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Santhakumar V, Manuel Mascarenhas N. The role of C-terminal helix in the conformational transition of an arginine binding protein. J Struct Biol X 2022; 6:100071. [PMID: 36035778 PMCID: PMC9402392 DOI: 10.1016/j.yjsbx.2022.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/06/2022] [Indexed: 11/27/2022] Open
Abstract
Probe the role of C-ter. helix (CTH) in conformational transition of TmArgBP. Presence of CTH almost doubles the barrier to access the closed-state. In the absence of CTH, the protein can fluctuate between the two conformations. CTH not only constraints the open-state conformation but also guides in accessing it.
The thermotoga maritima arginine binding protein (TmArgBP) is a periplasmic binding protein that has a short helix at the C-terminal end (CTH), which is swapped between the two chains. We apply a coarse-grained structure-based model (SBM) and all-atom MD simulation on this protein to understand the mechanism and the role of CTH in the conformational transition. When the results of SBM simulations of TmArgBP in the presence and absence of CTH are compared, we find that CTH is strategically located at the back of the binding pocket restraining the open-state conformation thereby disengaging access to the closed-state. We also ran all-atom MD simulations of open-state TmArgBP with and without CTH and discovered that in the absence of CTH the protein could reach the closed-state within 250 ns, while in its presence, the protein remained predominantly in its open-state conformation. In the simulation started from unliganded closed-state conformation without CTH, the protein exhibited multiple transitions between the two states, suggesting CTH as an essential structural element to stabilize the open-state conformation. In another simulation that began with an unliganded closed-state conformation with CTH, the protein was able to access the open-state. In this simulation the CTH was observed to reorient itself to interact with the protein emphasizing its role in assisting the conformational change. Based on our findings, we believe that CTH not only acts as a structural element that constraints the protein in its open-state but it may also guide the protein back to its open-state conformation upon ligand unbinding.
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2
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Vergara R, Romero‐Romero S, Velázquez‐López I, Espinoza‐Pérez G, Rodríguez‐Hernández A, Pulido NO, Sosa‐Peinado A, Rodríguez‐Romero A, Fernández‐Velasco DA. The interplay of protein–ligand and water‐mediated interactions shape affinity and selectivity in the LAO binding protein. FEBS J 2019; 287:763-782. [DOI: 10.1111/febs.15019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/25/2019] [Accepted: 07/24/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Renan Vergara
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Sergio Romero‐Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Isabel Velázquez‐López
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Georgina Espinoza‐Pérez
- Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Annia Rodríguez‐Hernández
- Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Nancy O. Pulido
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Alejandro Sosa‐Peinado
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
| | - Adela Rodríguez‐Romero
- Laboratorio de Química de Biomacromoléculas 3, Departamento de Química de Biomacromoléculas, Instituto de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Daniel Alejandro Fernández‐Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina Universidad Nacional Autónoma de México Ciudad de México México
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3
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Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein. Nat Chem Biol 2018; 14:542-547. [PMID: 29686357 DOI: 10.1038/s41589-018-0043-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 03/01/2018] [Indexed: 11/09/2022]
Abstract
The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme-substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations. Our work reveals the molecular evolutionary processes that underlie the emergence of enzymes de novo, which are notably mirrored by recent examples of computational enzyme design and directed evolution.
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4
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Cortes-Hernandez P, Domínguez-Ramírez L. Role of cis-trans proline isomerization in the function of pathogenic enterobacterial Periplasmic Binding Proteins. PLoS One 2017; 12:e0188935. [PMID: 29190818 PMCID: PMC5708682 DOI: 10.1371/journal.pone.0188935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 11/15/2017] [Indexed: 12/31/2022] Open
Abstract
Periplasmic Binding Proteins (PBPs) trap nutrients for their internalization into bacteria by ABC transporters. Ligand binding triggers PBP closure by bringing its two domains together like a Venus flytrap. The atomic determinants that control PBP opening and closure for nutrient capture and release are not known, although it is proposed that opening and ligand release occur while in contact with the ABC transporter for concurrent substrate translocation. In this paper we evaluated the effect of the isomerization of a conserved proline, located near the binding site, on the propensity of PBPs to open and close. ArgT/LAO from Salmonella typhimurium and HisJ from Escherichia coli were studied through molecular mechanics at two different temperatures: 300 and 323 K. Eight microseconds were simulated per protein to analyze protein opening and closure in the absence of the ABC transporter. We show that when the studied proline is in trans, closed empty LAO and HisJ can open. In contrast, with the proline in cis, opening transitions were much less frequent and characterized by smaller changes. The proline in trans also renders the open trap prone to close over a ligand. Our data suggest that the isomerization of this conserved proline modulates the PBP mechanism: the proline in trans allows the exploration of conformational space to produce trap opening and closure, while in cis it restricts PBP movement and could limit ligand release until in productive contact with the ABC transporter. This is the first time that a proline isomerization has been related to the control of a large conformational change like the PBP flytrap mechanism.
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Affiliation(s)
- Paulina Cortes-Hernandez
- Centro de Investigacion Biomedica de Oriente (CIBIOR), Instituto Mexicano del Seguro Social (IMSS), Metepec, Puebla, Mexico
| | - Lenin Domínguez-Ramírez
- Chemical and Biological Sciences, Universidad de las Américas Puebla (UDLAP), Cholula, Puebla, Mexico
- * E-mail:
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5
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Ameen S, Ahmad M, Mohsin M, Qureshi MI, Ibrahim MM, Abdin MZ, Ahmad A. Designing, construction and characterization of genetically encoded FRET-based nanosensor for real time monitoring of lysine flux in living cells. J Nanobiotechnology 2016; 14:49. [PMID: 27334743 PMCID: PMC4917951 DOI: 10.1186/s12951-016-0204-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 06/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Engineering microorganisms in order to improve the metabolite flux needs a detailed knowledge of the concentrations and flux rates of metabolites and metabolic intermediates in vivo. Fluorescence resonance energy transfer (FRET) based genetically encoded nanosensors represent a promising tool for measuring the metabolite levels and corresponding rate changes in live cells. Here, we report the development of a series of FRET based genetically encoded nanosensor for real time measurement of lysine at cellular level, as the improvement of microbial strains for the production of L-lysine is of major interest in industrial biotechnology. RESULTS The lysine binding periplasmic protein (LAO) from Salmonella enterica serovar typhimurium LT2 strain was used as the reporter element for the sensor. The LAO was sandwiched between GFP variants i.e. cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). Affinity, pH stability, specificity and metal ions effects was scrutinized for the in vitro characterization of this nanosensor, named as FLIPK. The FLIPK is specific to lysine and found to be stable with the pH within the physiological range. The calculated affinity (K d ) of FLIPK was 97 µM. For physiological applications, mutants with different binding affinities were also generated and investigated in vitro. The developed nanosensor efficiently monitored the intracellular level of lysine in bacterial as well as yeast cell. CONCLUSION The developed novel lysine fluorescence resonance energy transfer sensors can be used for in vivo monitoring of lysine levels in prokaryotes as well as eukaryotes. The potential of these sensors is that they can be used as reporter tools in the development of metabolically engineered microbial strains or for real-time monitoring of intracellular lysine during fermentation.
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Affiliation(s)
- Seema Ameen
- Department of Botany, Faculty of Science, Hamdard University, New Delhi, India
| | - Mohammad Ahmad
- Department of Botany, Faculty of Science, Hamdard University, New Delhi, India
| | - Mohd Mohsin
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - M Irfan Qureshi
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamed M Ibrahim
- Department of Botany & Microbiology, Science College, King Saud University, P.O. Box 2455, Riyadh, Saudi Arabia.,Department of Botany & Microbiology, Faculty of Science, Alexandria University, P.O. Box 21511, Alexandria, Egypt
| | - Malik Z Abdin
- Department of Biotechnology, Faculty of Science, Hamdard University, New Delhi, India
| | - Altaf Ahmad
- Department of Botany, Faculty of Science, Hamdard University, New Delhi, India. .,Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India.
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6
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Clifton BE, Jackson CJ. Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins. Cell Chem Biol 2016; 23:236-245. [PMID: 26853627 DOI: 10.1016/j.chembiol.2015.12.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/30/2015] [Accepted: 12/19/2015] [Indexed: 11/15/2022]
Abstract
The promiscuous functions of proteins are an important reservoir of functional novelty in protein evolution, but the molecular basis for binding promiscuity remains elusive. We used ancestral protein reconstruction to experimentally characterize evolutionary intermediates in the functional expansion of the polar amino acid-binding protein family, which has evolved to bind a variety of amino acids with high affinity and specificity. High-resolution crystal structures of an ancestral arginine-binding protein in complex with l-arginine and l-glutamine show that the promiscuous binding of l-glutamine is enabled by multi-scale conformational plasticity, water-mediated interactions, and selection of an alternative conformational substate productive for l-glutamine binding. Evolution of specialized glutamine-binding proteins from this ancestral protein was achieved by displacement of water molecules from the protein-ligand interface, reducing the entropic penalty associated with the promiscuous interaction. These results provide a structural and thermodynamic basis for the co-option of a promiscuous interaction in the evolution of binding specificity.
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Affiliation(s)
- Ben E Clifton
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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7
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Pulido NO, Silva DA, Tellez LA, Pérez-Hernández G, García-Hernández E, Sosa-Peinado A, Fernández-Velasco DA. On the molecular basis of the high affinity binding of basic amino acids to LAOBP, a periplasmic binding protein fromSalmonella typhimurium. J Mol Recognit 2015; 28:108-16. [DOI: 10.1002/jmr.2434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/20/2014] [Accepted: 09/15/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Nancy O. Pulido
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
| | - Daniel-Adriano Silva
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
- Biochemistry Department; University of Washington; Seattle WA USA
| | - Luis A. Tellez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
- Department of Psychiatry; Yale University School of Medicine; New Haven CT USA
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales; Universidad Autónoma Metropolitana- Cuajimalpa; México DF Mexico
| | - Enrique García-Hernández
- Instituto de Química; Universidad Nacional Autónoma de México; Circuito Exterior, Ciudad Universitaria México 04510 DF Mexico
| | - Alejandro Sosa-Peinado
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
| | - D. Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina; Universidad Nacional Autónoma de México; México DF Mexico
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8
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Horn AHC. A consistent force field parameter set for zwitterionic amino acid residues. J Mol Model 2014; 20:2478. [PMID: 25338816 DOI: 10.1007/s00894-014-2478-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 09/21/2014] [Indexed: 12/20/2022]
Abstract
Isolated amino acids play an important role in biochemistry and are therefore an interesting object of study. Atomistic molecular dynamics (MD) simulations can provide a high-resolution picture of the dynamic features of these species, especially in their biological environment. Unfortunately, most standard force field packages lack libraries for isolated amino acids in their zwitterionic form. Although several studies have used ad-hoc parameterizations for single amino acids, a consistent force-field parameter set for these molecules is still missing. Here, we present such a parameter library derived from the widely used parm99SB set from the AMBER program package. The parameter derivation for all 20 proteinogenic amino acids transparently followed established procedures with histidine treated in three different protonation states. All amino acids were subjected to MD simulations in four different forms for comparison: zwitterionic, N-teminally capped with acetyl, C-terminally capped with N-methyl, and capped at both termini. Simulation results show similarities between the different forms. Five zwitterionic amino acids-arginine, glutamate, glycine, phenylalanine, leucine-were simulated in a protein environment. Proteins and ligands generally retained their initial structure. The new parameter set will thus facilitate future atomistic simulations of these species.
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Affiliation(s)
- Anselm H C Horn
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstr. 17, 91054, Erlangen, Germany,
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9
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Gu S, Silva DA, Meng L, Yue A, Huang X. Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis. PLoS Comput Biol 2014; 10:e1003767. [PMID: 25101697 PMCID: PMC4125059 DOI: 10.1371/journal.pcbi.1003767] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 06/22/2014] [Indexed: 01/05/2023] Open
Abstract
Protein-ligand recognition plays key roles in many biological processes. One of the most fascinating questions about protein-ligand recognition is to understand its underlying mechanism, which often results from a combination of induced fit and conformational selection. In this study, we have developed a three-pronged approach of Markov State Models, Molecular Dynamics simulations, and flux analysis to determine the contribution of each model. Using this approach, we have quantified the recognition mechanism of the choline binding protein (ChoX) to be ∼90% conformational selection dominant under experimental conditions. This is achieved by recovering all the necessary parameters for the flux analysis in combination with available experimental data. Our results also suggest that ChoX has several metastable conformational states, of which an apo-closed state is dominant, consistent with previous experimental findings. Our methodology holds great potential to be widely applied to understand recognition mechanisms underlining many fundamental biological processes.
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Affiliation(s)
- Shuo Gu
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Daniel-Adriano Silva
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Luming Meng
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Alexander Yue
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Division of Biomedical Engineering, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, Institute for Advance Study and School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- * E-mail:
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10
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Chu BCH, Chan DI, DeWolf T, Periole X, Vogel HJ. Molecular dynamics simulations reveal that apo-HisJ can sample a closed conformation. Proteins 2013; 82:386-98. [DOI: 10.1002/prot.24396] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 11/11/2022]
Affiliation(s)
- B. C. H. Chu
- Department of Biological Sciences; University of Calgary; Calgary Alberta T2N 1N4 Canada
| | - D. I. Chan
- Department of Biological Sciences; University of Calgary; Calgary Alberta T2N 1N4 Canada
| | - T. DeWolf
- Department of Biological Sciences; University of Calgary; Calgary Alberta T2N 1N4 Canada
| | - X. Periole
- Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - H. J. Vogel
- Department of Biological Sciences; University of Calgary; Calgary Alberta T2N 1N4 Canada
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11
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Siuda I, Thøgersen L. Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics. J Mol Model 2013; 19:4931-45. [DOI: 10.1007/s00894-013-1991-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 08/29/2013] [Indexed: 11/24/2022]
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12
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Chu BCH, DeWolf T, Vogel HJ. Role of the two structural domains from the periplasmic Escherichia coli histidine-binding protein HisJ. J Biol Chem 2013; 288:31409-22. [PMID: 24036119 DOI: 10.1074/jbc.m113.490441] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Escherichia coli HisJ is a type II periplasmic binding protein that functions to reversibly capture histidine and transfer it to its cognate inner membrane ABC permease. Here, we used NMR spectroscopy to determine the structure of apo-HisJ (26.5 kDa) in solution. HisJ is a bilobal protein in which domain 1 (D1) is made up of two noncontiguous subdomains, and domain 2 (D2) is expressed as the inner domain. To better understand the roles of D1 and D2, we have isolated and characterized each domain separately. Structurally, D1 closely resembles its homologous domain in apo- and holo-HisJ, whereas D2 is more similar to the holo-form. NMR relaxation experiments reveal that HisJ becomes more ordered upon ligand binding, whereas isolated D2 experiences a significant reduction in slower (millisecond to microsecond) motions compared with the homologous domain in apo-HisJ. NMR titrations reveal that D1 is able to bind histidine in a similar manner as full-length HisJ, albeit with lower affinity. Unexpectedly, isolated D1 and D2 do not interact with each other in the presence or absence of histidine, which indicates the importance of intact interdomain-connecting elements (i.e. hinge regions) for HisJ functioning. Our results shed light on the binding mechanism of type II periplasmic binding proteins where ligand is initially bound by D1, and D2 plays a supporting role in this dynamic process.
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Affiliation(s)
- Byron C H Chu
- From the Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
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13
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Lama D, Modi V, Sankararamakrishnan R. Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations. PLoS One 2013; 8:e54397. [PMID: 23468841 PMCID: PMC3585337 DOI: 10.1371/journal.pone.0054397] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/13/2012] [Indexed: 11/19/2022] Open
Abstract
Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME) scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.
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Affiliation(s)
- Dilraj Lama
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Vivek Modi
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
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14
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 731] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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15
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Yao P, Zhang L, Latombe JC. Sampling-based exploration of folded state of a protein under kinematic and geometric constraints. Proteins 2011; 80:25-43. [DOI: 10.1002/prot.23134] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 07/08/2011] [Accepted: 07/12/2011] [Indexed: 11/09/2022]
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16
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Silva DA, Bowman GR, Sosa-Peinado A, Huang X. A role for both conformational selection and induced fit in ligand binding by the LAO protein. PLoS Comput Biol 2011; 7:e1002054. [PMID: 21637799 PMCID: PMC3102756 DOI: 10.1371/journal.pcbi.1002054] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 03/31/2011] [Indexed: 11/30/2022] Open
Abstract
Molecular recognition is determined by the structure and dynamics of both a protein and its ligand, but it is difficult to directly assess the role of each of these players. In this study, we use Markov State Models (MSMs) built from atomistic simulations to elucidate the mechanism by which the Lysine-, Arginine-, Ornithine-binding (LAO) protein binds to its ligand. We show that our model can predict the bound state, binding free energy, and association rate with reasonable accuracy and then use the model to dissect the binding mechanism. In the past, this binding event has often been assumed to occur via an induced fit mechanism because the protein's binding site is completely closed in the bound state, making it impossible for the ligand to enter the binding site after the protein has adopted the closed conformation. More complex mechanisms have also been hypothesized, but these have remained controversial. Here, we are able to directly observe roles for both the conformational selection and induced fit mechanisms in LAO binding. First, the LAO protein tends to form a partially closed encounter complex via conformational selection (that is, the apo protein can sample this state), though the induced fit mechanism can also play a role here. Then, interactions with the ligand can induce a transition to the bound state. Based on these results, we propose that MSMs built from atomistic simulations may be a powerful way of dissecting ligand-binding mechanisms and may eventually facilitate a deeper understanding of allostery as well as the prediction of new protein-ligand interactions, an important step in drug discovery.
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Affiliation(s)
- Daniel-Adriano Silva
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Biochemistry, Medicine School, Universidad Nacional Autónoma de México, México D.F., México
| | - Gregory R. Bowman
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Alejandro Sosa-Peinado
- Department of Biochemistry, Medicine School, Universidad Nacional Autónoma de México, México D.F., México
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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