The conformations of polypeptide chains where the main-chain parts of successive residues are enantiomeric. Their occurrence in cation and anion-binding regions of proteins 1 1 Edited by J. Thornton

Watson, James D.; Milner‐White, E. James

doi:10.1006/jmbi.2001.5228

Cited by 87 publications

(98 citation statements)

References 34 publications

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“…The search required that all four residues be within Ϯ45°of ideal ␣-sheet (,) angles: [(,) ϭ (45, 90°)] and [(,) ϭ (Ϫ90°, Ϫ45°)], and Ͼ40 unique PDB entries were found to have this conformation (data not shown). Another recent study of protein structures in the PDB has shown that a short alternation of residues in the ␣ R and the ␣ L conformations can create anion and cation binding site ''nests'' in native protein crystal structures (40,41).…”

Section: Methodsmentioning

confidence: 99%

Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease

Armen

DeMarco²,

Alonso³

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

132

170

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Transthyretin, ␤2-microglobulin, lysozyme, and the prion protein are four of the best-characterized proteins implicated in amyloid disease. Upon partial acid denaturation, these proteins undergo conformational change into an amyloidogenic intermediate that can self-assemble into amyloid fibrils. Many experiments have shown that pH-mediated changes in structure are required for the formation of the amyloidogeneic intermediate, but it has proved impossible to characterize these conformational changes at high resolution using experimental means. To probe these conformational changes at atomic resolution, we have performed molecular dynamics simulations of these proteins at neutral and low pH. In low-pH simulations of all four proteins, we observe the formation of ␣-pleated sheet secondary structure, which was first proposed by L. Pauling and R. B. Corey [(1951) Proc. Natl. Acad. Sci. USA 37, 251-256]. In all ␤-sheet proteins, transthyretin and ␤2-microglobulin, ␣-pleated sheet structure formed over the strands that are highly protected in hydrogen-exchange experiments probing amyloidogenic conditions. In lysozyme and the prion protein, ␣-sheets formed in the specific regions of the protein implicated in the amyloidogenic conversion. We propose that the formation of ␣-pleated sheet structure may be a common conformational transition in amyloidosis.

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Section: Methodsmentioning

confidence: 99%

Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease

Armen

DeMarco²,

Alonso³

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

132

170

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“…In our view, the answer to this riddle can be found in the ''nestsand-eggs'' motif recently described by Milner-White and co-workers. 14,15 This term describes a binding motif, composed of the three NHs of three sequential amide groups of peptide main chains. This motif (the ''nest'') is able to bind fully or partially negatively charged entities (the ''eggs'').…”

Section: Discussionmentioning

confidence: 99%

“…A wellknown example for a ''nest'' functioning in this sense is the oxy-anion hole of Ser hydrolases, which binds and stabilizes the so-called tetrahedral intermediate (6, Figure 6). [14][15][16][17] In the case of the Juliá-Colonna reaction, the addition of the hydroperoxy anion to the enone -carbon atom leads to a -peroxyenolate anion (7, Figure 6). We believe this is the ''crossing point'' of biological evolution and the ''nonbiological'' Juliá-Colonna epoxidation, i.e., a ''nest'' stabilizing the anionic transition state (or the anionic intermediate) of the Weitz-Scheffer epoxidation* The question arises whether typical ''nest'' sequences 14,15 may serve as even more efficient catalysts.…”

Section: Discussionmentioning

confidence: 99%

Asymmetric enone epoxidation by short solid‐phase bound peptides: Further evidence for catalyst helicity and catalytic activity of individual peptide strands

Berkessel¹,

Koch²,

Toniolo

et al. 2005

Biopolymers

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In the presence of short solid-phase bound peptide catalysts, the Juliá-Colonna epoxidation of enones (such as chalcone) with hydrogen peroxide can be performed with high enantiomeric excess (> or = 95% ee). It was proposed earlier (A. Berkessel, N. Gasch, K. Glaubitz, C. Koch, Organic Letters, 2001, Vol. 3, pp. 3839-3842) that this remarkable catalysis is governed by the N-terminus of individual and helical peptide strands. This mechanistic proposal was scrutinized further. (i) Nonaggregation of the peptide catalysts: five solid-phase bound statistic mixtures (0/100; 30/70; 50/50; 70/30; 100/0) of D-Leu and L-Leu heptamers were generated and assayed as catalysts. A linear dependence of the epoxide ee on the enantiomeric composition of the catalysts resulted. (ii) Catalyst helicity [introduction of the helix-stabilizing C(alpha)-methyl-L-leucine, L-(alphaMe)Leu]: solid-phase bound Leu/(alphaMe)Leu-pentamers of composition TentaGel-NH-[(alphaMe)-L-Leu]n-(L-Leu)m-H (n = 0-4; m = 5-n) were prepared and assayed as catalysts. The introduction of up to two (alphaMe)-L-Leu residues (n = 1, 2) significantly enhanced the catalyst activity relative to the L-Leu homopentamer (n = 0). Higher (alphaMe)-L-Leu contents (n = 3, 4) led to a decrease in both catalyst activity and enantiopurity of the product epoxide. In summary, both the individual catalytic action of the peptide strands and the helical conformation as the catalytically competent state of the peptide catalysts were further supported.

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“…The functionally active regions, possible nests or enzyme catalytic sites were explored in the modeled Actin-1 protein using ProFunc server (Watson and Milner-White, 2002a;Watson and Milner-White, 2002b;Pal et al, 2002;Laskowski, Watson and Thornton, 2005a;Porter, Bartlett and Thornton, 2004). Sequences showing significant sequence similarity (cut off…”

Section: Function Characterizationmentioning

confidence: 99%

Research paper In silico prediction and characterization of three-dimensional structure of Actin-1 of Arabidopsis thaliana

Sahu¹,

Dehury²,

Sarmah³

et al. 2013

bta

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Actin-1 is a ubiquitous protein belonging to the reproductive class of Actin family in Arabidopsis thaliana . This protein is involved in the formation of filaments that are major components of the cytoskeleton. Despite the importance of this protein, very little information is available regarding its structure and function in plants. In this study, analysis of the protein sequence was done and comparative model of Actin-1 was constructed (UNIPROT ID: P0CJ46) from Arabidopsis thaliana using the crystal structure of Dictyostelium discoideum actin (PDB ID:1NLV-A) as template employing Modeller version 9.9. The stable structure was generated by 5 nanosecond molecular dynamics simulation steps using GROMOS43A1 96 force field that characterized its structural and dynamic feature. The biochemical function of the final simulated structure was also investigated using PROFUNC. The molecular simulation study suggested that the modeled Actin-1 protein retain its stable conformation in aqueous solution. The predicted binding sites in the modeled Actin-1 protein are very informative for further protein-ligand interaction study.

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The conformations of polypeptide chains where the main-chain parts of successive residues are enantiomeric. Their occurrence in cation and anion-binding regions of proteins 1 1 Edited by J. Thornton

Cited by 87 publications

References 34 publications

Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease

Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease

Asymmetric enone epoxidation by short solid‐phase bound peptides: Further evidence for catalyst helicity and catalytic activity of individual peptide strands

Research paper In silico prediction and characterization of three-dimensional structure of Actin-1 of Arabidopsis thaliana

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