Unknown Three-Dimensional Structures

Lipases with Unknown Three-Dimensional Structures 

A broad variety of lipases isolated and purified to a varying degree from many organisms have been investigated to date. It is beyond the scope of this review to discuss the wealth of biochemical data generated 

Human Lipases Involved in Lipid Lipoprotein Metabolism I. Human Lipase Gene Family 

The human pancreatic lipase is homologous to two other lipases playing pivotal roles in lipoprotein metabolism lipoprotein lipase and hepatic lipase. Together these three proteins constitute the human lipase gene family. 

Lipoprotein and hepatic lipases are important enzymes involved in the metabolism of chylomicrons and various fractions of lipoproteins. Both have been the subject of attention, as evidenced by numerous reviews (e.g., Garfinkel and Schotz, 1987 Wang eta/., 1992). This interest stems from the fact that abnormal lipoprotein metabolism has been linked to various disorders, including hyperchylomicronemia, hypercholesterolemia, hypertriglyceridemia, obesity, diabetes, and premature atherosclerosis. Genetic defects in both HL and LPL are now known to be the cause of at least some familial disorders of lipoprotein metabolism. 

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Lipases with Unknown Three-Dimensional Structures. 38... 

M. J. Sippl, S. Weitckus. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins. 1992, 13, 258-271. 

Statistical surveys on the exposure to solvent of amino acid side chains in globular proteins have been used to arrive at special amino acid hydrophobicity scales, which in turn can be used to predict the exposure of peptide segments in proteins of unknown structure. Such prediction schemes have been used successfully to identify antigenic recognition sites at the surface of proteins of unknown three-dimensional structures [16]. 

A sequence alignment establishes the correspondences between the amino adds in th unknown protein and the template protein (or proteins) from wliich it will be built. Th three-dimensional structures of two or more related proteins are conveniently divided int structurally conserved regions (SCRs) and structurally variable regions (SVRs). Ihe structural conserved regions correspond to those stretches of maximum sequence identity or sequenc... 

A receptor is a surface membrane component, usually a protein, which regulates some biological event in response to reversible binding of a relatively small molecule40 . The precise three-dimensional structures of the binding sites of receptors still remain unknown today. Thus, this section mainly describes the correlation of shape similarity between the molecules which would bind to a given receptor with their biological activity. 

This example is one where the accurate three-dimensional structure of the protein is unknown under these circumstances, it is necessary to create a computer model. The development of inhibitors that are designed to overcome the effects of this mutation could not be based on the accurate structure of a ligand-binding site here, ligand-based design would be appropriate (see Sect. 7.9). 

When we have the information from the sequencing of the human genome, and want to understand the properties of those proteins that are coded by some of the genes but not yet known experimentally, we need to solve the protein-folding problem. Then we can translate the gene sequence—which specifies the sequence of amino acids—into the three-dimensional structure of the unknown protein. 

First the structures of cytochrome cytochrome c peroxidase [21] are both known at high resolution. Although the precise three dimensional structure of the protein-protein complex is unknown (and, we shall argue, unknowable), molecular modeling has produced detailed stereochemical models for the c ccp complex which are subject to experimental testing and subsequent improvement, as detailed below. 

Recently, Hwang et al. have performed conceptually similar predictions using three-dimensional structural information (Hwang et al., 1999). Here, structural similarities between a protein of unknown function and others available in the public databases were used to infer the general function of the URF as a new nucleotide triphosphosphatase. It is expected that as many new structures of URFs are solved over the next few years, the conceptual approaches described here will be useful in interpreting characteristics of such proteins even in the absence of a clear understanding of overall function or identification of specific substrates and products. 

The three-dimensional structure of human extracellular superoxide dismutase (EC-SOD) is unknown. Studies of structure-function relationships have been severely limited by its poor production in mammalian cell lines and failure to be expressed in prokaryotic and yeast systems. In contrast, extra- and intracellular Cu- and Zn-containing superoxide dismutases (CuZn-SOD) are expressed very well in E. coli and yeast. CuZn-SOD is homologous to a large interior fragment of EC-SOD, but lacks its extra N-terminal and C-terminal domains. Fusions of either the N-terminal domain of EC-SOD or both the N- and C-terminal domains of EC-SOD to CuZn-SOD resulted in a domain-swapped enzyme that expressed well and whose characteristics resemble EC-SOD (Stenlund and Tibell, 1999). 

We also totally lack a leadership role in the proper places, such as Washington. Why does the FDA ask us questions about the process They don t know what the three-dimensional structure is. The covalent structure is easier to define, the secondary and tertiary structures are more difficult. The only way they can be sure of what s happening is to make certain our processes are identical, because all else is unknown. Why are the biologists doing everything Because they have a presence there. We have to make our own destiny. One example is involvement with clinical trials. We need to do more, because we can do things in a quantitative way. 

We have investigated peptides whose structures were known beforehand from NMR or x-ray spectroscopy and related these structures to 2D-IR spectroscopy. Ultimately, one would like to deduce the structure of an unknown sample from a 2D-IR spectrum. In the case of 2D NMR spectroscopy, two different phenomena are actually needed to determine peptide structures. Essentially, correlation spectroscopy (COSY) is utilized in a first step to assign protons that are adjacent in the chemical structure of the peptide so that J coupling gives rise to cross peaks in these 2D spectra. However, this through-bond effect cannot be directly related to the three-dimensional structure of the sample, since that would require quantum chemistry calculations, which presently cannot be performed with sufficient accuracy. The nuclear Overhauser effect (NOE), which is an incoherent population transfer process and has a simple distance dependence, is used as an additional piece of information in order to measure the distance in... 

When we don t show bold and dashed bonds to indicate the three-dimensional structure of the molecule, we mean that we are talking about both enantiomers of the molecule. Another useful way of representing this is with wiggly bonds. Wiggly bonds are in fact slightly ambiguous chemists use them to mean, as they do here, both stereoisomers, but also to mean just one stereoisomer, but unknown stereochemistry. 

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