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 volume...

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All-atom empirical potential for molecular modeling and dynamics studies of proteins.

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

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The Amber biomolecular simulation programs

Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage).

Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Infrared spectroscopy of proteins.

Publisher Summary This chapter investigates the anatomy and taxonomy of protein structures. A protein is a polypeptide chain made up of amino acid residues linked together in a definite sequence. Amino acids are “handed,” and naturally occurring proteins contain only L-amino acids. A simple mnemonic for that purpose is the “corncrib.” The sequence of side chains determines all that is unique about a particular protein, including its biological function and its specific three-dimensional structure. The major possible routes to knowledge of three-dimensional protein structure are prediction from the amino acid sequence and analysis of spectroscopic measurements such as circular dichroism, laser Raman spectroscopy, and nuclear magnetic resonance. The analysis and discussion of protein structure is based on the results of three-dimensional X-ray crystallography of globular proteins. The basic elements of protein structures are discussed. The most useful level at which protein structures are to be categorized is the domain, as there are many cases of multiple-domain proteins in which each separate domain resembles other entire smaller proteins. The simplest type of stable protein structure consists of polypeptide backbone wrapped more or less uniformly around the outside of a single hydrophobic core. The outline of the taxonomy is also provided in the chapter.

The anatomy and taxonomy of protein structure.

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Vibrational spectra in the CH stretching region and the structure of the polymethylene chain

Infrared spectra of polyethylene terephthalate and three of its deuterated analogs have been obtained in the region of 70 to 3600 cm-i, polarized spect,ra having been obtained down to 330 cm-l On the basis of analysis of the predicted spectrum, and with the aid of data from benzene and substituted benzenes, a complete assignment of the spectrum has been made This assignment suggests a modification of the proposed chain structure of this polymer It also leads to the conclusion that the changes in the spectrum which occur upon crystallization of the polymer are not associated with different isomeric forms of the -OCH2CH20portion of the chain, but rather with changes in the symmetry and resonance characteristics of the substituted benzenoid ring framework

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Infrared spectra of high polymers

The infrared spectrum of polyethylene has been obtained between about 3000 cm—1 and 70 cm—1, polarization measurements on oriented specimens having been obtained to about 350 cm—1. Assignments of the fundamentals are made with the help of a group theory analysis. The assignment of the controversial CH2 wagging mode is discussed in detail and especially in terms of new evidence from the spectra of n‐paraffins, both as single crystals and as polycrystalline aggregates. It is shown that this mode is to be assigned to a weak band at 1369 cm—1. A satisfactory determination of the bands which arise from CH3 groups is also made possible by a study of the paraffin spectra. The splitting of bands in the spectrum is conclusively shown to arise from interactions between molecules in the crystalline phase. The nature of this interaction is discussed in terms of recent theories.

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Infrared Spectra of High Polymers. II. Polyethylene

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New chain conformations of poly(glutamic acid) and polylysine

Previous perturbation treatments of the Amide I vibrations of β polypeptides are inconsistent with a detailed normal coordinate analysis of crystalline polyglycine I. This analysis indicates that the D10 interaction constant is essentially zero, rather than the large value (about 20 cm-1) required by the earlier application of the perturbation theory. It is suggested that the previously neglected D11 term should be included in the perturbation expression, and it is shown that the physical origin of such a term can be accounted for by transition dipole coupling. This mechanism is shown to give a reasonable explanation of splittings of the C=O stretching vibrations in hydrogenbonded carboxylic acid dimers. Its application to β polypeptides provides a satisfactory interpretation of splittings in the Amide I modes.

https://www.pnas.org/content/pnas/69/10/2788.full.pdf

Samuel Krimm

Papers

Vibrational spectra in the CH stretching region and the structure of the polymethylene chain

Infrared spectra of high polymers

Infrared Spectra of High Polymers. II. Polyethylene

New chain conformations of poly(glutamic acid) and polylysine

Intermolecular Interaction Effects in the Amide I Vibrations of β Polypeptides