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Structure-Based Prediction Reveals Capping Motifs That Inhibit Β-Helix Aggregation

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Structure-Based Prediction Reveals Capping Motifs That Inhibit Β-Helix Aggregation Structure-based prediction reveals capping motifs that inhibit β-helix aggregation Allen W. Bryan, Jr.a,b,c, Jennifer L. Starner-Kreinbrinkd, Raghavendra Hosurc, Patricia L. Clarkd,1, and Bonnie Bergerc,e,1 aHarvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139; bWhitehead Institute, 9 Cambridge Center, Cambridge, MA 02139; cComputer Science and Artificial Intelligence Laboratory, 77 Massachusetts Avenue, Cambridge, MA 02139; dDepartment of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556; and eDepartment of Mathematics, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA 02139 Edited* by Susan Lindquist, Whitehead Institute for Biomedical Research, Cambridge, MA, and approved May 13, 2011 (received for review November 23, 2010) The parallel β-helix is a geometrically regular fold commonly found in the proteomes of bacteria, viruses, fungi, archaea, and some vertebrates. β-helix structure has been observed in monomeric units of some aggregated amyloid fibers. In contrast, soluble β- helices, both right- and left-handed, are usually “capped” on each end by one or more secondary structures. Here, an in-depth classi- fication of the diverse range of β-helix cap structures reveals subtle commonalities in structural components and in interactions with the β-helix core. Based on these uncovered commonalities, a toolkit of automated predictors was developed for the two distinct types of cap structures. In vitro deletion of the toolkit-predicted C-terminal cap from the pertactin β-helix resulted in increased aggregation and the formation of soluble oligomeric species. These results suggest that β-helix cap motifs can prevent specific, β-sheet- mediated oligomeric interactions, similar to those observed in BIOPHYSICS AND amyloid formation. COMPUTATIONAL BIOLOGY beta-helix ∣ hidden Markov model ∣ threading ∣ aggregation prediction ∣ beta-sheet oligomerization Fig. 1. Pectin methylesterase, 1GQ8; a typical β-helix. 1GQ8 is a right- arallel β-helices (1–3) are defined by the regular nature of handed β-helix, three-sided, with a single α-helix cap at its N terminus and Ptheir rungs, each of which consists of two or three β-strands a previous-strand visor cap at its C terminus. Inset, the assignment of β-strand arranged in sequential repeats separated by loops of various and turn names in a β-helix rung as seen in residues 167-225 of pectate lyase C β lengths (Fig. 1). Helical stacking of these rungs produces two (2PEC), a similar -helix. or three parallel β-sheets surrounding a central core filled with β inward-facing amino acid side chains. -helices form structurally In this paper we present an in-depth study of β-helix cap struc- and geometrically regular domains, despite the presence of loops tures, describe beta-helix β-helix cap detectors based on our struc- of various lengths, which can themselves include regular struc- β tural results, and report experimental evidence demonstrating a ture. The regularity of the -helix structure persists despite great β disparity in primary sequence (4–6). While right-handed parallel role for cap structures in preventing -helix aggregation. The β β-helices were the first to be described (3), left-handed (4, 7) and available structures in the PDB are classified by -helix cap fold α two-stranded (8) β-helices have now also been identified. Nota- into -helix and visor cap motifs that cross-correlate with estab- bly, β-helices are overrepresented in bacterial Protein Data Bank lished β-helix families. Despite wide variety in both sequence and (PDB) (9) entries but rare in eukaryotic entries (5). structure, these motifs display subtle but consistent themes that Richardson and Richardson (10) noted that β-helices often were revealed by focused modeling using hidden Markov models begin and end with a loop at either end, termed a β-helix cap. This (HMMs) and threading approaches. These models were com- cap is amphipathic: one side, sometimes incorporating charged piled into a prediction toolkit that accurately identifies β-helix residues, is exposed to solvent, while the other side caps the hy- caps from protein sequences with high specificity, even across β β drophobic core of the -helix. Caps thus protect -helix cores superfamilies. In vitro deletion of a toolkit-predicted result, from solvent exposure. Richardson and Richardson, among the C-terminal cap of the pertactin β-helix, is shown to promote others (11), speculated that caps could also prevent aggregation intermolecular interactions and aggregation. of β-helices. Many agglutinative proteins, including prion and amyloid proteins, are suspected to consist of repeating and inde- finitely extendable β-sheets assembled from monomers. Without a mechanism to interrupt formation of potential intermolecular β β Author contributions: A.W.B., J.L.S.-K., P.L.C., and B.B. designed research; A.W.B., hydrogen bonds at the ends of -helices, -helix-forming peptides J.L.S.-K., and R.H. performed research; R.H., P.L.C., and B.B. contributed new reagents/ could associate to form multimeric fibers similar to amyloid. analytic tools; J.L.S.-K. and R.H. rendered figures; A.W.B., J.L.S.-K., R.H., P.L.C., and Thus, disruption of β-helix caps could sequester β-helices into B.B. analyzed data; and A.W.B., J.L.S.-K., P.L.C., and B.B. wrote the paper. aggregate fibrils. However, despite the possible importance of The authors declare no conflict of interest. β-helix caps as preventers of aggregation, and despite interest *This Direct Submission article had a prearranged editor. in β-helices as potential models of prion and aggregative protein Freely available online through the PNAS open access option. assembly (12–15), no survey of the presumably analogous assem- 1To whom correspondence may be addressed. E-mail: [email protected] or [email protected]. — — bly interfaces the known caps and the adjacent structures has This article contains supporting information online at www.pnas.org/lookup/suppl/ been made. doi:10.1073/pnas.1017504108/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1017504108 PNAS ∣ July 5, 2011 ∣ vol. 108 ∣ no. 27 ∣ 11099–11104 Downloaded by guest on October 2, 2021 Results Structural Characterization of β-Helix Caps. In order to understand β-helix cap structures in sufficient detail to make β-helix cap classification possible, clear definitions and characterization of β-helix caps were required. Therefore, a survey of available β-helix structures from the PDB was conducted (see SI Text). For purposes of analysis, the extent of each cap was defined as the minimum continuous set of residues necessary to fulfill three requirements: (i) at least one continuous subset of cap residues maintains van der Waals contact with the hydrophobic core of the β-helix; (ii) at least one continuous subset of cap re- sidues maintains van der Waals contact with at least one strand of the terminal rung of the β-helix such that the cap backbone inter- sects the plane of its β-sheet, and (iii) caps do not begin or end within an element of regular secondary structure. The first two requirements reflect the functions of β-helix caps. Contact with the hydrophobic core adds stability and solubility to the β-helix, while intersecting at least one β-sheet plane provides steric hin- drance against H-bonding of the terminal rung with other pro- teins, especially other monomers or oligomers of the β-helix. The third requirement forced the inclusion of the entirety of each element of secondary structure, ensuring sufficient data for accurate sequence/secondary structure comparison. This survey revealed the vast majority of β-helix caps to follow one of two loose structural patterns. The definitions of these pat- terns, the α-helix and visor caps, are derived from the general definition above and described in more detail in SI Text. The α-helix caps (Fig. 2 A–C) are characterized by two secondary α structures, at least one of which is an -helix, lying approximately Fig. 2. α-helix and visor cap structures. All α-helix caps displayed are N-caps parallel to each other and to β-strand(s) of the adjacent β-helix and all visor caps displayed are C-caps, except for (I), where both N- and rung. In contrast, visor caps (Fig. 2 D–I) have in common a more C-caps are visors. For visibility, other domains and distant portions of the acute angle between structural elements than the angles connect- β-helices have been removed. All images were produced using PyMol ing β-strands in the adjacent β-helix, and a near-perpendicular, (www.pymol.org). (A–C) Representative α-helix N-caps. Structural compo- as opposed to aligned, intersection with the plane of at least nents used in HELIXCAP-HMM prediction are labeled: black labels, AE; red β labels, α-helix; and green labels, first rung. (A) 1BN8 (residues 33–46 shown); one -sheet. Aside from the common patterns of turns and con- – – – tact points, and the presence of at least one α-helix in α-helix (B) 1GQ8 (residues 8 32 shown); (C) 1KQA (residues 22 54 shown). (D I) Re- presentative visor family caps. (D) 1KQA (residues 53–190 shown), a previous- caps, β-helix caps display a wide variety of sequence and structure β – α strand visor on a left-handed -helix; (E) 1JTA (residues 260 340 shown), a diversity, incorporating loops, additional -helices, and short previous-strand visor on a right-handed β-helix; (F) 1G95 (residues 376–441 β-strands. shown), a cross-helix visor on a left-handed β-helix; (G) 1DBG (residues Despite this diversity, models were effectively developed to 379–433 shown), a cross-helix visor on a right-handed β-helix; (H) 2PEC (re- describe the commonalities of each type of cap.
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