Structure and Functionality

Carbohydrates are characterized by the presence of polyhydroxylic aldehyde or polyhydroxy-lic ketone structures or polymers made of such units. Sugars and polysaccharides have definite 

---

Cantor C R and Schimmel P R 1980 Biophysical Chemistry, Part II Techniques for the Study of Biological Structure and Function (San Francisco Freeman)... 

Uchida M, Tanizaki T, Gda T and Ka]iyama T 1991 Control of surface chemical-structure and functional property of Langmuir-Blodgett-film composed of new polymerizable amphiphile with a sodium-sulfonate Maoromoieouies 24 3238-43... 

The catalytic subunit then catalyzes the direct transfer of the 7-phosphate of ATP (visible as small beads at the end of ATP) to its peptide substrate. Catalysis takes place in the cleft between the two domains. Mutual orientation and position of these two lobes can be classified as either closed or open, for a review of the structures and function see e.g. [36]. The presented structure shows a closed conformation. Both the apoenzyme and the binary complex of the porcine C-subunit with di-iodinated inhibitor peptide represent the crystal structure in an open conformation [37] resulting from an overall rotation of the small lobe relative to the large lobe. 

Our work is targeted to biomolecular simulation applications, where the objective is to illuminate the structure and function of biological molecules (proteins, enzymes, etc) ranging in size from dozens of atoms to tens of thousands of atoms today, with the desire to increase this limit to millions of atoms in the near future. Such molecular dynamics (MD) simulations simply apply Newton s law to each atom in the system, with the force on each atom being determined by evaluating the gradient of the potential field at each atom s position. The potential includes contributions from bonding forces. 

Having settled on a definition of chemoinformatics, it is time for us to reflect on the distinction between chemoinformatics and bioinformatics. The objects of interest of bioinformatics are mainly genes and proteins. But genes, DNA and RNA, and proteins are chemical compounds They are objects of high interest in chemistry, Chemists have made substantial contributions to the elucidation of the structure and function of nucleic adds and proteins. The message is dear there is no clearcut distinction between bioinfonnatics and chemoinformatics I... 

This difference m reactivity especially toward hydrolysis has an important result We 11 see m Chapter 27 that the structure and function of proteins are critical to life Itself The bonds mainly responsible for the structure of proteins are amide bonds which are about 100 times more stable to hydrolysis than ester bonds These amide bonds are stable enough to maintain the structural integrity of proteins m an aqueous environment but susceptible enough to hydrolysis to be broken when the occasion demands... 

The relationship between structure and function reaches its ultimate expression in the chemistry of ammo acids peptides and proteins... 

Unlike DNA most of which is m the nucleus RNA is found mostly m the cell s mam compartment the cytoplasm There are three different kinds of RNA which differ sub stantially from one another m both structure and function... 

These pohcy statements are founded on the existing language and authorities in Clean Water Act Sections 303 (c) (2) (A) and (Bf EPA defined biological criteria as numerical values or narrative expressions used to describe the expected structure and function of the aquatic community. ... 

A prior distribution for sequence profiles can be derived from mixtures of Dirichlet distributions [16,51-54]. The idea is simple Each position in a multiple alignment represents one of a limited number of possible distributions that reflect the important physical forces that determine protein structure and function. In certain core positions, we expect to get a distribution restricted to Val, He, Met, and Leu. Other core positions may include these amino acids plus the large hydrophobic aromatic amino acids Phe and Trp. There will also be positions that are completely conserved, including catalytic residues (often Lys, GIu, Asp, Arg, Ser, and other polar amino acids) and Gly and Pro residues that are important in achieving certain backbone conformations in coil regions. Cys residues that form disulfide bonds or coordinate metal ions are also usually well conserved. 

RH Holm, P Kennepohl, El Solomon. Structural and functional aspects of metal sites in biology. Chem Rev 96 2239-2341, 1996. 

I Qumkal, V Davasse, 1 Gaillard, J-M Mouhs. On the role of conserved prohne residues in the structure and function of Clostridium pasteurianum 2[4Ee-4S] ferredoxm. Protein Eng 7 681-687, 1994. 

The globin fold has been used to study evolutionary constraints for maintaining structure and function. Evolutionary divergence is primarily constrained by conservation of the hydrophobicity of buried residues. In contrast, neither conserved sequence nor size-compensatory mutations in the hydrophobic core are important. Proteins adapt to mutations in buried residues by small changes of overall structure that in the globins involve movements of entire helices relative to each other. 

Weber, PC., Salemme, ER. Structural and functional diversity in 4-a-helical proteins. Nature 287 82-84, 1980. 

We have described a general relationship between structure and function for the a/p-barrel structures. They all have the active site at the same position with respect to their common structure in spite of having different functions as well as different amino acid sequences. We can now ask if similar relationships also occur for the open a/p-sheet structures in spite of their much greater variation in structure. Can the position of the active sites be predicted from the structures of many open-sheet a/p proteins ... 

Ohlsson, I., Nordstrom, B., Branden, C.-I. Structural and functional similarities within the coenzyme binding domains of dehydrogenases. /. Mol. Biol. 89 339-354, 1974. 

The simplest topology is obtained if each successive p strand is added adjacent to the previous strand until the last strand is joined by hydrogen bonds to the first strand and the barrel is closed (Figure 5.2). These are called up-and-down P sheets or barrels. The arrangement of p strands is similar to that in the a/P-barrel structures we have just described in Chapter 4, except that here the strands are antiparallel and all the connections are hairpins. The structural and functional versatility of even this simple arrangement will be illustrated by two examples. 

Wiley, D.C., Skehel, JJ. The structure and function of the hemagglutinin membrane glycoprotein of influenza virus. Annu. Rev. Biochem. 56 365-394, 1987. 

Saibil, H.R. The lid that shapes the pot structure and function of the chaperonin GroES. Structure 4 1-4, 1996. 

Phillips, S.E.V. Built by association structure and function of helix-loop-helix DNA-binding proteins. Strueture 2 1-4, 1994. 

James, M.N.G. An x-ray crystallographic approach to enzyme structure and function. Can. J. Biochem. 

Kiihlbrandt, W. Structure and function of bacterial lightharvesting complexes. Structure 3 521-525, 1995. 

Proteins are usually separated into two distinct functional classes passive structural materials, which are built up from long fibers, and active components of cellular machinery in which the protein chains are arranged in small compact domains, as we have discussed in earlier chapters. In spite of their differences in structure and function, both these classes of proteins contain a helices and/or p sheets separated by regions of irregular structure. In most cases the fibrous proteins contain specific repetitive amino acid sequences that are necessary for their specific three-dimensional structure. 

Homologous proteins have similar structure and function... 

---