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Tamman H, Ernits K, Roghanian M, Ainelo A, Julius C, Perrier A, Talavera A, Ainelo H, Dugauquier R, Zedek S, Thureau A, Pérez J, Lima-Mendez G, Hallez R, Atkinson GC, Hauryliuk V, Garcia-Pino A. Structure of SpoT reveals evolutionary tuning of catalysis via conformational constraint. Nat Chem Biol 2023; 19:334-345. [PMID: 36470996 PMCID: PMC9974481 DOI: 10.1038/s41589-022-01198-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022]
Abstract
Stringent factors orchestrate bacterial cell reprogramming through increasing the level of the alarmones (p)ppGpp. In Beta- and Gammaproteobacteria, SpoT hydrolyzes (p)ppGpp to counteract the synthetase activity of RelA. However, structural information about how SpoT controls the levels of (p)ppGpp is missing. Here we present the crystal structure of the hydrolase-only SpoT from Acinetobacter baumannii and uncover the mechanism of intramolecular regulation of 'long'-stringent factors. In contrast to ribosome-associated Rel/RelA that adopt an elongated structure, SpoT assumes a compact τ-shaped structure in which the regulatory domains wrap around a Core subdomain that controls the conformational state of the enzyme. The Core is key to the specialization of long RelA-SpoT homologs toward either synthesis or hydrolysis: the short and structured Core of SpoT stabilizes the τ-state priming the hydrolase domain for (p)ppGpp hydrolysis, whereas the longer, more dynamic Core domain of RelA destabilizes the τ-state priming the monofunctional RelA for efficient (p)ppGpp synthesis.
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Affiliation(s)
- Hedvig Tamman
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium.
| | - Karin Ernits
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Chemistry, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Mohammad Roghanian
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Departement of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Andres Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | | | - Anthony Perrier
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- Bacterial Cell Cycle and Development, Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | - Hanna Ainelo
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | - Rémy Dugauquier
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Safia Zedek
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
| | | | - Javier Pérez
- Synchrotron SOLEIL, Saint-Aubin - BP 48, Gif sur Yvette, France
| | - Gipsi Lima-Mendez
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
| | - Régis Hallez
- Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- Bacterial Cell Cycle and Development, Biology of Microorganisms Research Unit, Namur Research Institute for Life Science, University of Namur, Namur, Belgium
- WELBIO, Brussels, Belgium
| | - Gemma C Atkinson
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medicine, University of Lund, Lund, Sweden.
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- University of Tartu, Institute of Technology, Tartu, Estonia.
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium.
- WELBIO, Brussels, Belgium.
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Clark LC, Atkin KE, Whelan F, Brentnall AS, Harris G, Towell AM, Turkenburg JP, Liu Y, Feizi T, Griffiths SC, Geoghegan JA, Potts JR. Staphylococcal Periscope proteins Aap, SasG, and Pls project noncanonical legume-like lectin adhesin domains from the bacterial surface. J Biol Chem 2023; 299:102936. [PMID: 36702253 PMCID: PMC9999234 DOI: 10.1016/j.jbc.2023.102936] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/08/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Staphylococcus aureus and Staphylococcus epidermidis are frequently associated with medical device infections that involve establishment of a bacterial biofilm on the device surface. Staphylococcal surface proteins Aap, SasG, and Pls are members of the Periscope Protein class and have been implicated in biofilm formation and host colonization; they comprise a repetitive region ("B region") and an N-terminal host colonization domain within the "A region," predicted to be a lectin domain. Repetitive E-G5 domains (as found in Aap, SasG, and Pls) form elongated "stalks" that would vary in length with repeat number, resulting in projection of the N-terminal A domain variable distances from the bacterial cell surface. Here, we present the structures of the lectin domains within A regions of SasG, Aap, and Pls and a structure of the Aap lectin domain attached to contiguous E-G5 repeats, suggesting the lectin domains will sit at the tip of the variable length rod. We demonstrate that these isolated domains (Aap, SasG) are sufficient to bind to human host desquamated nasal epithelial cells. Previously, proteolytic cleavage or a deletion within the A domain had been reported to induce biofilm formation; the structures suggest a potential link between these observations. Intriguingly, while the Aap, SasG, and Pls lectin domains bind a metal ion, they lack the nonproline cis peptide bond thought to be key for carbohydrate binding by the lectin fold. This suggestion of noncanonical ligand binding should be a key consideration when investigating the host cell interactions of these bacterial surface proteins.
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Affiliation(s)
- Laura C Clark
- Department of Biology, University of York, York, United Kingdom
| | - Kate E Atkin
- Department of Biology, University of York, York, United Kingdom
| | - Fiona Whelan
- Department of Biology, University of York, York, United Kingdom; Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, South Australia, Australia.
| | | | - Gemma Harris
- Department of Biology, University of York, York, United Kingdom
| | - Aisling M Towell
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | | | - Yan Liu
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ten Feizi
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | - Joan A Geoghegan
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland; Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Jennifer R Potts
- Department of Biology, University of York, York, United Kingdom; School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia.
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Nascimento KS, Silva MTL, Oliveira MV, Lossio CF, Pinto-Junior VR, Osterne VJS, Cavada BS. Dalbergieae lectins: A review of lectins from species of a primitive Papilionoideae (leguminous) tribe. Int J Biol Macromol 2019; 144:509-526. [PMID: 31857177 DOI: 10.1016/j.ijbiomac.2019.12.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/06/2019] [Accepted: 12/14/2019] [Indexed: 01/24/2023]
Abstract
Lectins are (glyco)proteins capable of reversibly binding to specific carbohydrates, thus having various functions and applications. Plant lectins are the best studied, and the Leguminoseae family is highlighted in a number of published works, especially species of the Papilionoideae subfamily. Dalbergieae is one of the tribes in this subfamily comprising 49 genera and over 1300 species. From this tribe, about 26 lectins were studied, among which we can highlight the Arachis hypogaea lectin, widely used in cancer studies. Dalbergieae lectins demonstrate various carbohydrate specificities and biological activities including anti-inflammatory, vasorelaxant, nociceptive, antibacterial, antiviral among others. Structurally, these lectins are quite similar in their three-dimensional folding but present significant differences in oligomerization patterns and in the conservation of carbohydrate-recognition domain. Despite the existence of structural data from some lectins, only sparse literature has reported on this tribe's diversity, not to mention the range of biological effects, determined through specific assays. Therefore, this work will review the most important studies on Dalbergieae lectins and their potential biomedical applications.
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Affiliation(s)
- Kyria Santiago Nascimento
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil.
| | - Mayara Torquato Lima Silva
- Departamento de Bioquímica, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Messias Vital Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil
| | - Claudia Figueiredo Lossio
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil
| | | | - Vinicius Jose Silva Osterne
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil
| | - Benildo Sousa Cavada
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará (UFC), Fortaleza, Ceará, Brazil.
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Van Nerom K, Tamman H, Takada H, Hauryliuk V, Garcia-Pino A. The Rel stringent factor from Thermus thermophilus: crystallization and X-ray analysis. Acta Crystallogr F Struct Biol Commun 2019; 75:561-569. [PMID: 31397328 PMCID: PMC6688660 DOI: 10.1107/s2053230x19010628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/26/2019] [Indexed: 11/11/2022] Open
Abstract
The stringent response, controlled by (p)ppGpp, enables bacteria to trigger a strong phenotypic resetting that is crucial to cope with adverse environmental changes and is required for stress survival and virulence. In the bacterial cell, (p)ppGpp levels are regulated by the concerted opposing activities of RSH (RelA/SpoT homologue) enzymes that can transfer a pyrophosphate group of ATP to the 3' position of GDP (or GTP) or remove the 3' pyrophosphate moiety from (p)ppGpp. Bifunctional Rel enzymes are notoriously difficult to crystallize owing to poor stability and a propensity for aggregation, usually leading to a loss of biological activity after purification. Here, the production, biochemical analysis and crystallization of the bifunctional catalytic region of the Rel stringent factor from Thermus thermophilus (RelTtNTD) in the resting state and bound to nucleotides are described. RelTt and RelTtNTD are monomers in solution that are stabilized by the binding of Mn2+ and mellitic acid. RelTtNTD crystallizes in space group P4122, with unit-cell parameters a = b = 88.4, c = 182.7 Å, at 4°C and in space group P41212, with unit-cell parameters a = b = 105.7, c = 241.4 Å, at 20°C.
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Affiliation(s)
- Katleen Van Nerom
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Hedvig Tamman
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
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5
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Malik A, Lin YF, Pratihar S, Angel LA, Hase WL. Direct Dynamics Simulations of Fragmentation of a Zn(II)-2Cys-2His Oligopeptide. Comparison with Mass Spectrometry Collision-Induced Dissociation. J Phys Chem A 2019; 123:6868-6885. [DOI: 10.1021/acs.jpca.9b05218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Abdul Malik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
| | - Yu-Fu Lin
- Department of Chemistry Texas A&M University—Commerce, 2600 South Neal Street, Commerce, Texas 75428, United States
| | - Subha Pratihar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
| | - Laurence A. Angel
- Department of Chemistry Texas A&M University—Commerce, 2600 South Neal Street, Commerce, Texas 75428, United States
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
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6
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Mechanism of regulation and neutralization of the AtaR–AtaT toxin–antitoxin system. Nat Chem Biol 2019; 15:285-294. [DOI: 10.1038/s41589-018-0216-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/14/2018] [Indexed: 11/08/2022]
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7
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Barre A, Bourne Y, Van Damme EJM, Rougé P. Overview of the Structure⁻Function Relationships of Mannose-Specific Lectins from Plants, Algae and Fungi. Int J Mol Sci 2019; 20:E254. [PMID: 30634645 PMCID: PMC6359319 DOI: 10.3390/ijms20020254] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/29/2018] [Accepted: 12/31/2018] [Indexed: 01/05/2023] Open
Abstract
To date, a number of mannose-binding lectins have been isolated and characterized from plants and fungi. These proteins are composed of different structural scaffold structures which harbor a single or multiple carbohydrate-binding sites involved in the specific recognition of mannose-containing glycans. Generally, the mannose-binding site consists of a small, central, carbohydrate-binding pocket responsible for the "broad sugar-binding specificity" toward a single mannose molecule, surrounded by a more extended binding area responsible for the specific recognition of larger mannose-containing N-glycan chains. Accordingly, the mannose-binding specificity of the so-called mannose-binding lectins towards complex mannose-containing N-glycans depends largely on the topography of their mannose-binding site(s). This structure⁻function relationship introduces a high degree of specificity in the apparently homogeneous group of mannose-binding lectins, with respect to the specific recognition of high-mannose and complex N-glycans. Because of the high specificity towards mannose these lectins are valuable tools for deciphering and characterizing the complex mannose-containing glycans that decorate both normal and transformed cells, e.g., the altered high-mannose N-glycans that often occur at the surface of various cancer cells.
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Affiliation(s)
- Annick Barre
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France.
| | - Yves Bourne
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Architecture et Fonction des Macromolécules Biologiques, 163 Avenue de Luminy, 13288 Marseille, France.
| | - Els J M Van Damme
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium.
| | - Pierre Rougé
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France.
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8
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Haji-Ghassemi O, Gilbert M, Spence J, Schur MJ, Parker MJ, Jenkins ML, Burke JE, van Faassen H, Young NM, Evans SV. Molecular Basis for Recognition of the Cancer Glycobiomarker, LacdiNAc (GalNAc[β1→4]GlcNAc), by Wisteria floribunda Agglutinin. J Biol Chem 2016; 291:24085-24095. [PMID: 27601469 DOI: 10.1074/jbc.m116.750463] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Indexed: 01/10/2023] Open
Abstract
Aberrant glycosylation and the overexpression of specific carbohydrate epitopes is a hallmark of many cancers, and tumor-associated oligosaccharides are actively investigated as targets for immunotherapy and diagnostics. Wisteria floribunda agglutinin (WFA) is a legume lectin that recognizes terminal N-acetylgalactosaminides with high affinity. WFA preferentially binds the disaccharide LacdiNAc (β-d-GalNAc-[1→4]-d-GlcNAc), which is associated with tumor malignancy in leukemia, prostate, pancreatic, ovarian, and liver cancers and has shown promise in cancer glycobiomarker detection. The mechanism of specificity for WFA recognition of LacdiNAc is not fully understood. To address this problem, we have determined affinities and structure of WFA in complex with GalNAc and LacdiNAc. Affinities toward Gal, GalNAc, and LacdiNAc were measured via surface plasmon resonance, yielding KD values of 4.67 × 10-4 m, 9.24 × 10-5 m, and 5.45 × 10-6 m, respectively. Structures of WFA in complex with LacdiNAc and GalNAc have been determined to 1.80-2.32 Å resolution. These high resolution structures revealed a hydrophobic groove complementary to the GalNAc and, to a minor extent, to the back-face of the GlcNAc sugar ring. Remarkably, the contribution of this small hydrophobic surface significantly increases the observed affinity for LacdiNAc over GalNAc. Tandem MS sequencing confirmed the presence of two isolectin forms in commercially available WFA differing only in the identities of two amino acids. Finally, the WFA carbohydrate binding site is similar to a homologous lectin isolated from Vatairea macrocarpa in complex with GalNAc, which, unlike WFA, binds not only αGalNAc but also terminal Ser/Thr O-linked αGalNAc (Tn antigen).
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Affiliation(s)
- Omid Haji-Ghassemi
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Michel Gilbert
- Human Health Therapeutics, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Jenifer Spence
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Melissa J Schur
- Human Health Therapeutics, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Matthew J Parker
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Meredith L Jenkins
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - John E Burke
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
| | - Henk van Faassen
- Human Health Therapeutics, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - N Martin Young
- Human Health Therapeutics, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Stephen V Evans
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3P6, Canada and
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9
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Structural characterization of a Vatairea macrocarpa lectin in complex with a tumor-associated antigen: A new tool for cancer research. Int J Biochem Cell Biol 2016; 72:27-39. [DOI: 10.1016/j.biocel.2015.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 12/05/2015] [Accepted: 12/31/2015] [Indexed: 11/22/2022]
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10
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Peptide Bond cis/trans Isomerases: A Biocatalysis Perspective of Conformational Dynamics in Proteins. Top Curr Chem (Cham) 2011; 328:35-67. [DOI: 10.1007/128_2011_151] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Optimizing Reaction Conditions for the Isomerization of Fatty Acids and Fatty Acid Methyl Esters to Their Branch Chain Products. J AM OIL CHEM SOC 2010. [DOI: 10.1007/s11746-010-1718-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Mathieu S, Poteau R, Trinquier G. Estimating the "steric clash" at cis peptide bonds. J Phys Chem B 2008; 112:7894-902. [PMID: 18543981 DOI: 10.1021/jp711082d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To account for the scarcity of cis peptide bonds in proteins, especially in nonproline (or secondary amide) cases, a steric-clash argument is often put forward, in a scheme where the R lateral chains are facing parallel one another, and the backbone is kept in an "all- trans"-like arrangement. Although such a steric conflict can be partly relieved through proper adjustment of the backbone dihedral angles, one can try to estimate its associated energy cost. To this end, quantum-chemistry approaches using a differential-torsion protocol and bond-separation-energy analyses are applied to N-ethyl propionamide CH3-CH2-CO-NH-CH2-CH3, regarded as a model capable of exhibiting C beta...C beta interaction as in alanine succession. The calculations provide an increment of 9 kcal/mol, quite close to that obtained in the nearly isostere (gsg) rotamer of n-hexane (10 kcal/mol), suggesting the local effects induced by methyl-methyl contact are similar in both cases. Analogous treatments on larger radicals as encountered in leucine or phenylalanine dimers do not change this increment much, which therefore defines the basic reference per-plaque quota to be overcome along all- cis chains. Explicit modeling indicated it can be reduced by up to a factor of 4.
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Affiliation(s)
- Simon Mathieu
- Laboratoire de Chimie et Physique Quantique, IRSAMC, Université Paul-Sabatier, Toulouse Cedex 9, France
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