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Evangelista-Falcón W, Denhez C, Baena-Moncada A, Ponce-Vargas M. Revisiting the Sweet Taste Receptor T1R2-T1R3 through Molecular Dynamics Simulations Coupled with a Noncovalent Interactions Analysis. J Phys Chem B 2023; 127:1110-1119. [PMID: 36705604 DOI: 10.1021/acs.jpcb.2c07180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
It is nowadays widely accepted that sweet taste perception is elicited by the activation of the heterodimeric complex T1R2-T1R3, customarily known as sweet taste receptor (STR). However, the interplay between STR and sweeteners has not yet been fully clarified. Here through a methodology coupling molecular dynamics and the independent gradient model (igm) approach we determine the main interacting signatures of the closed (active) conformation of the T1R2 Venus flytrap domain (VFD) toward aspartame. The igm methodology provides a rapid and reliable quantification of noncovalent interactions through a score (Δginter) based on the attenuation of the electronic density gradient when two molecular fragments approach each other. Herein, this approach is coupled to a 100 ns molecular dynamics simulation (MD-igm) to explore the ligand-cavity contacts on a per-residue basis as well as a series of key inter-residue interactions that stabilize the closed form of VFD. We also apply an atomic decomposition scheme of noncovalent interactions to quantify the contribution of the ligand segments to the noncovalent interplay. Finally, a series of structural modification on aspartame are conducted in order to obtain guidelines for the rational design of novel sweeteners. Given that innovative methodologies to reliably quantify the extent of ligand-protein coupling are strongly demanded, this approach combining a noncovalent analysis and MD simulations represents a valuable contribution, that can be easily applied to other relevant biomolecular systems.
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Affiliation(s)
- Wilfredo Evangelista-Falcón
- Laboratory of Biomolecules, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima15023, Perú
| | - Clément Denhez
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse 51687, ReimsCedex 02 BP39, France
| | - Angélica Baena-Moncada
- Laboratorio de Investigación de Electroquímica Aplicada, Facultad de Ciencias de la Universidad Nacional de Ingeniería, Av. Túpac Amaru 210, Rímac, Lima31-139, Perú
| | - Miguel Ponce-Vargas
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse 51687, ReimsCedex 02 BP39, France
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Yaacob N, Ahmad Kamarudin NH, Leow ATC, Salleh AB, Raja Abd Rahman RNZ, Mohamad Ali MS. The Role of Solvent-Accessible Leu-208 of Cold-Active Pseudomonas fluorescens Strain AMS8 Lipase in Interfacial Activation, Substrate Accessibility and Low-Molecular Weight Esterification in the Presence of Toluene. Molecules 2017; 22:E1312. [PMID: 28805665 PMCID: PMC6152135 DOI: 10.3390/molecules22081312] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/31/2017] [Accepted: 08/04/2017] [Indexed: 11/23/2022] Open
Abstract
The alkaline cold-active lipase from Pseudomonas fluorescens AMS8 undergoes major structural changes when reacted with hydrophobic organic solvents. In toluene, the AMS8 lipase catalytic region is exposed by the moving hydrophobic lid 2 (Glu-148 to Gly-167). Solvent-accessible surface area analysis revealed that Leu-208, which is located next to the nucleophilic Ser-207 has a focal function in influencing substrate accessibility and flexibility of the catalytic pocket. Based on molecular dynamic simulations, it was found that Leu-208 strongly facilitates the lid 2 opening via its side-chain. The KM and Kcat/KM of L208A mutant were substrate dependent as it preferred a smaller-chain ester (pNP-caprylate) as compared to medium (pNP-laurate) or long-chain (pNP-palmitate) esters. In esterification of ethyl hexanoate, L208A promotes a higher ester conversion rate at 20 °C but not at 30 °C, as a 27% decline was observed. Interestingly, the wild-type (WT) lipase's conversion rate was found to increase with a higher temperature. WT lipase AMS8 esterification was higher in toluene as compared to L208A. Hence, the results showed that Leu-208 of AMS8 lipase plays an important role in steering a broad range of substrates into its active site region by regulating the flexibility of this region. Leu-208 is therefore predicted to be crucial for its role in interfacial activation and catalysis in toluene.
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Affiliation(s)
- Norhayati Yaacob
- Enzyme Technology/Molecular Biomedicine Laboratory, Enzyme and Microbial Technology Research Centre, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Department of Cell Biology and Molecule, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
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Cha HJ, Jang DS, Kim YG, Hong BH, Woo JS, Kim KT, Choi KY. Rescue of deleterious mutations by the compensatory Y30F mutation in ketosteroid isomerase. Mol Cells 2013; 36:39-46. [PMID: 23740430 PMCID: PMC3887930 DOI: 10.1007/s10059-013-0013-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 04/29/2013] [Accepted: 04/30/2013] [Indexed: 01/07/2023] Open
Abstract
Proteins have evolved to compensate for detrimental mutations. However, compensatory mechanisms for protein defects are not well understood. Using ketosteroid isomerase (KSI), we investigated how second-site mutations could recover defective mutant function and stability. Previous results revealed that the Y30F mutation rescued the Y14F, Y55F and Y14F/Y55F mutants by increasing the catalytic activity by 23-, 3- and 1.3-fold, respectively, and the Y55F mutant by increasing the stability by 3.3 kcal/mol. To better understand these observations, we systematically investigated detailed structural and thermodynamic effects of the Y30F mutation on these mutants. Crystal structures of the Y14F/Y30F and Y14F/Y55F mutants were solved at 2.0 and 1.8 previoulsy solved structures of wild-type and other mutant KSIs. Structural analyses revealed that the Y30F mutation partially restored the active-site cleft of these mutant KSIs. The Y30F mutation also increased Y14F and Y14F/Y55F mutant stability by 3.2 and 4.3 kcal/mol, respectively, and the melting temperatures of the Y14F, Y55F and Y14F/Y55F mutants by 6.4°C, 5.1°C and 10.0°C, respectively. Compensatory effects of the Y30F mutation on stability might be due to improved hydrophobic interactions because removal of a hydroxyl group from Tyr30 induced local compaction by neighboring residue movement and enhanced interactions with surrounding hydrophobic residues in the active site. Taken together, our results suggest that perturbed active-site geometry recovery and favorable hydrophobic interactions mediate the role of Y30F as a secondsite suppressor.
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Affiliation(s)
- Hyung Jin Cha
- Department of Life Science, Division of Molecular and Life Sciences, Division of Integrative Biosciences and Biotechnology, WCU Program, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Do Soo Jang
- Research Institute, Genexine Co., Seongnam 463-400,
Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Bee Hak Hong
- Research Institute, Genexine Co., Seongnam 463-400,
Korea
| | - Jae-Sung Woo
- Institute for Basic Science, Seoul National University, Seoul 151-742,
Korea
| | - Kyong-Tai Kim
- Department of Life Science, Division of Molecular and Life Sciences, Division of Integrative Biosciences and Biotechnology, WCU Program, Pohang University of Science and Technology, Pohang 790-784,
Korea
| | - Kwan Yong Choi
- Department of Life Science, Division of Molecular and Life Sciences, Division of Integrative Biosciences and Biotechnology, WCU Program, Pohang University of Science and Technology, Pohang 790-784,
Korea
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Nikitina J, Shutova T, Melnik B, Chernyshov S, Marchenkov V, Semisotnov G, Klimov V, Samuelsson G. Importance of a single disulfide bond for the PsbO protein of photosystem II: protein structure stability and soluble overexpression in Escherichia coli. PHOTOSYNTHESIS RESEARCH 2008; 98:391-403. [PMID: 18709441 DOI: 10.1007/s11120-008-9327-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 07/01/2008] [Indexed: 05/09/2023]
Abstract
PsbO protein is an important constituent of the water-oxidizing complex, located on the lumenal side of photosystem II. We report here the efficient expression of the spinach PsbO in E. coli where the solubility depends entirely on the formation of the disulfide bond. The PsbO protein purified from a pET32 system that includes thioredoxin fusion is properly folded and functionally active. Urea unfolding experiments imply that the reduction of the single disulfide bridge decreases stability of the protein. Analysis of inter-residue contact density through the PsbO molecule shows that Cys51 is located in a cluster with high contact density. Reduction of the Cys28-Cys51 bond is proposed to perturb the packing interactions in this cluster and destabilize the protein as a whole. Taken together, our results give evidence that PsbO exists in solution as a compact highly ordered structure, provided that the disulfide bridge is not reduced.
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Affiliation(s)
- Julia Nikitina
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umea, Sweden
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Sandgren M, Ståhlberg J, Mitchinson C. Structural and biochemical studies of GH family 12 cellulases: improved thermal stability, and ligand complexes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2004; 89:246-91. [PMID: 15950056 DOI: 10.1016/j.pbiomolbio.2004.11.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this review we will describe how we have gathered structural and biochemical information from several homologous cellulases from one class of glycoside hydrolases (GH family 12), and used this information within the framework of a protein-engineering program for the design of new variants of these enzymes. These variants have been characterized to identify some of the positions and the types of mutations in the enzymes that are responsible for some of the biochemical differences in thermal stability and activity between the homologous enzymes. In this process we have solved the three-dimensional structure of four of these homologous GH 12 cellulases: Three fungal enzymes, Humicola grisea Cel12A, Hypocrea jecorina Cel12A and Hypocrea schweinitzii Cel12A, and one bacterial, Streptomyces sp. 11AG8 Cel12A. We have also determined the three-dimensional structures of the two most stable H. jecorina Cel12A variants. In addition, four ligand-complex structures of the wild-type H. grisea Cel12A enzyme have been solved and have made it possible to characterize some of the interactions between substrate and enzyme. The structural and biochemical studies of these related GH 12 enzymes, and their variants, have provided insight on how specific residues contribute to protein thermal stability and enzyme activity. This knowledge can serve as a structural toolbox for the design of Cel12A enzymes with specific properties and features suited to existing or new applications.
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Affiliation(s)
- Mats Sandgren
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden.
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Sandgren M, Gualfetti PJ, Paech C, Paech S, Shaw A, Gross LS, Saldajeno M, Berglund GI, Jones TA, Mitchinson C. The Humicola grisea Cel12A enzyme structure at 1.2 A resolution and the impact of its free cysteine residues on thermal stability. Protein Sci 2004; 12:2782-93. [PMID: 14627738 PMCID: PMC2366986 DOI: 10.1110/ps.03220403] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
As part of a program to discover improved glycoside hydrolase family 12 (GH 12) endoglucanases, we have extended our previous work on the structural and biochemical diversity of GH 12 homologs to include the most stable fungal GH 12 found, Humicola grisea Cel12A. The H. grisea enzyme was much more stable to irreversible thermal denaturation than the Trichoderma reesei enzyme. It had an apparent denaturation midpoint (T(m)) of 68.7 degrees C, 14.3 degrees C higher than the T. reesei enzyme. There are an additional three cysteines found in the H. grisea Cel12A enzyme. To determine their importance for thermal stability, we constructed three H. grisea Cel12A single mutants in which these cysteines were exchanged with the corresponding residues in the T. reesei enzyme. We also introduced these cysteine residues into the T. reesei enzyme. The thermal stability of these variants was determined. Substitutions at any of the three positions affected stability, with the largest effect seen in H. grisea C206P, which has a T(m) 9.1 degrees C lower than that of the wild type. The T. reesei cysteine variant that gave the largest increase in stability, with a T(m) 3.9 degrees C higher than wild type, was the P201C mutation, the converse of the destabilizing C206P mutation in H. grisea. To help rationalize the results, we have determined the crystal structure of the H. grisea enzyme and of the most stable T. reesei cysteine variant, P201C. The three cysteines in H. grisea Cel12A play an important role in the thermal stability of this protein, although they are not involved in a disulfide bond.
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Affiliation(s)
- Mats Sandgren
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, S-751 24 Uppsala, Sweden
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Sandgren M, Gualfetti PJ, Shaw A, Gross LS, Saldajeno M, Day AG, Jones TA, Mitchinson C. Comparison of family 12 glycoside hydrolases and recruited substitutions important for thermal stability. Protein Sci 2003; 12:848-60. [PMID: 12649442 PMCID: PMC2323842 DOI: 10.1110/ps.0237703] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
As part of a program to discover improved glycoside hydrolase family 12 (GH 12) endoglucanases, we have studied the biochemical diversity of several GH 12 homologs. The H. schweinitzii Cel12A enzyme differs from the T. reesei Cel12A enzyme by only 14 amino acids (93% sequence identity), but is much less thermally stable. The bacterial Cel12A enzyme from S. sp. 11AG8 shares only 28% sequence identity to the T. reesei enzyme, and is much more thermally stable. Each of the 14 sequence differences from H. schweinitzii Cel12A were introduced in T. reesei Cel12A to determine the effect of these amino acid substitutions on enzyme stability. Several of the T. reesei Cel12A variants were found to have increased stability, and the differences in apparent midpoint of thermal denaturation (T(m)) ranged from a 2.5 degrees C increase to a 4.0 degrees C decrease. The least stable recruitment from H. schweinitzii Cel12A was A35S. Consequently, the A35V substitution was recruited from the more stable S. sp. 11AG8 Cel12A and this T. reesei Cel12A variant was found to have a T(m) 7.7 degrees C higher than wild type. Thus, the buried residue at position 35 was shown to be of critical importance for thermal stability in this structural family. There was a ninefold range in the specific activities of the Cel12 homologs on o-NPC. The most and least stable T. reesei Cel12A variants, A35V and A35S, respectively, were fully active. Because of their thermal tolerance, S. sp. 11AG8 Cel12A and T. reesei Cel12A variant A35V showed a continual increase in activity over the temperature range of 25 degrees C to 60 degrees C, whereas the less stable enzymes T. reesei Cel12A wild type and the destabilized A35S variant, and H. schweinitzii Cel12A showed a decrease in activity at the highest temperatures. The crystal structures of the H. schweinitzii, S. sp. 11AG8, and T. reesei A35V Cel12A enzymes have been determined and compared with the wild-type T. reesei Cel12A enzyme. All of the structures have similar Calpha traces, but provide detailed insight into the nature of the stability differences. These results are an example of the power of homolog recruitment as a method for identifying residues important for stability.
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Affiliation(s)
- Mats Sandgren
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, SE-75124 Uppsala, Sweden
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