Current Protein and Peptide Science - Volume 6, Issue 5, 2005

The glycosyl carrier lipids, dolichylphosphate (C95-P) and undecapreylphosphate (C55-P) are key molecular players in the synthesis and translocation of complex glycoconjugates across cell membranes. The molecular mechanism of how these processes occur remains a mystery. Failure to completely catalyze C95-P-mediated N-linked protein glycosylation is lethal, as are defects in the C55-P-mediated synthesis of bacterial cell surface polymers. Our recent NMR studies have sought to understand the role these "super-lipids" play in biosynthetic and translocation pathways, which are of critical importance to problems in human biology and molecular medicine. The PIs can alter membrane structure by inducing in the lamellar phospholipids (PL) bilayer a non-lamellar or hexagonal (HexII) structure. Membrane proteins that bind PIs contain a transmembrane binding motif, designated a PI recognition sequence (PIRS). Herein we review our recent combination of 1H- and 31P NMR spectroscopy and energy minimized molecular modeling studies that have determined the preferred orientation of PIs in model phospholipids membranes. They also show that the addition of a PIRS peptide to nonlamellar membranes induced by the PIs can reverse the HexII phase back to a lamellar structure. Our molecular modeling calculations have also shown that as many as five PIRS peptides can bind to a single PI molecule. These findings lead to the hypothesis that the PI-induced HexII structure may have the potential of forming a membrane channel that could facilitate glycoconjugate translocation processes. This is an alternate hypothesis to the possible existence of hypothetical "flippases" to accomplish movement of hydrophilic sugar chains across hydrophobic membranes.

HIV-1 cell entry is mediated by sequential interactions of the envelope protein gp120 with the receptor CD4 and a coreceptor, usually CCR5 or CXCR4, depending on the individual virion. Considerable efforts on exploiting the HIV coreceptors as drug targets have led to the new class of coreceptor antagonists. While these antiretroviral drugs aim at preventing virus/coreceptor interaction by binding to host proteins, neutralizing antibodies directed against the coreceptor- binding sites on gp120 have attracted attention as possible vaccine candidates. However, both approaches are complicated by the multiple protective mechanisms of gp120 which allow for rapid escape from selective pressures exerted by drugs or antibodies. Thus, advances in rational drug and vaccine design rely heavily on improved insights into the relation between genotype and phenotype, the evolution of coreceptor usage, and, ultimately the structural biology of coreceptor usage and inhibition. The third variable (V3) loop of gp120, crucially involved in all these aspects, will be a major focus of this review.

The structural class is an important attribute used to characterize the overall folding type of a protein or its domain. Since the concept of protein structural class was developed about 3 decades ago based on a visual inspection of polypeptide chain topologies in a dataset of only 31 gloular proteins, the number of structure-known proteins has been increased rapidly. For example, as of 12-July-2005, the entries deposited into RCSB PDB Protein Data Bank for proteins, peptides, and viruses whose 3-dimensional structures were determined by X-ray and NMR techniques have been increased to 28,920. To properly cover more and more structure-known proteins, some modification and expansion from the original structural classification scheme have been developed. Meanwhile, many different approaches have been proposed for predicting the structural class of proteins. In this review, the new classification schemes are briefly introduced. The attention is focused on the progress in structural class prediction and its impact in stimulating the development of identifying the other attributes of proteins. It is interesting to point out that the development of the latter has actually in turn greatly enriched the power of the former. Also, some promising approaches for the further development of protein structural class prediction are also addressed.

This review briefly covers recent literature of research on the phosphoryl transfer mechanism of PKA. Combining experimental and theoretical calculation results on enzymes with experimentally observed biomimic activities of phosphoryl amino acids and a small molecular model of catalytic core in PKA, a novel mechanism was proposed. The cooperative participation roles of both Asp166 and Lys168 via a penta-coodinate phosphoric intermediate was elucidated to conciliate the current different views of the phosphoryl transfer mechanism of PKA. Since many ATP-binding enzymes may share a similar phosphoryl transfer mechanism, this proposed mechanism might also apply to the mechanism of these enzymes, e.g., molecular motor and phosphatase among others.

Protein-protein interactions play a central role in numerous processes in cell and are one of the main research fields in current functional proteomics. The increase of finished genomic sequences has greatly stimulated the progress for detecting the functions of the genes and their encoded proteins. As complementary ways to the high through-put experimental methods, various methods of bioinformatics have been developed for the study of the protein-protein interaction. These methods range from the sequence homology-based to the genomic-context based. Recently, it tends to integrate the data from different methods to build the protein-protein interaction network, and to predict the protein function from the analysis of the network structure. Efforts are ongoing to improve these methods and to search for novel aspects in genomes that could be exploited for function prediction. This review highlights the recent advances of the bioinformatics methods in protein-protein interaction researches. In the end, the application of the protein-protein interaction has also been discussed.

The nicotinic acetylcholine receptor (AChR) is the archetype of the Cys-loop ligand-gated ion channel receptor superfamily. Noncompetitive antagonists inhibit the AChR without interacting directly with agonist sites. Among noncompetitive antagonists, general and local anesthetics have been used for decades to study the structure and function of muscle- as well as neuronal-type AChRs. In this review, we address and update all information regarding the characterization of binding sites and the mechanism of action for n-alkanols, barbiturates, inhalational and dissociative general anesthetics, as well as for tertiary and quaternary local anesthetics. The experimental evidence outlined in this review suggest that: (1) several neuronal-type AChRs might be targets for the pharmacological action of distinct anesthetics; (2) the molecular components of a specific anesthetic locus on a certain receptor type are different from the structural determinants of the site for the same anesthetic on a different receptor type; (3) there are unique binding sites for distinct anesthetics in the same receptor; (4) the affinity of a specific anesthetic depends on the AChR conformational state; (5) anesthetics may inhibit AChRs by different mechanisms including open-channel-blocking, augmenting the desensitization process, and/or inactivating the opening of resting receptors; and (6) some anesthetics may potentiate AChR activity.

Neuronal guidance cues attract or repel axons and/or neurons and play important roles in the pathfinding of neuronal networks and the functioning of nervous system. Prominent among them are the families of ephrins, semaphorins, Slits and netrins and their cognate cell-surface receptors. Due to their biological significance, extensive research has been carried out in the last ten years or so. Angiogenesis is a cellular process of capillary sprouting and configuring of neovasculatures, which shares many developmental, anatomical, physiological and pathophysiological features with the neural counterparts. This review will summarize the emerging evidence indicating the common molecular mechanisms underlying both axon guidance (including neuronal migration) and angiogenesis for exquisite regulation of proper wiring of both systems.

Protein functional site prediction is closely related to drug design, hence to public health. In order to save the cost and the time spent on identifying the functional sites in sequenced proteins in biology laboratory, computer programs have been widely used for decades. Many of them are implemented using the state-of-the-art pattern recognition algorithms, including decision trees, neural networks and support vector machines. Although the success of this effort has been obvious, advanced and new algorithms are still under development for addressing some difficult issues. This review will go through the major stages in developing pattern recognition algorithms for protein functional site prediction and outline the future research directions in this important area.