1
|
Vergara R, Berrocal T, Juárez Mejía EI, Romero-Romero S, Velázquez-López I, Pulido NO, López Sanchez HA, Silva DA, Costas M, Rodríguez-Romero A, Rodríguez-Sotres R, Sosa-Peinado A, Fernández-Velasco DA. Thermodynamic and kinetic analysis of the LAO binding protein and its isolated domains reveal non-additivity in stability, folding and function. FEBS J 2023; 290:4496-4512. [PMID: 37178351 DOI: 10.1111/febs.16819] [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] [Received: 03/29/2023] [Accepted: 05/12/2023] [Indexed: 05/15/2023]
Abstract
Substrate-binding proteins (SBPs) are used by organisms from the three domains of life for transport and signalling. SBPs are composed of two domains that collectively trap ligands with high affinity and selectivity. To explore the role of the domains and the integrity of the hinge region between them in the function and conformation of SBPs, here, we describe the ligand binding, conformational stability and folding kinetics of the Lysine Arginine Ornithine (LAO) binding protein from Salmonella thiphimurium and constructs corresponding to its two independent domains. LAO is a class II SBP formed by a continuous and a discontinuous domain. Contrary to the expected behaviour based on their connectivity, the discontinuous domain shows a stable native-like structure that binds l-arginine with moderate affinity, whereas the continuous domain is barely stable and shows no detectable ligand binding. Regarding folding kinetics, studies of the entire protein revealed the presence of at least two intermediates. While the unfolding and refolding of the continuous domain exhibited only a single intermediate and simpler and faster kinetics than LAO, the folding mechanism of the discontinuous domain was complex and involved multiple intermediates. These findings suggest that in the complete protein the continuous domain nucleates folding and that its presence funnels the folding of the discontinuous domain avoiding nonproductive interactions. The strong dependence of the function, stability and folding pathway of the lobes on their covalent association is most likely the result of the coevolution of both domains as a single unit.
Collapse
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, Mexico
| | - Tania Berrocal
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Eva Isela Juárez Mejía
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Department of Biochemistry, University of Bayreuth, Germany
| | - Isabel Velázquez-López
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Nancy O Pulido
- Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Haven A López Sanchez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Rogelio Rodríguez-Sotres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alejandro Sosa-Peinado
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Uncertainty in protein-ligand binding constants: asymmetric confidence intervals versus standard errors. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:661-670. [PMID: 33837826 DOI: 10.1007/s00249-021-01518-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/05/2021] [Accepted: 03/13/2021] [Indexed: 01/18/2023]
Abstract
Equilibrium binding constants (Kb) between chemical compounds and target proteins or between interacting proteins provide a quantitative understanding of biological interaction mechanisms. Reported uncertainties of measured experimental parameters are critical for decision-making in many scientific areas, e.g., in lead compound discovery processes and in comparing computational predictions with experimental results. Uncertainties in measured Kb values are commonly represented by a symmetric normal distribution, often quoted in terms of the experimental value plus-minus the standard deviation. However, in general, the distributions of measured Kb (and equivalent Kd) values and the corresponding free energy change ΔGb are all asymmetric to varying degree. Here, using a simulation approach, we illustrate the effect of asymmetric Kb distributions within the realm of isothermal titration calorimetry (ITC) experiments. Further we illustrate the known, but perhaps not widely appreciated, fact that when distributions of any of Kb, Kd and ΔGb are transformed into each other, their degree of asymmetry is changed. Consequently, we recommend that a more accurate way of expressing the uncertainties of Kb, Kd, and ΔGb values is to consistently report 95% confidence intervals, in line with other authors' suggestions. The ways to obtain such error ranges are discussed in detail and exemplified for a binding reaction obtained by ITC.
Collapse
|
4
|
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
| |
Collapse
|
5
|
Paiardini A, Mantoni F, Giardina G, Paone A, Janson G, Leoni L, Rampioni G, Cutruzzolà F, Rinaldo S. A novel bacterial l-arginine sensor controlling c-di-GMP levels in Pseudomonas aeruginosa. Proteins 2018; 86:1088-1096. [PMID: 30040157 DOI: 10.1002/prot.25587] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 01/16/2023]
Abstract
Nutrients such as amino acids play key roles in shaping the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond taking part to cellular metabolism and to protein synthesis, amino acids are also signaling molecules able to influence group behavior in microorganisms, such as biofilm formation. This lifestyle switch involves complex metabolic reprogramming controlled by local variation of the second messenger 3', 5'-cyclic diguanylic acid (c-di-GMP). The intracellular levels of this dinucleotide are finely tuned by the opposite activity of dedicated diguanylate cyclases (GGDEF signature) and phosphodiesterases (EAL and HD-GYP signatures), which are usually allosterically controlled by a plethora of environmental and metabolic clues. Among the genes putatively involved in controlling c-di-GMP levels in P. aeruginosa, we found that the multidomain transmembrane protein PA0575, bearing the tandem signature GGDEF-EAL, is an l-arginine sensor able to hydrolyse c-di-GMP. Here, we investigate the basis of arginine recognition by integrating bioinformatics, molecular biophysics and microbiology. Although the role of nutrients such as l-arginine in controlling the cellular fate in P. aeruginosa (including biofilm, pathogenicity and virulence) is already well established, we identified the first l-arginine sensor able to link environment sensing, c-di-GMP signaling and biofilm formation in this bacterium.
Collapse
Affiliation(s)
- A Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
| | - F Mantoni
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
| | - G Giardina
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
| | - A Paone
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy
| | - G Janson
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy
| | - L Leoni
- Department of Science, University Roma Tre (I), Roma, Italy
| | - G Rampioni
- Department of Science, University Roma Tre (I), Roma, Italy
| | - F Cutruzzolà
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
| | - S Rinaldo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
| |
Collapse
|
6
|
Banda-Vázquez J, Shanmugaratnam S, Rodríguez-Sotres R, Torres-Larios A, Höcker B, Sosa-Peinado A. Redesign of LAOBP to bind novel l-amino acid ligands. Protein Sci 2018. [PMID: 29524280 DOI: 10.1002/pro.3403] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Computational protein design is still a challenge for advancing structure-function relationships. While recent advances in this field are promising, more information for genuine predictions is needed. Here, we discuss different approaches applied to install novel glutamine (Gln) binding into the Lysine/Arginine/Ornithine binding protein (LAOBP) from Salmonella typhimurium. We studied the ligand binding behavior of two mutants: a binding pocket grafting design based on a structural superposition of LAOBP to the Gln binding protein QBP from Escherichia coli and a design based on statistical coupled positions. The latter showed the ability to bind Gln even though the protein was not very stable. Comparison of both approaches highlighted a nonconservative shared point mutation between LAOBP_graft and LAOBP_sca. This context dependent L117K mutation in LAOBP turned out to be sufficient for introducing Gln binding, as confirmed by different experimental techniques. Moreover, the crystal structure of LAOBP_L117K in complex with its ligand is reported.
Collapse
Affiliation(s)
| | - Sooruban Shanmugaratnam
- Max Planck Institute for Developmental Biology, Tübingen, Germany.,Universität Bayreuth, Bayreuth, Germany
| | | | | | - Birte Höcker
- Max Planck Institute for Developmental Biology, Tübingen, Germany.,Universität Bayreuth, Bayreuth, Germany
| | | |
Collapse
|
7
|
Paul S, Banerjee S, Vogel HJ. Ligand binding specificity of the Escherichia coli periplasmic histidine binding protein, HisJ. Protein Sci 2016; 26:268-279. [PMID: 27865021 DOI: 10.1002/pro.3079] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022]
Abstract
The HisJ protein from Escherichia coli and related Gram negative bacteria is the periplasmic component of a bacterial ATP-cassette (ABC) transporter system. Together these proteins form a transmembrane complex that can take up L-histidine from the environment and translocate it into the cytosol. We have studied the specificity of HisJ for binding L-His and many related naturally occurring compounds. Our data confirm that L-His is the preferred ligand, but that 1-methyl-L-His and 3-methyl-L-His can also bind, while the dipeptide carnosine binds weakly and D-histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind. L-Arg, homo-L-Arg, and post-translationally modified methylated Arg-analogs also bind with reasonable avidity, with the exception of symmetric dimethylated-L-Arg. In contrast, L-Lys and L-Orn have considerably weaker interactions with HisJ and methylated and acetylated Lys variants show relatively poor binding. It was also observed that the carboxylate group of these amino acids and their variants was very important for proper recognition of the ligand. Taken together our results are a key step towards designing HisJ as a specific protein-based reagentless biosensor.
Collapse
Affiliation(s)
- Subrata Paul
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta, T2N 1N4, Canada
| | - Sambuddha Banerjee
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta, T2N 1N4, Canada
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta, T2N 1N4, Canada
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|