (namely, NMR, fluorescence, FTIR, and circular dichroism). The unfolded character of the domain also explains, first, the impossibility of its overexpression in several Escherichia coli strains and, second, its insolubility in aqueous buffers. To the best of our knowledge, this is the first extensive study of the conformational preferences of a bHLH domain under different solution conditions. Upon binding to two DNA E-boxes, the protein forms "fuzzy" complexes (that is, the complexes were not fully folded). The affinities of bHLHN for both DNA boxes were smaller than those of other bHLH domains, which might explain why the protein-DNA complexes were not fully folded.
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Affiliation(s)
- David Aguado-Llera
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
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14
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Chicken ileal bile-acid-binding protein: a promising target of investigation to understand binding co-operativity across the protein family. Biochem J 2009; 425:413-24. [PMID: 19874274 DOI: 10.1042/bj20091209] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Protein-bile acid interactions are crucial microscopic events at the basis of both physiological and pathological biochemical pathways. BABPs (bile-acid-binding proteins) are intracellular transporters able to bind ligands with different stoichiometry, selectivity and co-operativity. The molecular determinants and energetics of interaction are the observables that connect the microscopic to the macroscopic frameworks. The present paper addresses the study and proposes a mechanism for the multi-site interaction of bile acids with chicken I-BABP (ileal BABP) with the aim of elucidating the determinants of ligand binding in comparison with homologous proteins from different species and tissues. A thermodynamic binding model describing two independent consecutive binding sites is derived from isothermal titration calorimetry experiments and validated on the basis of both protein-observed and ligand-observed NMR titration data. It emerges that a singly bound protein is relatively abundant at low ligand/protein molar ratios assessing the absence of strong co-operativity. Both the measured energetics of binding and the distributed protein chemical-shift perturbations are in agreement with a first binding event triggering a global structural rearrangement. The enthalpic and entropic contributions associated with binding of the first ligand indicate that the interaction increases stability and order of the bound protein. The results described in the present study point to the presence of a protein scaffold which is able to establish long-range communication networks, but does not manifest positive-binding co-operativity, as observed for the human protein. We consider chicken I-BABP a suitable model to address the molecular basis for a gain-of-function on going from non-mammalian to mammalian species.
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