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Kobori S, Huh S, Appavoo SD, Yudin AK. Two-Dimensional Barriers for Probing Conformational Shifts in Macrocycles. J Am Chem Soc 2021; 143:5166-5171. [PMID: 33754700 DOI: 10.1021/jacs.1c01248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We describe the development and use of composite two-dimensional barriers in macrocyclic backbones. These tunable constructs derive their mode of action from heterocyclic rearrangements. The Boulton-Katritzky reaction has been identified as a particularly versatile means to effect a composite barrier, allowing the examination of the influence of heterocycle translocation on conformation. Kinetic studies using 1H NMR have revealed that the in-plane atom movement is fast in 17, 18, 19-membered rings but slows down in 16-membered rings. The analysis by NMR and MD simulation experiments is consistent with the maintenance of rare cis-amide motifs during conformational interconversion. Taken together, our investigation demonstrates that heterocyclic rearrangement reactions can be used to control macrocyclic backbones and provides fundamental insights that may be applicable to the development of a wide range of other conformational control elements.
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Affiliation(s)
- Shinya Kobori
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario Canada, M5S 3H6
| | - Sungjoon Huh
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario Canada, M5S 3H6
| | - Solomon D Appavoo
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario Canada, M5S 3H6
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario Canada, M5S 3H6
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2
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Kellner R, Malempré R, Vandenameele J, Brans A, Hennen AF, Rochus N, Di Paolo A, Vandevenne M, Matagne A. Protein formulation through automated screening of pH and buffer conditions, using the Robotein® high throughput facility. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:473-490. [PMID: 33611612 DOI: 10.1007/s00249-021-01510-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/26/2021] [Accepted: 02/08/2021] [Indexed: 12/30/2022]
Abstract
Among various factors, the direct environment (e.g. pH, buffer components, salts, additives, etc.…) is known to have a crucial effect on both the stability and activity of proteins. In particular, proper buffer and pH conditions can improve their stability and function significantly during purification, storage and handling, which is highly relevant for both academic and industrial applications. It can also promote data reproducibility, support the interpretation of experimental results and, finally, contribute to our general understanding of the biophysical properties of proteins. In this study, we have developed a high throughput screen of 158 different buffers/pH conditions in which we evaluated: (i) the protein stability, using differential scanning fluorimetry and (ii) the protein function, using either enzymatic assays or binding activity measurements, both in an automated manner. The modular setup of the screen allows for easy implementation of other characterization methods and parameters, as well as additional test conditions. The buffer/pH screen was validated with five different proteins used as models, i.e. two active-site serine β-lactamases, two metallo-β-lactamases (one of which is only active as a tetramer) and a single-domain dromedary antibody fragment (VHH or nanobody). The formulation screen allowed automated and fast determination of optimum buffer and pH profiles for the tested proteins. Besides the determination of the optimum buffer and pH, the collection of pH profiles of many different proteins may also allow to delineate general concepts to understand and predict the relationship between pH and protein properties.
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Affiliation(s)
- Ruth Kellner
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Romain Malempré
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Julie Vandenameele
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - Alain Brans
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | | | - Noémie Rochus
- Eurogentec S.A., Rue Bois Saint-Jean, 5, 4102, Seraing, Belgium
| | - Alexandre Di Paolo
- Eurogentec S.A., Rue Bois Saint-Jean, 5, 4102, Seraing, Belgium.,Xpress Biologics SA, Accessia Pharma Site, Avenue du Parc Industriel, 89, 4041, Milmort, Belgium
| | - Marylène Vandevenne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000, Liège (Sart-Tilman), Belgium.
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3
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Thakkar BS, Svendsen JSM, Engh RA. Density Functional Studies on Secondary Amides: Role of Steric Factors in Cis/Trans Isomerization. Molecules 2018; 23:molecules23102455. [PMID: 30257481 PMCID: PMC6222500 DOI: 10.3390/molecules23102455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 11/16/2022] Open
Abstract
Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine methyl ester, can suitably represent the isomerization and complexities arising out of a larger molecular backbone, and can serve as the primary scaffold for model structures with different substitution patterns in order to assess and compare the steric effect of the substitution patterns. Here, we describe our theoretical assessment of such steric effects using tert-butyl as a representative bulky substitution. We analyze the geometries and relative stabilities of both trans and cis isomers, and effects on the cis/trans isomerization barrier. We also use the additivity principle to calculate absolute steric effects with a gradual increase in bulk. The study establishes that bulky substitutions significantly destabilize cis isomers and also increases the isomerization barrier, thereby synergistically hindering the cis/trans isomerization of secondary amides. These results provide a basis for the rationalization of kinetic and thermodynamic properties of peptides with potential applications in synthetic and medicinal chemistry.
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Affiliation(s)
- Balmukund S Thakkar
- Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
| | | | - Richard A Engh
- Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
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4
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Thakkar BS, Svendsen JSM, Engh RA. Cis/Trans Isomerization in Secondary Amides: Reaction Paths, Nitrogen Inversion, and Relevance to Peptidic Systems. J Phys Chem A 2017; 121:6830-6837. [DOI: 10.1021/acs.jpca.7b05584] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Balmukund S. Thakkar
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø-9037, Norway
| | | | - Richard A. Engh
- Department of Chemistry, UiT The Arctic University of Norway, Tromsø-9037, Norway
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5
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Vandenameele J, Lejeune A, Di Paolo A, Brans A, Frère JM, Schmid FX, Matagne A. Folding of Class A β-Lactamases Is Rate-Limited by Peptide Bond Isomerization and Occurs via Parallel Pathways. Biochemistry 2010; 49:4264-75. [DOI: 10.1021/bi100369d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Julie Vandenameele
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Annabelle Lejeune
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Alexandre Di Paolo
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Alain Brans
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Jean-Marie Frère
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Franz X. Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - André Matagne
- Laboratoire d’Enzymologie et Repliement des Protéines, Centre d’Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
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6
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Aumüller T, Fischer G. Bioactivity of Folding Intermediates Studied by the Recovery of Enzymatic Activity during Refolding. J Mol Biol 2008; 376:1478-92. [DOI: 10.1016/j.jmb.2007.12.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 12/17/2007] [Accepted: 12/21/2007] [Indexed: 10/22/2022]
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7
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Guan RJ, Xiang Y, He XL, Wang CG, Wang M, Zhang Y, Sundberg EJ, Wang DC. Structural mechanism governing cis and trans isomeric states and an intramolecular switch for cis/trans isomerization of a non-proline peptide bond observed in crystal structures of scorpion toxins. J Mol Biol 2004; 341:1189-204. [PMID: 15321715 DOI: 10.1016/j.jmb.2004.06.067] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2004] [Revised: 06/15/2004] [Accepted: 06/22/2004] [Indexed: 11/20/2022]
Abstract
Non-proline cis peptide bonds have been observed in numerous protein crystal structures even though the energetic barrier to this conformation is significant and no non-prolyl-cis/trans-isomerase has been identified to date. While some external factors, such as metal binding or co-factor interaction, have been identified that appear to induce cis/trans isomerization of non-proline peptide bonds, the intrinsic structural basis for their existence and the mechanism governing cis/trans isomerization in proteins remains poorly understood. Here, we report the crystal structure of a newly isolated neurotoxin, the scorpion alpha-like toxin Buthus martensii Karsch (BmK) M7, at 1.4A resolution. BmK M7 crystallizes as a dimer in which the identical non-proline peptide bond between residues 9 and 10 exists either in the cis conformation or as a mixture of cis and trans conformations in either monomer. We also determined the crystal structures of several mutants of BmK M1, a representative scorpion alpha-like toxin that contains an identical non-proline cis peptide bond as that observed in BmK M7, in which residues within or neighboring the cis peptide bond were altered. Substitution of an aspartic acid residue for lysine at residue 8 in the BmK M1 (K8D) mutant converted the cis form of the non-proline peptide bond 9-10 into the trans form, revealing an intramolecular switch for cis-to-trans isomerization. Cis/trans interconversion of the switch residue at position 8 appears to be sequence-dependent as the peptide bond between residues 9 and 10 retains its wild-type cis conformation in the BmK M1 (K8Q) mutant structure. The structural interconversion of the isomeric states of the BmK M1 non-proline cis peptide bond may relate to the conversion of the scorpion alpha-toxins subgroups.
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Affiliation(s)
- Rong-Jin Guan
- Center for Structural and Molecular Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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8
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Martin A, Schmid FX. A proline switch controls folding and domain interactions in the gene-3-protein of the filamentous phage fd. J Mol Biol 2003; 331:1131-40. [PMID: 12927547 DOI: 10.1016/s0022-2836(03)00864-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The amino-terminal domains N1 and N2 of the gene-3-protein of phage fd form a bilobal structural and functional entity that protrudes from the phage tip. Domain N2 initiates the infection of Escherichia coli by binding to the F pilus. This binding results in the dissociation of the two domains and allows N1 to interact with the TolA receptor at the cell surface. The refolding of the N1-N2 fragment begins with the folding of domain N1, which takes a few milliseconds, followed by the folding of domain N2, which is complete within five minutes. The subsequent domain assembly is unusually slow and shows a time-constant of 6200 s at 25 degrees C. We found that the rate of this reaction is controlled by the trans to cis isomerization of the Gln212-Pro213 bond in the hinge subdomain of N2, a region that provides many interactions between N1 and N2 in the gene-3-protein. The substitution of Pro213 by Gly accelerated domain association 30-fold and revealed that the folding of the two individual domains and their assembly are indeed sequential steps in the refolding of the gene-3-protein. In the course of infection, the domains must separate to expose the binding site for TolA on domain N1. The kinetic block of domain reassembly caused by Pro213 isomerization could ensure that after the initial binding of N2 to the F pilus the open state persists until N1 and TolA are close enough for their mutual interaction. Pro213 isomerization might thus serve as a slow conformational switch in the function of the gene-3-protein.
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Affiliation(s)
- Andreas Martin
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440, Bayreuth, Germany
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9
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Peimbert M, Segovia L. Evolutionary engineering of a beta-Lactamase activity on a D-Ala D-Ala transpeptidase fold. Protein Eng Des Sel 2003; 16:27-35. [PMID: 12646690 DOI: 10.1093/proeng/gzg008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The beta-Lactamase hydrolytic activity has arisen several times from DD-transpeptidases. We have been able to replicate the evolutionary process of beta-Lactamase activity emergence on a PBP2X DD-transpeptidase. Some of the most interesting changes, like modifying the catalytic properties of an enzyme, may require several mutations in concert; therefore it is essential to explore efficiently sequence space by generating the right diversity. We designed a biased combinatorial library in which biochemical and structural information were incorporated by site directed mutagenesis on relevant residues and then subjected to random mutagenesis to allow for mutations in unforeseen positions. We isolated mutants from this library conferring 10-fold higher cefotaxime resistance levels than the background wild-type through mutations exclusively in the coding sequence. We demonstrate that only three substitutions in the DD-transpeptidase active site, two produced by the directed and one by the random mutagenesis, are sufficient to acquire this activity. The purified product of one mutant (MutE) had a 10(5)-fold increase in cefotaxime deacylation rate allowing it to hydrolyze beta-Lactams yet it has apparently conserved DD-peptidase activity. This work is the first to show a possible evolutionary intermediate between a beta-Lactamase and a DD-transpeptidase necessary for the development of antibiotic resistance.
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Affiliation(s)
- Mariana Peimbert
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62250 México.
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10
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Affiliation(s)
- F X Schmid
- Biochemisches Laboratorium, Universität Bayreuth, D-95440 Bayreuth, Germany
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11
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Lejeune A, Vanhove M, Lamotte-Brasseur J, Pain RH, Frère JM, Matagne A. Quantitative analysis of the stabilization by substrate of Staphylococcus aureus PC1 beta-lactamase. CHEMISTRY & BIOLOGY 2001; 8:831-42. [PMID: 11514231 DOI: 10.1016/s1074-5521(01)00053-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND The stabilization of enzymes in the presence of substrates has been recognized for a long time. Quantitative information regarding this phenomenon is, however, rather scarce since the enzyme destroys the potential stabilizing agent during the course of the experiments. In this work, enzyme unfolding was followed by monitoring the progressive decrease of the rate of substrate utilization by the Staphylococcus aureus PC1 beta-lactamase, at temperatures above the melting point of the enzyme. RESULTS Enzyme inactivation was directly followed by spectrophotometric measurements. In the presence of substrate concentrations above the K(m) values, significant stabilization was observed with all tested compounds. A combination of unfolding kinetic measurements and enzymatic studies, both under steady-state and non-steady-state regimes, allowed most of the parameters characteristic of the two concurrent phenomena (i.e. substrate hydrolysis and enzyme denaturation) to be evaluated. In addition, molecular modelling studies show a good correlation between the extent of stabilization, and the magnitude of the energies of interaction with the enzyme. CONCLUSIONS Our analysis indicates that the enzyme is substantially stabilized towards heat-induced denaturation, independently of the relative proportions of non-covalent Henri-Michaelis complex (ES) and acyl-enzyme adduct (ES*). Thus, for those substrates with which the two catalytic intermediates are expected to be significantly populated, both species (ES and ES*) appear to be similarly stabilized. This analysis contributes a new quantitative approach to the problem.
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Affiliation(s)
- A Lejeune
- Laboratoire d' Enzymologie, Centre d' Ingénierie des Protéines, Institut de Chimie, Université de Liège, Belgium
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