Current Protein & Peptide Science

ISSN: 1389-2042

Current Protein and Peptide Science
Volume 7, Number 3, June 2006

Contents


Exploring the Molecular Function of PIN1 by Nuclear Magnetic Resonance Pp. 179-194
Isabelle Landrieu, C. Smet, J.-M. Wieruszeski, A.-V. Sambo, R. Wintjens, L. Buée and G. Lippens
[Abstract]


Molecular Dynamics of Nicotinic Acetylcholine Receptor Correlating Biological Functions Pp. 195-200
Yechun Xu, Xiaomin Luo, Jianhua Shen, Weiliang Zhu, Kaixian Chen and Hualiang Jiang
[Abstract]


Biological Significance of Polymorphism in Legume Protease Inhibitors from the Bowman-Birk Family Pp. 201-216
Alfonso Clemente and C. Domoney
[Abstract]


Advances in Homology Protein Structure Modeling Pp. 217-227
Zhexin Xiang
[Abstract]


The Roles of Corticotropin-Releasing Factor-Related Peptides and Their Receptors in the Cardiovascular System Pp. 229-239
Hossein Pournajafi Nazarloo, P.M. Buttrick, H. Saadat and A.J. Dunn
[Abstract]


Development of Inhibitors of the Aspartyl Protease Renin for the Treatment of Hypertension Pp. 241-254
Boyd B. Scott, Gerard M. McGeehan and Richard K. Harrison
[Abstract]


Cellobiose Dehydrogenase – A Flavocytochrome from Wood Degrading, Phytopathogenic, and Saprotropic Fungi Pp. 255-280
Marcel Zamocky, R. Ludwig, C. Peterbauer, B.M. Hallberg, C. Divne, P. Nicholls and D. Haltrich
[Abstract]




Abstracts

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Exploring the Molecular Function of PIN1 by Nuclear Magnetic Resonance
Isabelle Landrieu, C. Smet, J.-M. Wieruszeski, A.-V. Sambo, R. Wintjens, L. Buée and G. Lippens

PIN1 participates in the regulation of a number of signalling pathways in the cell involving protein phosphorylation/dephosphorylation. Its role seems to be an essential control level in addition to the protein phosphorylation by proline-directed kinases. Its cellular function includes regulation of the cell cycle by interaction with phosphorylated mitotic proteins such as Cdc25 and transcription factors such as p53. PIN1 was shown to be involved in the malignant transformation of cells in breast cancer, by up regulation of cyclinD1 and is thought to be involved in the development of the AD by regulating the function of phosphorylated Tau. We propose here to discuss the molecular function of PIN1 at the atomic level based on data from the recent literature and our own results obtained by the technique of Nuclear Magnetic Resonance.

PIN1 specifically interacts with pThr/pSer-Pro motifs and is constituted by two domains: a WW N-terminal domain that binds pThr/pSer-Pro epitopes and a prolyl cis/trans isomerase C-terminal catalytic domain. An exception to this organisation is found in the plant PIN1 homologous enzymes, like PIN1At from Arabidopsis thaliana, that are constituted of the sole catalytic domain. The molecular function of PIN1, binding to and isomerization of pThr/pSer-Pro bonds, are thought to lead to several functional consequences. In a first mode of action, exemplified by its competition with the CKS protein, the interaction with PIN1 prevents interaction with other regulatory proteins, like ubiquitin-ligases that lead to degradation pathways. In a second mode of action, the idea is largely accepted that the local isomerization modifies the global conformation of the protein substrate and hence its intrinsic activity, although this has never been directly demonstrated. Finally, isomerization catalysis is thought to regulate the (de)phosphorylation of specific pThr/pSer-Pro motifs, exemplified by the stimulation of the dephosphorylation of pThr231 of Tau by the PP2A phosphatase.


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Molecular Dynamics of Nicotinic Acetylcholine Receptor Correlating Biological Functions
Yechun Xu, Xiaomin Luo, Jianhua Shen, Weiliang Zhu, Kaixian Chen and Hualiang Jiang

The nicotinic acetylcholine receptor (nAChR) that mediates fast intercellular communication in response to neurotransmitters is a paradigm of ligand-gated ion channels. Molecular dynamics (MD) simulations are valuable in understanding membrane protein function at atomic level, providing useful clues for further experimental/theoretical studies. In this brief review, recent progress in MD simulations of the nAChR has been illustrated, mainly focusing on the latest simulation of the whole transmembrane domain of the receptor. On the basis of MD simulations, asymmetrical and asynchronous motions of five subunits were observed both in the ligand binding and transmembrane domains; a closed-to-open conformational shift of the gate was captured in different simulation systems; the contributions from the lipid molecules and other transmembrane segments rather than M2 to the gate switch as well as the conformational change of the whole channel were assessed; the dynamic behavior and related physical/chemical properties of the water molecules and cations within the ion channel were examined; and an experimentally comparable single-channel conductance and ion selectivity were obtained.


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Biological Significance of Polymorphism in Legume Protease Inhibitors from the Bowman-Birk Family
Alfonso Clemente and C. Domoney

Naturally occurring protease inhibitors (PI) of the Bowman-Birk type constitute a major PI family in cereal and legume seeds. The family name is derived from the names of the two investigators who characterised the first inhibitor of this type, the Bowman-Birk inhibitor from soybean (BBI). These proteins have the capacity to inhibit one or more of a range of serine proteases, including the digestive enzymes trypsin and chymotrypsin. PI from this family interact with the active sites of serine proteases in a `canonical´, i.e. substrate-like, manner via exposed reactive site loops of conserved conformation within the inhibitor. Multiple BBI variants can be found within and among species. A limited number of amino acids located within the inhibitory domain is responsible for the primary functional and biological activities of BBI-like proteins. However, sequence variation in binding loops, post-translational modifications at the amino- and carboxy-terminal ends, as well as differences in the multimeric nature of the inhibitors may act in combination to influence the functional properties and the physiological role of BBI-like proteins.

Recently, BBI and proteins homologous to BBI (BBI-like proteins) have emerged as highly promising cancer chemopreventive agents. BBI has been shown to be capable of preventing or suppressing carcinogenic processes in a wide variety of in vitro and in vivo animal model systems. The potential exploitation of BBI-like proteins in human health-promotion programmes will depend on elucidating in detail the molecular basis for the variation in biological activities among the many variant forms. New knowledge, derived both from the use of synthetic cyclic peptides that mimic the inhibitory loops of BBI-like proteins, and from genomic data pertaining to the structure of BBI gene classes, together facilitate the manipulation, screening and selection of appropriate variants through biotechnology.


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Advances in Homology Protein Structure Modeling
Zhexin Xiang

Homology modeling plays a central role in determining protein structure in the structural genomics project. The importance of homology modeling has been steadily increasing because of the large gap that exists between the over-whelming number of available protein sequences and experimentally solved protein structures, and also, more importantly, because of the increasing reliability and accuracy of the method. In fact, a protein sequence with over 30% identity to a known structure can often be predicted with an accuracy equivalent to a low-resolution X-ray structure. The recent advances in homology modeling, especially in detecting distant homologues, aligning sequences with template structures, modeling of loops and side chains, as well as detecting errors in a model, have contributed to reliable prediction of protein structure, which was not possible even several years ago. The ongoing efforts in solving protein structures, which can be time-consuming and often difficult, will continue to spur the development of a host of new computational methods that can fill in the gap and further contribute to understanding the relationship between protein structure and function.


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The Roles of Corticotropin-Releasing Factor-Related Peptides and Their Receptors in the Cardiovascular System
Hossein Pournajafi Nazarloo, P.M. Buttrick, H. Saadat and A.J. Dunn

Corticotropin-releasing factor (CRF), CRF-related peptides and their receptors are present in the central nervous system and in peripheral tissues including the immune, reproductive and cardiovascular systems. CRF and urocortin (urocortin 1) bind to the CRF receptor type 1 (CRF₁ receptor) and the CRF receptor type 2 (CRF₂ receptor), whereas urocortin 2 (formerly known as stresscopin related peptide) and urocortin 3 (formerly known as stresscopin) bind with high affinity to the CRF₂ receptor. Recent studies show that urocortin 1, urocortin 2 and urocortin 3 are potent regulators of cardiovascular function. This review highlights the role of cardiovascular CRF and related peptides and its relevance in mediating the adaptive response of the cardiovascular system to stressful conditions.


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Development of Inhibitors of the Aspartyl Protease Renin for the Treatment of Hypertension
Boyd B. Scott, Gerard M. McGeehan and Richard K. Harrison

Renin is the rate-limiting enzyme in the renin-angiotensin-aldosterone system (RAS) which controls blood pressure and volume. The biological function of renin is to cleave the N-terminus of angiotensinogen releasing the decapeptide, angiotensin I (ANGI). Subsequently, angiotensin I is further processed by the angiotensin converting enzyme (ACE) to produce angiotensin II (ANGII). The RAS cascade is a major target for the clinical management of hypertension. Current clinical treatments include angiotensin converting enzyme inhibitors (ACEi) and ANGII receptor blockers (ARBs). As the rate-limiting enzyme in ANGII production, renin inhibitors have been pursued as an additional class of anti-hypertensives. Clinical studies conducted with renin inhibitors have shown them to be as effective as ACE inhibitors in lowering blood pressure. Most importantly, inhibitors of renin may have a number of potential advantages over ACEi and ARBs. Renin is specific for angiotensinogen and will not carry the ancillary pharmacology associated with ACEi or ARBs.

To date, no renin inhibitors have made it to market. The development of these inhibitors has been hindered by poor bioavailability and complex synthesis. However, despite the pharmacokinetic challenges of designing renin inhibitors, the enzyme remains a promising target for the development of novel treatments for hypertension.

This review will consist of an overview of renin biology, the pharmacology of renin and RAS and focus in on renin as a target for blood pressure regulation. We also cover the evaluation of renin inhibitors in animal models and clinical studies. Presently a number of new generation inhibitors of renin are in development with at least one in the clinic and these will be discussed. Finally we will discuss what might distinguish renin inhibitors from current therapeutic options and discuss other therapeutic indications renin inhibitors might have.


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Cellobiose Dehydrogenase – A Flavocytochrome from Wood Degrading, Phytopathogenic, and Saprotropic Fungi
Marcel Zamocky, R. Ludwig, C. Peterbauer, B.M. Hallberg, C. Divne, P. Nicholls and D. Haltrich

Cellobiose dehydrogenase, the only currently known extracellular flavocytochrome, is formed not only by a number of wood-degrading but also by various phytopathogenic fungi. This inducible enzyme participates in early events of lignocellulose degradation, as investigated in several basidiomycete fungi at the transcriptional and translational level. However, its role in the ascomycete fungi is not yet obvious. Comprehensive sequence analysis of CDH-encoding genes and their translational products reveals significant sequence similarities along the entire sequences and also a common domain architecture. All known cellobiose dehydrogenases fall into two related subgroups. Class-I members are represented by sequences from basidiomycetes whereas class-II comprises longer, more complex sequences from ascomycete fungi. Cellobiose dehydrogenase is typically a monomeric protein consisting of two domains joined by a protease-sensitive linker region. Each larger (dehydrogenase) domain is flavin-associated while the smaller (cytochrome) domains are haem-binding. The latter shorter domains are unique sequence motifs for all currently known flavocytochromes. Each cytochrome domain of CDH can bind a single haem b as prosthetic group. The larger dehydrogenase domain belongs to the glucose-methanol-choline (GMC) oxidoreductase superfamily – a widespread flavoprotein evolutionary line. The larger domains can be further divided into a flavin-binding subdomain and a substrate-binding subdomain. In addition, the class-II (but not class-I) proteins can possess a short cellulose-binding module of type 1 at their C-termini. All the cellobiose dehydrogenases oxidise cellobiose, cellodextrins, and lactose to the corresponding lactones using a wide spectrum of different electron acceptors. Their flexible specificity serves as a base for the development of possible biotechnological applications.