A sequence preference for nucleation of α‐helix—crystal structure of Gly‐<scp>L</scp>‐Ala‐<scp>L</scp>‐Val and Gly‐<scp>L</scp>‐Ala‐<scp>L</scp>‐Leu: Some comments on the geometry of leucine zippers

Chaturvedi, Sanjeev; Go, K.; Parthasarathy, R.

doi:10.1002/bip.360310405

Cited by 25 publications

(22 citation statements)

References 17 publications

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“…Special attention is paid to intermolecular interactions involving water molecules. Crystal studies were performed on the noncyclical tripeptides Gly-Ala-Val‚3H 2 O and Gly-Ala-Leu‚3H 2 O, 51 which are in helical conformations, and Ala-Ala-Ala, which is a parallel pleated sheet model. 52 These peptides include water molecules and ionic functional groups.…”

Section: Resultsmentioning

confidence: 99%

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

et al. 1998

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New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.

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Section: Resultsmentioning

confidence: 99%

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

et al. 1998

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“…We have measured the 13 C α CSA of the central alanine in three crystal forms of the tripeptides glycyl- l -alanyl- l -valine (G*AV) and l -alanyl- l -alanyl- l -alanine , (A*AA and A*AA-hemihydrate) by slow CPMAS experiments. The measured values correlate well with those calculated by ab initio methods using φ and ψ angles around the central alanine C α taken from the known crystal structures.…”

Section: Introductionmentioning

confidence: 99%

Determination of Dihedral Angles in Peptides through Experimental and Theoretical Studies of α-Carbon Chemical Shielding Tensors

et al. 1997

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A simple method for the determination of backbone dihedral angles in peptides and proteins is presented. The chemical-shift anisotropies (CSA) of the central alanine α-carbon in powdered crystalline tripeptides, whose structures have been determined previously by X-ray crystallography, were measured by cross-polarization magic-angle-spinning nuclear magnetic resonance. The experimental CSA values were correlated with ab initio chemical-shielding calculations over Ramanchandran φ/ψ space on an N-formyl-l-alanine amide fragment. Using this correlation, φ/ψ probability surfaces for one of the tripeptides were calculated based only on the α-carbon CSA, allowing a prediction of backbone angles. Dihedral angles predicted by these calculations fall within ±12° of the values determined by crystallography. This approach should be useful in the determination of solid-state protein structure.

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“…The hydrated structure is ahelix-like and formed when crystallized from a water-methanol solution. 11 The structure contains three unique water molecules labeled W A , W B and W H . The backbone of a tripeptide is too small to form an (i, i + 4) hydrogen bond of an a-helix.…”

Section: Thz Results Of the Tripeptide Gly-ala-leu (Gal)mentioning

confidence: 99%

“…New experimental THz data and QM results are reported on the tripeptide, Gly-Ala-Leu (GAL), which is known from X-ray studies to crystallize from water-methanol solution into an a-helical secondary structure. 11 The co-crystallization of three different types of water molecules occurs at the hydrophilic sites in this tripeptide to form two types of hydrogen bonding networks, including one 13-atom (R13) and one nine-atom (R9) hydrogen bonded ring. In the R13 form, the water molecule bridges the N-and C-termini and thus critically functions to retain the helical conformation of the peptide.…”

Section: Introductionmentioning

confidence: 99%

State-resolved THz spectroscopy and dynamics of crystalline peptide–water systems

et al. 2011

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Vibrationally state-resolved THz spectra are obtained at cryogenic temperatures for three crystalline peptide-water systems that represent different structural motifs. The systems include two types of secondary structures and a hydrophobic peptide nanopore structure. Almost all of these systems are shown to undergo exchange with water at room temperature that alters the hydrogen bonding network in ways easily detectable in the THz region at cryogenic temperatures. Stark differences are observed in the spectra of model a-helical and b-sheet structures upon water removal at hydrophilic binding sites. However, within the confined pore of a hydrophobic nanotube, water in the form of helical wires has a subtle but significant impact on the phonon modes of the tube. The THz spectra are shown to easily distinguish between the different hydration states of the system that have been independently characterized by mass change measurements. Spectral comparisons with quantum chemical predictions of fully relaxed crystal structures confirm the hydration states and give detailed information about the free energies associated with dehydration. The vibrational free energies are shown to make significant contributions to the overall energy balance of the dehydration processes.

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A sequence preference for nucleation of α‐helix—crystal structure of Gly‐L‐Ala‐L‐Val and Gly‐L‐Ala‐L‐Leu: Some comments on the geometry of leucine zippers

Cited by 25 publications

References 17 publications

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

Determination of Dihedral Angles in Peptides through Experimental and Theoretical Studies of α-Carbon Chemical Shielding Tensors

State-resolved THz spectroscopy and dynamics of crystalline peptide–water systems

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