A Chemical Approach to Protein Design—Template‐Assembled Synthetic Proteins (TASP)

Mutter, Manfred; Vuilleumier, Stéphane

doi:10.1002/anie.198905353

Cited by 406 publications

(159 citation statements)

References 287 publications

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“…Four-helix bundle proteins representing selected sequences are generated by attachment of four identical peptides to a nine-amino acid template molecule &KKPGKEKG) (Mutter & Vuilleumier, 1989) at the 6-amino groups of indicated lysines (underlined). The template is modeled as two antiparallel ,&sheets connected by a type I1 &turn and designed to provide a suitable arrangement of attached peptide modules (Mutter & Vuilleumier, 1989).…”

Section: Design Considerationsmentioning

confidence: 99%

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Design of a functional calcium channel protein: Inferences about an ion channel‐forming motif derived from the primary structure of voltage‐gated calcium channels

et al. 1993

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To identify sequence-specific motifs associated with the formation of an ionic pore, we systematically evaluated the channel-forming activity of synthetic peptides with sequence of predicted transmembrane segments of the voltage-gated calcium channel. The amino acid sequence of voltage-gated, dihydropyridine (DHP)-sensitive calcium channels suggests the presence in each of four homologous repeats (I-IV) of six segments (SI-S6) predicted to form membrane-spanning, a-helical structures. Only peptides representing amphipathic segments S2 or S3 form channels in lipid bilayers. To generate a functional calcium channel based on a four-helix bundle motif, four-helix bundle proteins representing IVS2 (T4CaIVS2) or IVS3 (T4CaIVS3) were synthesized. Both proteins form cationselective channels, but with distinct characteristics: the single-channel conductance in 50 mM BaCI, is 3 pS and 10 pS. For T4CaIVS3, the conductance saturates with increasing concentration of divalent cation. The dissociation constants for Ba2+, Ca2+, and SrZf are 13.6 mM, 17.7 mM, and 15.0 mM, respectively. The conductance of T4CaIVS2 does not saturate up to 150 mM salt. Whereas T4CaIVS3 is blocked by pM Ca2+ and Cd2+, T4CaIVS2 is not blocked by divalent cations. Only T4CaIVS3 is modulated by enantiomers of the DHP derivative BayK 8644, demonstrating sequence requirement for specific drug action. Thus, only T4CaIVS3 exhibits pore properties characteristic also of authentic calcium channels. The designed functional calcium channel may provide insights into fundamental mechanisms of ionic permeation and drug action, information that may in turn further our understanding of molecular determinants underlying authentic pore structures.Keywords: calcium channel; dihydropyridines; lipid bilayer; protein design; four-helix bundle; single-channel recording Voltage-gated channels, comprising a large superfamily of integral membrane proteins fundamentally involved in electrical excitability (Hille, 1992), facilitate the flux of ions across the cell membrane in response to changes in transmembrane electric field. Because voltage-gated channel proteins have not yet yielded to high-resolution structural analysis, the unequivocal localization of even fundamental motifs, such as the actual ionic pathway, is lacking. However, understanding the unique functional attributes of channel proteins requires that structural elements underlying specific properties are identified. Extensive efforts are currently directed toward elucidating molecular determinants underlying the ionic pore.

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Section: Design Considerationsmentioning

confidence: 99%

“…The template is modeled as two antiparallel ,&sheets connected by a type I1 &turn and designed to provide a suitable arrangement of attached peptide modules (Mutter & Vuilleumier, 1989).…”

Section: Design Considerationsmentioning

confidence: 99%

Design of a functional calcium channel protein: Inferences about an ion channel‐forming motif derived from the primary structure of voltage‐gated calcium channels

et al. 1993

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“…However, the usefulness of this scaffold for the generation of multifunctional serine protease mimetic libraries remains to be proven. This design was based on an earlier proposition called Template Assembled Synthetic Peptides (TASP) [25,26]. In this approach, cyclic decapeptides, derived from the antibiotic gramicidin S containing four Lysines, were used as attachment sites.…”

Section: Accepted M Manuscriptmentioning

confidence: 99%

Molecular Dynamics as a pattern recognition tool: An automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site

Tatsis¹,

Stavrakoudis²,

Demetropoulos³

2008

Biophysical Chemistry

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Recently, the synthesis of a molecule has been reported that belongs to a Lysine based, branched cyclic peptide class. This work explores the ability of such molecules to preserve the 3D geometry of the Trypsin's Active Site (TAS) by applying an integrated framework of automated computer procedures. The following four factors a) D/L chirality, b) different amino acids at different positions of the molecular scaffold's cyclic part, c) the application of AMBER and CHARMM force fields and d) different implicit solvation models were evaluated against TAS similarity. It was found that a number of molecules exhibit satisfactory geometric affinity to the TAS during extended Molecular Dynamics runs. We estimated that more than 2000 molecules (belonging to this class) could retain good similarity to the TAS arrangement.

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“…Our approach to the design of a t a was to rely upon the large body of work with peptide assemblies (Lau et al, 1984;Eisenberg et al, 1986;DeGrado et al, 1987DeGrado et al, , 1989DeGrado, 1988;Mutter & Vuilleumier, 1989;O'Shea et al, 1989;Hodges et al, 1990;Mutter & Hersperger, 1990;O'Neil & DeGrado, 1990) and monomeric helices in solution (Scholtz & Baldwin, 1992). The goal was to develop a peptide system that would meet the requirements outlined above without trying to predict the structure to atomic detail.…”

Section: Rationale Goals Definition Of Success and Approachmentioning

confidence: 99%

“…The next step was to choose a pattern for the hydrophobic amino acids. Because the stability of many monomeric peptide helices in solution is quite small (Scholtz & Baldwin, 1992) and because assemblies of peptides containing hydrophobic interfaces can be quite stable (DeGrado, 1988;Mutter & Vuilleumier, 1989;Hodges et al, 1990;Mutter & Hersperger, 1990), it was clear that a proper hydrophobic interface was crucial to the stability of the peptide. Further, because the aggregation state of designed peptides correlates roughly with the extent and pattern of the hydrophobic interface (DeCrado, 1988;Mutter & Vuilleumier, 1989;O'Shea et al, 1989;Hodges et al, 1990;Mutter & Hersperger, 1990;Chin et al, 1992), a narrow hydrophobic interface similar to that in coiled-coil peptides might be appropriate both for stability and lack of nonspecific aggregation.…”

Section: Designmentioning

confidence: 99%

Strategies and rationales for the de novo design of a helical hairpin peptide

Fezoui

Weaver²,

Osterhout³

1995

Protein Science

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The de novo design of a t a , a helical hairpin peptide, is described. a t a (u-helix/turn/a-helix) was developed to provide a model system for protein folding at the level of secondary structure association and stabilization. According t o the prevailing models of protein folding, the second step in the folding process is the association and stabilization of secondary structural elements or microdomains. A brief description of the design, along with CD and NMR evidence confirming the conformation of the peptide in solution, has been published (Fezoui Y, Weaver DL, Osterhout JJ, 1994, Proc Natl Acad Sci USA 91:3675-3679). The present work includes a full description of the design process, including the trade-offs that were made during the development of the peptide, a discussion of recent experimental results that were not available at the time of the original design, indications of areas where, in retrospect, the design might have been done differently, and a discussion of how the present work fits into the field of de novo protein design.Keywords: diffusion-collision model; molten globule; NMR; peptide; secondary structure; tertiary structure a t a is a de novo designed 38-amino acid peptide that has been shown by CD and two-dimensional NMR to exhibit in solution the designed aspects of secondary and tertiary structure (Fezoui et al., 1994). The purpose of the present paper is to present a full description of the process that led to the sequence of the peptide. Although the paper cited above contains a brief description of the design, space limitations precluded a complete discussion of the design process. In addition, the original peptide design was completed in the fall of 1990. Since then, there has been considerable progress made in the understanding of peptide conformation and the intervening work would have a bearing on any subsequent design.The goal of the design was to produce a peptide containing two interacting helices connected by a turn region. Such a peptide was desired as an experimental model of secondary structure association that could be used to investigate the early stages of protein folding as envisioned in the diffusion-collision model (Karplus & Weaver, 1976 protein folding are transiently folded elements of secondary structure (microdomains) that associate by diffusion and collision and become mutually stabilizing during the second stage of folding (Karplus & Weaver, 1976.Because the helix-forming properties of isolated monomeric helices had received considerable attention (reviewed by Scholtz & Baldwin, 1992), it seemed reasonable to extend the range of inquiry into the mechanisms of protein folding by studying connected helices. Connected and interacting helices might be expected to be stabilized by both short-range and tertiary interactions. The relative contributions to helix stability among the various short-range and tertiary interactions could be investigated with a helical hairpin peptide. Rationale, goals, definition of success, and approachThe first consideration in un...

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A Chemical Approach to Protein Design—Template‐Assembled Synthetic Proteins (TASP)

Cited by 406 publications

References 287 publications

Design of a functional calcium channel protein: Inferences about an ion channel‐forming motif derived from the primary structure of voltage‐gated calcium channels

Design of a functional calcium channel protein: Inferences about an ion channel‐forming motif derived from the primary structure of voltage‐gated calcium channels

Molecular Dynamics as a pattern recognition tool: An automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site

Strategies and rationales for the de novo design of a helical hairpin peptide

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