Biological macromolecule structural information

BIOLOGICAL MACROMOLECULE STRUCTURAL INFORMATION HCCH-COSY and -TOCSY Experiments... 

Time-resolved fluorescence spectroscopy is widely used as a research tool in biochemistry and biophysics. These uses of fluorescence have resulted in extensive knowledge of the structure and dynamics of biological macromolecules. This information has been gained by studies of phenomena that affect the excited state, such as the local environment, quenching processes, and energy transfer. 

Biochemical applications have been made more recently O, ). Here, cyclic photochemical reactions are employed to generate nuclear spin-polarization in biological macromolecules. The information obtained is of a structural nature rather than mechanistic. In the case of proteins aromatic amino acid residues (tyrosine, histidine and tryptophan) can be polarized by reversible hydrogen atom or electron transfer reactions with a photo-excited dye. These reactions require direct contact of the dye with the amino acid side-chains so that they only occur for residues lying at the surface of the protein. 

Inorganic Three-dimensional Structure Databases Molecular Docking and Structure-based Design Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases Structure Representation Three-dimensional Structure Searching,... 

Many complex systems have been spread on liquid interfaces for a variety of reasons. We begin this chapter with a discussion of the behavior of synthetic polymers at the liquid-air interface. Most of these systems are linear macromolecules however, rigid-rod polymers and more complex structures are of interest for potential optoelectronic applications. Biological macromolecules are spread at the liquid-vapor interface to fabricate sensors and other biomedical devices. In addition, the study of proteins at the air-water interface yields important information on enzymatic recognition, and membrane protein behavior. We touch on other biological systems, namely, phospholipids and cholesterol monolayers. These systems are so widely and routinely studied these days that they were also mentioned in some detail in Chapter IV. The closely related matter of bilayers and vesicles is also briefly addressed. 

Besides the MDL Molfile formal, other file formats are often used in chemistry SMILES has already been mentioned in Section 2.3.3. Another one, the PDB file format, is primarily used for storing 3D structure information on biological macromolecules such as proteins and polynucleotides (Tutorial, Section 2.9.7) [52, 53). GIF (Crystallographic Information File) [54, 55] is also a 3D structure information file format with more than three incompatible file versions and is used in crystallography. GIF should not be confused with the Chiron Interchange Formal, which is also extended with. cif. In spectroscopy, JCAMP is apphed as a spectroscopic exchange file format [56]. Here, two modifications can be... 

PDB files were designed for storage of crystal structures and related experimental information on biological macromolecules, primarily proteins, nucleic acids, and their complexes. Over the years the PDB file format was extended to handle results from other experimental (NM.R, cryoelectron microscopy) and theoretical methods... 

Energy-transfer measurements are often used to estimate the distances between sites on biological macromolecules such as proteins, and the effects of conformational changes on these distances. In this type of experiment, the efficiency of energy transfer is used to calculate the distance between donor and acceptor fluorophores in order to obtain structural information about the macromolecule. 

Our discussion of globular protein structure begins with the principles gleaned from the earliest protein structures to be elucidated. This is followed by a detailed description of protein substructure and comparative categorization. Such discussions are possible only because of the vast amount of information available over the Internet from resources such as the Protein Data Bank (PDB www.rcsb.org/pdb), an archive of experimentally determined three-dimensional structures of biological macromolecules. 

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