A program for evaluating the solution scattering from macromolecules with known atomic structure is presented. The program uses multipole expansion for fast calculation of the spherically averaged scattering pattern and takes into account the hydration shell. Given the atomic coordinates (e.g. from the Brookhaven Protein Data Bank) it can either predict the solution scattering curve or fit the experimental scattering curve using only two free parameters, the average displaced solvent volume per atomic group and the contrast of the hydration layer. The program runs on IBM PCs and on the major UNIX platforms. Journal of Applied CrystallographyISSN0021-8898 © 1995

A program suite for one-dimensional small-angle scattering data processing running on IBM-compatible PCs under Windows 9x/NT/2000/XP is presented. The main program, PRIMUS, has a menu-driven graphical user interface calling computational modules to perform data manipulation and analysis. Experimental data in binary OTOKO format can be reduced by calling the program SAPOKO, which includes statistical analysis of time frames, averaging and scaling. Tools to generate the angular axis and detector response ®les from diffraction patterns of calibration samples, as well as binary to ASCII transformation programs, are available. Several types of ASCII ®les can be directly imported into PRIMUS, in particular, sasCIF or ILL-type ®les are read without modi®cation. PRIMUS provides basic data manipulation functions (averaging, background subtraction, merging of data measured in different angular ranges, extrapolation to zero sample concentration, etc.) and computes invariants from Guinier and Porod plots. Several external modules coupled with PRIMUS via pop-up menus enable the user to evaluate the characteristic functions by indirect Fourier transformation, to perform peak analysis for partially ordered systems and to ®nd shape approximations in terms of threeparametric geometrical bodies. For the analysis of mixtures, PRIMUS enables model-independent singular value decomposition or linear ®tting if the scattering from the components is known. An interface is also provided to the general non-linear ®tting program MIXTURE, which is designed for quantitative analysis of multicomponent systems represented by simple geometrical bodies, taking shape and size polydispersity as well as interparticle interference effects into account.

An ab initio method for building structural models of proteins from x-ray solution scattering data is presented. Simulated annealing is employed to find a chain-compatible spatial distribution of dummy residues which fits the experimental scattering pattern up to a resolution of 0.5 nm. The efficiency of the method is illustrated by the ab initio reconstruction of models of several proteins, with known and unknown crystal structure, from experimental scattering data. The new method substantially improves the resolution and reliability of models derived from scattering data and makes solution scattering a useful technique in large-scale structural characterization of proteins.

The structure of the protein-solvent interface is the subject of controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal structure (lysozyme, Escherichia coli thioredoxin reductase, and protein R1 of E. coli ribonucleotide reductase) were investigated in parallel by x-ray and neutron scattering in H 2 O and D 2 O solutions. The analysis of the protein-solvent interface is based on the significantly different contrasts for the protein and for the hydration shell. The results point to the existence of a first hydration shell with an average density Ϸ10% larger than that of the bulk solvent in the conditions studied. Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces.Hydration, ion binding, and hydrophobic effects are major factors in the stabilization of the tertiary and quaternary structure as well as in the interactions between macromolecules. Despite their importance, macromolecule-solvent interactions are understood inadequately because of the considerable difficulty associated with their experimental study (for a review, see ref.

Small-angle scattering (SAS) of x-rays and neutrons is a fundamental tool in the study of biological macromolecules. The major advantage of the method lies in its ability to provide structural information about partially or completely disordered systems. SAS allows one to study the structure of native particles in near physiological environments and to analyse structural changes in response to variations in external conditions. In this review we concentrate on SAS studies of isotropic systems, in particular, solutions of biological macromolecules, an area where major progress has been achieved during the last decade. Solution scattering studies are especially important, given the challenge of the 'post-genomic' era with vast numbers of protein sequences becoming available. Numerous structural initiatives aim at large-scale expression and purification of proteins for subsequent structure determination using x-ray crystallography and NMR spectroscopy. Because of the requirement of good crystals for crystallography and the low molecular mass requirement of NMR, a significant fraction of proteins cannot be analysed using these two high-resolution methods. Progress in SAS instrumentation and novel analysis methods, which substantially improve the resolution and reliability of the structural models, makes the method an important complementary tool for these initiatives. The review covers the basics of x-ray and neutron SAS, instrumentation, mathematical methods used in data analysis and major modelling techniques. Examples of applications of SAS to different types of biomolecules (proteins, nucleic acids, macromolecular complexes, polyelectrolytes) are presented. A brief account of the new opportunities offered by third and fourth generation synchrotron radiation sources (time-resolved studies, coherent scattering and single molecule scattering) is also given.

A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies--on ribosomes and on the allosteric protein aspartate transcarbamoylase--illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

Lipopolysaccharide (LPS) represents a major virulence factor of Gram-negative bacteria (`endotoxin') that can cause septic shock in mammals including man. The lipid anchor of LPS to the outer membrane, lipid A, has a peculiar chemical structure, harbours the`endotoxic principle' of LPS and is responsible for the expression of pathophysiological effects. Chemically modified lipid A can be endotoxically inactive, but may express strong antagonistic activity against LPS, a property that can be utilized in antisepsis treatment. We show here that these different biological activities are directly correlated with the molecular shape of lipid A. Only (hexaacyl) lipid A with a conical/concave shape, the cross-section of the hydrophobic region being larger than that of the hydrophilic region, exhibited strong interleukin-6 (IL-6)-inducing capacity. Most strikingly, a correlation between a cylindrical molecular shape of lipid A and antagonistic activity was established: IL-6 induction by enterobacterial LPS was inhibited by cylindrically shaped lipid A except for compounds with reduced headgroup charge. The antagonistic action is interpreted by assuming that lipid A molecules intercalate into the cytoplasmic membrane of mononuclear cells, and subsequently blocking of the putative signaling protein by the lipid A with cylindrical shape.

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