Tertiary structural folds

J. R. Gunn, A. Monge, R. A. Friesner, and C. H. Marshall, /. Phys. Chem., 98,702 (1994). Hierarchical Algorithm for Computer Modeling of Protein Tertiary Structure Folding of Myoglobin to 6.2 A Resolution. 

Ion dehydration effects can be responsible for a variety of ion-dependent RNA folding properties, especially for the tertiary structure folding (Draper, 2008). Refinement of the TBI model should include a more accurate treatment for the possible ion dehydration effect. Further development of the model should also consider the all-atom details of the RNA structure and the improvements of computational efficiency. 

Zinc finger proteins have recently been classified into eight distinct structural groups distinguished by their tertiary structural folds around the zinc coordination complex and the spatial arrangement of secondary structural elements that contribute zinc ligands. Table 1 lists representative members from each of six of these eight stmctural classes that are known to interact directly with nucleic acids. These are discussed in turn. 

On the other hand, in a minimal catalytic model system, the ribozymes have advantages over protein enzymes. Even short oligonucleotides can effectively use duplex formation to bind substrates and the known ribozymes are generally smaller than their protein counterparts. This substrate recognition through secondary structure is not a common feature of protein binding sites, where tertiary structural folds are necessary to optimize close packing of residues distant in primary sequence [42],... 

The architecture of protein molecules is complex and can be described according to structural organization as primary structure (amino acid sequence), secondary structure (regular structures such as helical, pleated sheet, and coil stractures), tertiary structure (fold in three-dimensional space), quaternary structure (subunit structure) and quintemary structure (biomacromolecular complexes). Usually the overall three-dimensional (3D) architecture of a protein molecule is termed as its conformation, which refers to its secondary and tertiary structures. Between these two stractures, motifs (supersecondary structures) refer to the packing of adjacent secondary stractures into distinct structural elements and domains refer to identifiable 3D structural units that may correspond to functional units. The structures of most proteins with more than 200 amino acid residues appear to consist of two or more domains. 

Hierarchical Algorithm for Computer Modeling of Protein Tertiary Structure Folding of Myoglobin to 6.2 A Resolution. 

Keywords, protein folding, tertiary structure, potential energy surface, global optimization, empirical potential, residue potential, surface potential, parameter estimation, density estimation, cluster analysis, quadratic programming... 

Section 27 20 The folding of a peptide chain is its tertiary structure The tertiary struc ture has a tremendous influence on the properties of the peptide and the biological role it plays The tertiary structure is normally determined by X ray crystallography... 

Tertiary structure (Section 27 20) A description of how a pro tein chain is folded... 

A Caflisch, M Karplus. Molecular dynamics studies of protein and peptide folding and unfolding. In K Merz Jr, S Le Grand, eds. The Protein Eoldmg Problem and Tertiary Structure Prediction. Boston Birkhauser, 1994, pp 193-230. 

Several motifs usually combine to form compact globular structures, which are called domains. In this book we will use the term tertiary structure as a common term both for the way motifs are arranged into domain structures and for the way a single polypeptide chain folds into one or several domains. In all cases examined so far it has been found that if there is significant amino acid sequence homology in two domains in different proteins, these domains have similar tertiary structures. 

The fundamental unit of tertiary structure is the domain. A domain is defined as a polypeptide chain or a part of a polypeptide chain that can fold independently into a stable tertiary structure. Domains are also units of function. Often, the different domains of a protein are associated with different functions. For example, in the lambda repressor protein, discussed in Chapter 8, one domain at the N-terminus of the polypeptide chain binds DNA, while a second domain at the C-terminus contains a site necessary for the dimerization of two polypeptide chains to form the dimeric repressor molecule. 

In the native protein these less stable ds-proline peptides are stabilized by the tertiary structure but in the unfolded state these constraints are relaxed and there is an equilibrium between ds- and trans-isomers at each peptide bond. When the protein is refolded a substantial fraction of the molecules have one or more proline-peptide bonds in the incorrect form and the greater the number of proline residues the greater the fraction of such molecules. Cis-trans isomerization of proline peptides is intrinsically a slow process and in vitro it is frequently the rate-limiting step in folding for those molecules that have been trapped in a folding intermediate with the wrong isomer. 

What can be done by predictive methods if the sequence search fails to reveal any homology with a protein of known tertiary structure Is it possible to model a tertiary structure from the amino acid sequence alone There are no methods available today to do this and obtain a model detailed enough to be of any use, for example, in drug design and protein engineering. This is, however, a very active area of research and quite promising results are being obtained in some cases it is possible to predict correctly the type of protein, a, p, or a/p, and even to derive approximations to the correct fold. 

For a 3-cm-long molecule of DNA to fit inside a cell so tiny that we can only see it with a microscope, the polynucleotide chain must be folded into a more compact form. Not only must the DNA be compacted, it must be folded in a way that allows it to cany out its main functions. The way the chain is folded defines the tertiary structure of a nucleic acid. 

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