Chemistry protein structure

Computer simulations of electron transfer proteins often entail a variety of calculation techniques electronic structure calculations, molecular mechanics, and electrostatic calculations. In this section, general considerations for calculations of metalloproteins are outlined in subsequent sections, details for studying specific redox properties are given. Quantum chemistry electronic structure calculations of the redox site are important in the calculation of the energetics of the redox site and in obtaining parameters and are discussed in Sections III.A and III.B. Both molecular mechanics and electrostatic calculations of the protein are important in understanding the outer shell energetics and are discussed in Section III.C, with a focus on molecular mechanics. 

Applications of neural networks are becoming more diverse in chemistry [31-40]. Some typical applications include predicting chemical reactivity, acid strength in oxides, protein structure determination, quantitative structure property relationship (QSPR), fluid property relationships, classification of molecular spectra, group contribution, spectroscopy analysis, etc. The results reported in these areas are very encouraging and are demonstrative of the wide spectrum of applications and interest in this area. 

The opening sentence above says it all. NMR is by far the most valuable spectroscopic technique for structure determination. Although wei) just give an overview of the subject in this chapter, focusing on NMR applications to small molecules, more advanced NMR techniques are also used in biological chemistry to study protein structure and folding. 

Iron-sulphur proteins structural chemistry of their chromophores and related systems. R. Mason and J. A. Zubieta, Angew. Chem., Int. Ed. Engl., 1973,12, 390-399 (101). 

West, K.A. and Crabb, J.W 1990 Performance evaluation automatic hydrolysis and PTC amino acid analysis. In Vallafraca, J.J., ed.. Current Research in Protein Chemistry Techniques, Structure, and Function. San Diego, Academic Press 37-48. 

The term ageing of polymers is usually reserved for long-term changes in properties of polymers exposed to weathering conditions. It may involve any of the above processes and include physical processes of polymer recrystallization and denaturation of, for example, protein structure in biopolymer chemistry. The term corrosion, used essentially for the deterioration (ageing) of metal... 

Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Aarhus C 8000 Aarhus, Denmark e-mail ncn chem.au.dk... 

The active site of an enzyme is generally a pocket or cleft that is specialized to recognize specific substrates and catalyze chemical transformations. It is formed in the three-dimensional structure by a collection of different amino acids (active-site residues) that may or may not be adjacent in the primary sequence. The interactions between the active site and the substrate occur via the same forces that stabilize protein structure hydrophobic interactions, electrostatic interactions (charge-charge), hydrogen bonding, and van der Waals interactions. Enzyme active sites do not simply bind substrates they also provide catalytic groups to facilitate the chemistry and provide specific interactions that stabilize the formation of the transition state for the chemical reaction. 

Christianson D (1991) Structural biology of zinc. In Anfinsen C, Richards F, Edsall J, Eisenberg D (eds) Advances in protein chemistry. Metalloproteins structural aspects, vol 42. Academic Press, p 281... 

Abstract Conjugated polymers have many unique photophysical properties that make them useful for a variety of applications within the fields of chemistry, molecular biology, and medicine, specifically their ability to produce a conformation-dependant spectral signature reflective of changes in their local environment. This physical property makes conjugated polymers an indispensible tool in the toolbox of fluorescent reporters, and within this chapter, their utilization as molecular probes for studying protein structure and conformation is emphasized. 

It is helpful to know the chemistry of fixatives in order to understand their action and avoid artifacts (4). Most commonly studied antigens are either proteins or carbohydrates. Many of these molecules are soluble in aqueous solutions and need to be fixed in place in cells. Insoluble antigens also need to be structurally preserved (/). All chemical fixatives will cause chemical and conformational changes in the protein structure of cells with lesser changes noted for carbohydrate antigens (5). Secondary and tertiary structures of proteins are the most important for eliciting antigenicity and chemical fixatives usually disturb these conformations (3). 

Software tools for virtual screening can be best classified by the input data available for screening. On the one side, there is always a collection of compounds to be screened, which differs in size (from a few tens to several millions) and in structure (from structurally unrelated compounds via combinatorial libraries to chemistry spaces). On the other side, there is the data that is used to create the screening query, which can be a protein structure, a known active compound or a pharmacophore created from several known actives (see Figure 4.1). In summary, we are ending up with four classes of screening tools ... 

Consider a molecular structure, which is the most important unifying information model in chemistry. Molecular structures appear in knowledgebases that represent catalogs of commercially available chemicals, pharmacology of named drugs, natural sources of bioactive molecules, protein-ligand interactions, measured molecular bioactivities, metabolic pathways, abstracted research literature, databases of synthetic reactions, and so on. 

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