Solvent-induced distortions and the curvature of α-helices

  title={Solvent-induced distortions and the curvature of $\alpha$-helices},
  author={Tom L. Blundell and David J. Barlow and Nivedita Borkakoti and Jesse Thornton},
The α-helix defined in 1951 by Pauling et al. 1 on the basis of model building and X-ray fibre diffraction data has 3.65 residues per turn (n) achieved with planar peptides, torsion angles of φ = −48° and ψ = −57° and hydrogen bonds which are close to linear. Although X-ray analyses of proteins have confirmed the general correctness of the model for the helix, recent high resolution (1.7–1.0 Å) diffraction studies have shown that the parameters described by Pauling et al. 1 and later by Perutz2… Expand
Peptide‐bond distortions and the curvature of α‐helices
Solvent accessible peptide bonds in proteins exhibit a 1–3° compression of the OCN bond angle and a corresponding expansion of the NCCa bond angle, relative to buried peptide bonds. These changes areExpand
High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics
A new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. Expand
The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR
One unexpected feature that emerged from the dynamics calculations was that a Thr side chain subtly disrupted the helical geometry 4–7 residues N‐terminal in sequence, which was reflected in the proton chemical shifts and the rates of amide proton exchange for several amides that engage in a mixed 310/α/π‐helical conformation. Expand
Influence of the environment in the conformation of alpha-helices studied by protein database search and molecular dynamics simulations.
There is a remarkable coincidence between the phi and Psi angles obtained in the analysis of residues exposed to the lipid in membrane proteins and the results from computer simulations in methane, which suggests that this simulation protocol properly mimic the lipidic cell membrane and reproduce several structural characteristics of membrane-embedded proteins. Expand
HELANAL-Plus: a web server for analysis of helix geometry in protein structures
This work follows the algorithm published by Shakarji (1998) to get the best fit linear and curved helix axis and shows that an evolutionary conservation of proline derived kinks is suggested even after the mutation of the prolines to other amino acids. Expand
Structural features of transmembrane helices
At the C‐termini of transmembrane helices structural motifs equivalent to the Gly‐caps of helices in globular proteins have been found, with two third of the trans Membrane Gly‐ Caps taking up a primary structure that is typically not found at helix termini exposed to a polar solvent. Expand
Solvated states of poly-L-alanine α-helix explored by Raman optical activity.
Simulation of ROA spectra utilizing the normal mode optimization and Cartesian tensor transfer methods indicate that the change in dielectric constant of the solvent is the main factor for the spectral intensity change, whereas the influence of the conformational change is minor. Expand
Helix geometry in proteins.
In alpha-helices where there are kinks caused by proline residues, it is shown that the angle of kink is relatively constant (approximately 26 degrees), and that there is minimal disruption of the helix hydrogen bonding. Expand
Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation.
An important role played by shortest 3(10)-helices in proteins with important structural and folding implications is ascribed, based on correlation matrices of site-specific amino acid composition, and the relative abundance of these short secondary structural elements. Expand
H-Bond Surrogate-Stabilized Shortest Single-Turn α-Helices: sp2 Constraints and Residue Preferences for the Highest α-Helicities
An HBS model that can be placed in unstructured tetrapeptides without excising any of its residues, and that biases them predominantly into remarkably stable single α-helical turns in varying solvents, pH values, and temperatures is introduced. Expand


Structure of actinidin, after refinement at 1.7 A resolution.
  • E. Baker
  • Chemistry, Medicine
  • Journal of molecular biology
  • 1980
The structure of the sulphydryl protease, actinidin, after refinement at 1.7 A resolution, is described and the geometry of hydrogen bonds in helices, β-structure and turns has been analysed. Expand
The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain.
This work has used information about interatomic distances, bond angles, and other configurational parameters to construct two reasonable hydrogen-bonded helical configurations for the polypeptide chain; it is likely that these configurations constitute an important part of the structure of both fibrous and globular proteins, as well as of syntheticpolypeptides. Expand
The helical hydrophobic moment: a measure of the amphiphilicity of a helix
The spatial distribution of the hydrophobic side chains in globular proteins is of considerable interest. It was recognized previously1 that most of the α-helices of myoglobin and haemoglobin areExpand
Conformational flexibility in a small globular hormone: X‐ray analysis of avian pancreatic polypeptide at 0.98‐Å resolution
For the first time, six‐parameter anisotropic thermal ellipsoids have been refined for each atom; these define the directions of the molecular motions in the polypeptide, indicating concerted vibrations. Expand
Solvent effects and polar interactions in the structural stability and dynamics of globular proteins.
Using detailed hydrogen bonding, surface exposure, internal environment, and solvent interaction calculations on several proteins, in conjunction wit data from quantum mechanical hydrogen-bondingExpand
Structure and function of haemoglobin: II. Some relations between polypeptide chain configuration and amino acid sequence
In a protein of unknown structure, a regular periodicity of invariant non-polar sites might serve to recognize helical regions, and the incidence of prolines to define their lengths, if all the proline sites observed are plotted along the sequence. Expand
Structure of erythrocruorin in different ligand states refined at 1.4 A resolution.
Spin state changes seem to have little influence on the porphyrin stereochemistry; it is determined primarily by the chemical properties of the ligand and its interaction with the haem and the globin. Expand
New X-Ray Evidence on the Configuration of Polypeptide Chains: Polypeptide Chains in Poly-γ-benzyl-L-glutamate, Keratin and Hæmoglobin
New X-Ray Evidence on the Configuration of Polypeptide Chains: Polypeptide Chains in Poly-γ-benzyl-L-glutamate, Keratin and Haemoglobin