The design of linear peptides that fold as monomeric beta-sheet structures

De novo protein design: Crystallographic characterization of a synthetic peptide containing independent helical and hairpin domains

The Meccano (or Lego) set approach to synthetic protein design envisages covalent assembly of prefabricated units of peptide secondary structure. Stereochemical control over peptide folding is achieved by incorporation of conformationally constrained residues like alpha-aminoisobutyric acid (Aib) or DPro that nucleate helical and beta-hairpin structures, respectively. The generation of a synthetic sequence containing both a helix and a hairpin is achieved in the peptide BH17, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Gly-Gly-Leu-Phe-Val-DPro-Gly-Leu- Phe-Val-OMe (where Boc is t-butoxycarbonyl), as demonstrated by a crystal structure determination. The achiral -Gly-Gly- linker permits helix termination as a Schellman motif and extension to the strand segment of the hairpin. Structure parameters for C(89)H(143)N(17)O(20) x 2H(2)O are space group P2(1), a = 14.935(7) A, b = 18.949(6) A, c = 19.231(8) A, beta = 101.79(4) degrees, Z = 2, agreement factor R(1) = 8.50% for 4,862 observed reflections > 4 sigma(F), and resolution of approximately 0.98 A.

De novo protein design: crystallographic characterization of a synthetic peptide containing independent helical and hairpin domains

The Meccano (or Lego) set approach to synthetic protein design envisages covalent assembly of prefabricated units of peptide secondary structure. Stereochemical control over peptide folding is achieved by incorporation of conformationally constrained residues like alpha-aminoisobutyric acid (Aib) or DPro that nucleate helical and beta-hairpin structures, respectively. The generation of a synthetic sequence containing both a helix and a hairpin is achieved in the peptide BH17, Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Gly-Gly-Leu-Phe-Val-DPro-Gly-Leu- Phe-Val-OMe (where Boc is t-butoxycarbonyl), as demonstrated by a crystal structure determination. The achiral -Gly-Gly- linker permits helix termination as a Schellman motif and extension to the strand segment of the hairpin. Structure parameters for C(89)H(143)N(17)O(20) x 2H(2)O are space group P2(1), a = 14.935(7) A, b = 18.949(6) A, c = 19.231(8) A, beta = 101.79(4) degrees, Z = 2, agreement factor R(1) = 8.50% for 4,862 observed reflections > 4 sigma(F), and resolution of approximately 0.98 A.

beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat

The stability and (un)folding of the 19-residue peptide, SCVTLYQSWRYSQADNGCA, corresponding to the first beta-hairpin (residues 10 to 28) of the alpha-amylase inhibitor tendamistat (PDB entry 3AIT) has been studied by molecular dynamics simulations in explicit water under periodic boundary conditions at several temperatures (300 K, 360 K and 400 K), starting from various conformations for simulation lengths, ranging from 10 to 30 ns. Comparison of trajectories of the reduced and oxidized native peptides reveals the importance of the disulphide bridge closing the beta-hairpin in maintaining a proper turn conformation, thereby insuring a proper side-chain arrangement of the conserved turn residues. This allows rationalization of the conservation of those cysteine residues among the family of alpha-amylase inhibitors. High temperature simulations starting from widely different initial configurations (native beta-hairpin, alpha and left-handed helical and extended conformations) begin sampling similar regions of the conformational space within tens of nanoseconds, and both native and non-native beta-hairpin conformations are recovered. Transitions between conformational clusters are accompanied by an increase in energy fluctuations, which is consistent with the increase in heat capacity measured experimentally upon protein folding. The folding events observed in the various simulations support a model for beta-hairpin formation in which the turn is formed first, followed by hydrogen bond formation closing the hairpin, and subsequent stabilization by side-chain hydrophobic interactions.

Design of single-layer beta-sheets without a hydrophobic core

The hydrophobic effect is the main thermodynamic driving force in the folding of water-soluble proteins. Exclusion of nonpolar moieties from aqueous solvent results in the formation of a hydrophobic core in a protein, which has been generally considered essential for specifying and stabilizing the folded structures of proteins. Outer surface protein A (OspA) from Borrelia burgdorferi contains a three-stranded beta-sheet segment which connects two globular domains. Although this single-layer beta-sheet segment is exposed to solvent on both faces and thus does not contain a hydrophobic core, the segment has a high conformational stability. Here we report the engineering of OspA variants that contain larger single-layer beta-sheets (comprising five and seven beta-strands) by duplicating a beta-hairpin unit within the beta-sheet. Nuclear magnetic resonance and small-angle X-ray scattering analyses reveal that these extended single-layer beta-sheets are formed as designed, and amide hydrogen-deuterium exchange and chemical denaturation show that they are stable. Thus, interactions within the beta-hairpin unit and those between adjacent units, which do not involve the formation of a hydrophobic core, are sufficient to specify and stabilize the single-layer beta-sheet structure. Our results provide an expanded view of protein folding, misfolding and design.

Fast kinetics and mechanisms in protein folding

This review describes how kinetic experiments using techniques with dramatically improved time resolution have contributed to understanding mechanisms in protein folding. Optical triggering with nanosecond laser pulses has made it possible to study the fastest-folding proteins as well as fundamental processes in folding for the first time. These include formation of alpha-helices, beta-sheets, and contacts between residues distant in sequence, as well as overall collapse of the polypeptide chain. Improvements in the time resolution of mixing experiments and the use of dynamic nuclear magnetic resonance methods have also allowed kinetic studies of proteins that fold too fast (greater than approximately 10(3) s-1) to be observed by conventional methods. Simple statistical mechanical models have been extremely useful in interpreting the experimental results. One of the surprises is that models originally developed for explaining the fast kinetics of secondary structure formation in isolated peptides are also successful in calculating folding rates of single domain proteins from their native three-dimensional structure.