Structure functions

Let us consider a small-angle scattering experiment. The radiation falls on molecules in a container at fixed pressure. Let us study the scattering in a volume V which is small with respect to the volume of the container but not microscopic (see Fig. 7.1). An elastic transfer wave vector q corresponds to each scattering angle 0 with q — 2k0 sin 0/2, (k0 being the incident wave vector) and the scattering is characterized by the differential cross-section 

we assume that the scattering is entirely coherent the incoherent contribution has been subtracted (see Chapter 6, Section 5.3). The cross-section is an extensive quantity, but we can introduce the cross-section per unit volume  

The cross-section can be used to calculate the turbidity S defined by eqn (6.4.14). 

The intensive quantity thus defined depends on the by and on the concentrations of the scatterers. It depends also on the internal geometrical structure of the sample. This is this structure which we wish to characterize, and this desire will lead us later to define the structure function. 

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Skourtis S S and Beratan D N 1999 Theories of structure-function reiationships for bridge-mediated eiectron transfer reactions Adv. Chem. Phys. 106 377-452... 

Fetisova Z G, Borisov A Y and Fok M V 1985 Analysis of structure-function correlations in light-harvesting photosynthetic antenna—structure optimization parameters J. Theoret. Biol. 112 41-75... 

Bryngelson J D, J N Onuchic, N D Socci and P G Wolynes 1995. Funnels, Pathways, and the Energy Landscape of Protein Folding A Synthesis. Proteins Structure, Function and Genetics 21 167-195. 

Cuff IA and G J Barton 1999. Evaluation and Improvement of Multiple Sequence Methods for P Secondary Structure Prediction. Proteins Structure, Function and Genetics 34 508-519. 

Kovacs H, A E Mark and W F van Gunsteren 1997. Solvent Structure at a Hydrophobic Protein Surface. Proteins Structure, Function and Genetics 27 395-404. 

Maiorov V N and G M Crippen 1994. Learning About Protein Folding via Potential Functions. Proteins Structure, Function and Genetics 20 167-173. 

Mosimann S, S Meleshko and M N G Jones 1995. A Critical Assessment of Comparative Molecular Modeling of Tertiary Structures of Proteins. Proteins Structure, Function and Genetics 23 301-317. 

Moult J, T Hubbard, K Fldelis and J T Pedersen 1999. Critical Assessment of Methods of Protein Structure Prediction (CASP) Round III. Proteins Structure, Function and Genetics Suppl. 3 2-6. 

Noble M E M, R K Wierenga, A-M Lambeir, F R Opperdoes, W H Thunnissen, K H Kalk, H Groendijk and W G J Hoi 1991. The Adaptability of the Active Site of Trypanosomal Triosephosphate Isomerase as Observed in the Crystal Structures of Three Different Complexes. Proteins Structure, Function and Genetics 10 50-69. 

Orengp C A, N P Brown and W R Taylor 1992. Fast Structure Alignment for Protein Datal Searching. Proteins Structure, Function and Genetics 14 139-167. 

Boresch S, G Archontis and M Karplus 1994. Free Energy Simulations The Meaning of the Indi-. id Contributions from a Component. Analysis. Proteins Structure, Function and Gau tics 20 25-33. 

Gilson M K and B Honig 1988. Calculation of the Total Electrostatic Energy of a Macromoleculai System Solvation Energies, Binding Energies and Conformational Analysis. Proteins Structure Function and Genetics 4 7-18. 

Klapper 1, R Hagstrom, RFine, K Sharp and B Honig 1986. Focusing of Electric Fields in tire Actir e Sit of CuZn Superoxide Dismutase Effects of Ionic Strength and Amino-Acid Substitution. Proteins Structure, Function and Genetics 1 47-59. 

Miyamoto S and P A Kollman 1993a. Absolute and Relative Binding Tree Energy Calculations of the Interaction of Biotin and its Analogues with Streptavidin Using Molecular Dynamics/Free Energy Perturbation Approaches. Proteins Structure, Function and Genetics 16 226-245. 

A, C W Murray, D E Clark, D R Westhead and M D Eldridge 1998. Flexible Docking using Tabu rch and an Empirical Estimate of Binding Affinity. Proteins Structure, Function and Genetics 167-382. 

D S and A J Olson 1990 Automated Docking of Substrates to Proteins by Simulated ealing. Proteins Structure, Function and Genetics 8 195-202. 

Kramer B, M Rarey and T Lengauer 1999. Evaluation of the FLEXX Incremental Constructioi Algorithm for Protein-Ligand Docking. Proteins Structure, Function and Genetics 37 228-241. 

B and W J Howe 1991. Computer Design of Bioactive Molecules - A Method for Receptor-Based Novo Ligand Design. Proteins Structure, Function and Genetics 11 314-328. i H L 1965. The Generation of a Unique Machine Description for Chemical Structures - A hnique Developed at Chemical Abstracts Service. Journal of Chemical Documentation 5 107-113. J 1995. Computer-aided Estimation of Symthetic Accessibility. PhD thesis. University of Leeds, itan R, N Bauman, J S Dixon and R Venkataraghavan 1987. Topological Torsion A New )lecular Descriptor for SAR Applications. Comparison with Other Descriptors. Journal of emical Information and Computer Science 27 82-85. 

Structure—function relationships of prolactin among a variety of species have been pubUshed (17,18). Only one gene for prolactin appears to exist (19). Although classically placed in the category of simple protein hormones, prolactin can be glycosylated. Carbohydrate attachment occurs at Asn-31, where the consensus glycosylation sequence Asn—X—Ser is found. 

R. E. Chance and co-workers, in D. H. Rich and E. Gross, eds.. Peptides Synthesis —Structure-function. Pierce Chemical Co. Press, Rockford, lU.,... 

A. W. Norman, R. Bouillon, and M. Thomasset, eds.. Vitamin D, Structure, Function Analysis and Clinical Application, Proceedings of the Eighth Workshop on Vitamin D, Paris, July 5, 1991, Walter de Gmyter, Berlin, 1991. 

Structure— Function Relationships. Since PCBs and related HAHs are found in the environment as complex mixtures of isomers and congeners, any meaninghil risk and hazard assessment of these mixtures must consider the quaUtative and quantitative stmcture—function relationships. Several studies have investigated the stmcture—activity relationships for PCBs that exhibit 2,3,7,8-tetrachlorodibenzo-p-dioxin [1746-01-6] (1)... 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

Antiparallel beta (P) structures comprise the second large group of protein domain structures. Functionally, this group is the most diverse it includes enzymes, transport proteins, antibodies, cell surface proteins, and virus coat proteins. The cores of these domains are built up by p strands that can vary in number from four or five to over ten. The P strands are arranged in a predominantly antiparallel fashion and usually in such a way that they form two P sheets that are joined together and packed against each other. 

Finn, B.E., Forsen, S. The evolving model of calmodulin structure, function and activation. Structure 3 7-11, 1995. 

Rossmann, M.G. Virus structure, function, and evolution. Harvey Lectures, Series 83 107-120, 1989. 

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