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Singular points of protein beta-sheets.

ABSTRACT: Protein beta-sheets can be regarded as surfaces. Two surfaces can be connected along a common edge to form a larger surface, or two edges of a surface can coalesce to form a closed sheet such as a beta-barrel. Singular points are locations where these connections are not perfect. In protein beta-sheets, a singular point is characterized by a residue separating two beta-ladders. In this paper, we study the singular points of protein beta-sheets from the surface topologic viewpoint, summarize our search results from the protein structural data in the Protein Data Bank, and present examples where singular points are near the active sites and may contribute to forming the proper relative positions of catalytic residues.

SUBMITTER: Liu WM

PROVIDER: S-EPMC2143876 | biostudies-other | 1998 Nov

REPOSITORIES: biostudies-other

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Singular points of protein beta-sheets.

Liu W M WM Chou K C KC

Protein science : a publication of the Protein Society 19981101 11

Protein beta-sheets can be regarded as surfaces. Two surfaces can be connected along a common edge to form a larger surface, or two edges of a surface can coalesce to form a closed sheet such as a beta-barrel. Singular points are locations where these connections are not perfect. In protein beta-sheets, a singular point is characterized by a residue separating two beta-ladders. In this paper, we study the singular points of protein beta-sheets from the surface topologic viewpoint, summarize our ...[more]

PMID: 9827998

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Project description:The development of peptide beta-hairpins is problematic, because folding depends on the amino acid sequence and changes to the sequence can significantly decrease folding. Robust beta-hairpins that can tolerate such changes are attractive tools for studying interactions involving protein beta-sheets and developing inhibitors of these interactions. This paper introduces a new class of peptide models of protein beta-sheets that addresses the problem of separating folding from the sequence. These model beta-sheets are macrocyclic peptides that fold in water to present a pentapeptide beta-strand along one edge; the other edge contains the tripeptide beta-strand mimic Hao [JACS 2000, 122, 7654] and two additional amino acids. The pentapeptide and Hao-containing peptide strands are connected by two delta-linked ornithine (deltaOrn) turns [JACS 2003, 125, 876]. Each deltaOrn turn contains a free alpha-amino group that permits the linking of individual modules to form divalent beta-sheets. These "cyclic modular beta-sheets" are synthesized by standard solid-phase peptide synthesis of a linear precursor followed by solution-phase cyclization. Eight cyclic modular beta-sheets 1a-1h containing sequences based on beta-amyloid and macrophage inflammatory protein 2 were synthesized and characterized by 1H NMR. Linked cyclic modular beta-sheet 2, which contains two modules of 1b, was also synthesized and characterized. 1H NMR studies show downfield alpha-proton chemical shifts, deltaOrn delta-proton magnetic anisotropy, and NOE cross-peaks that establish all compounds but 1c and 1g to be moderately or well folded into a conformation that resembles a beta-sheet. Pulsed-field gradient NMR diffusion experiments show little or no self-association at low (</=2 mM) concentrations. Changes to the residues in the Hao-containing strands of 1c and 1g improve folding and show that folding of the structures can be enhanced without altering the sequence of the pentapeptide strand. Well-folded cyclic modular beta-sheets 1a, 1b, and 1f each have a phenylalanine directly across from Hao, suggesting that cyclic modular beta-sheets containing aromatic residues across from Hao are better folded.

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Singular points of protein beta-sheets.

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Singular points of protein beta-sheets.

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