MOLMOL: a program for display and analysis of macromolecular structures.

The interpretation of protein structures: estimation of static accessibility.

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.

Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an atomic level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone is crucial to achieve representative conformational distributions in simulation studies. To improve the treatment of the peptide backbone, quantum mechanical (QM) and molecular mechanical (MM) calculations were undertaken on the alanine, glycine, and proline dipeptides, and the results from these calculations were combined with molecular dynamics (MD) simulations of proteins in crystal and aqueous environments. QM potential energy maps of the alanine and glycine dipeptides at the LMP2/cc-pVxZ//MP2/6-31G* levels, where x = D, T, and Q, were determined, and are compared to available QM studies on these molecules. The LMP2/cc-pVQZ//MP2/6-31G* energy surfaces for all three dipeptides were then used to improve the MM treatment of the dipeptides. These improvements included additional parameter optimization via Monte Carlo simulated annealing and extension of the potential energy function to contain peptide backbone phi, psi dihedral crossterms or a phi, psi grid-based energy correction term. Simultaneously, MD simulations of up to seven proteins in their crystalline environments were used to validate the force field enhancements. Comparison with QM and crystallographic data showed that an additional optimization of the phi, psi dihedral parameters along with the grid-based energy correction were required to yield significant improvements over the CHARMM22 force field. However, systematic deviations in the treatment of phi and psi in the helical and sheet regions were evident. Accordingly, empirical adjustments were made to the grid-based energy correction for alanine and glycine to account for these systematic differences. These adjustments lead to greater deviations from QM data for the two dipeptides but also yielded improved agreement with experimental crystallographic data. These improvements enhance the quality of the CHARMM force field in treating proteins. This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general.

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.

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.

The paper describes an investigation of the intensity of Bragg reflection when the incident X-rays are polarized and the azimuth of the electric vector is varied with respect to the plane of reflection. It is observed, using natural and ground (211) faces of NaNO3, that the variation of intensity with azimuth of polarization is different for a mosaic and a perfect crystal. Such a difference is in fact to be expected from theoretical considerations. The actual behaviour of both the ground and the natural faces was found to be intermediate between what is predicted by theory for an ideally perfect and an ideally mosaic crystal. By comparing the observed azimuthal variation of the integrated reflection with the theoretical expectation for the two limiting cases, it is possible to assess the degree of perfection of the crystal.

Investigation of the degree of perfection of a crystal by means of polarized X-rays

The absolute configuration of glucosamine

(of. Internationale Tabellen, 1935, vol . 2, pp . 562, 564). H e r e 0 is t h e B r a g g ang le a n d t h e f o r m u l a e refer to s y m m e t r i c a l ' surface ' ref lexions. I f , howeve r , t h e inc iden t X r a y s a re c o m p l e t e l y po la r i zed a n d t h e e lect r ic v e c t o r m a k e s a n angle ~ w i t h t h e n o r m a l to t h e p l ane of ref lexion, t h e n t h e i n t e g r a t e d ref lexions in t h e two cases a re : OM¢ = RM [COS 9\" ~P-{-Sin ~ ~0 COS ~\" 9.0] , (2a)

http://journals.iucr.org/q/issues/1953/04/00/a00884/a00884.pdf

Influence of mosaicity on the Bragg reflexion of polarized X-rays

Laue photographs with the X-ray beam normal to the surface (111) planes have been taken for two typical bluc-fluorescent diamonds exhibiting widely different intensities of fluorescence, but similar in other respects. Microphotometry of the peak intensity of the various spots shows that although the intensity of all the spots is greater with the more fluorescent diamond, the ratio (r) of the intensities of the corresponding spots varies. Empirically, it is found that (r−1) is proportional to the product of the structure factor, the wave-length reflected and a function of the angle of incidence.

G. N. Ramachandran

Papers

Investigation of the degree of perfection of a crystal by means of polarized X-rays

The absolute configuration of glucosamine

Influence of mosaicity on the Bragg reflexion of polarized X-rays

X-ray reflection and the structure of diamond

Hydroxyproline stabilizes both intrafibrillar structure as well as inter-protofibrillar linkages in collagen