Current Protein and Peptide Science - Volume 11, Issue 1, 2010

Current Protein and Peptide Science (CPPS) has now completed ten years of publication. As we embark on the next ten years it is useful to look back over the past and reflect on our successes as well as our problems. I am very pleased that CPPS has featured high quality review articles from laboratories around the world. Interacting with authors from so many countries has been one of the most rewarding aspects of my job as Editor-in-Chief. I am also very happy that the papers published in CPPS over these years have featured a wide variety of topic in protein chemistry, structure, and function. While we are close to having a general understanding of protein structure, the various properties of proteins including alternate conformations and varying solubility characteristics have provided explanations for diseases. Newly discovered proteins from the various genomic sequencing projects provide challenges for determining the functional activities. Clearly, the future of protein science is unlimited. I also wish to thank the many referees who have contributed to the peer review process for CPPS. Again, I have been fortunate to rely on scientists from many countries and laboratories to handle the difficult task of assessing the quality of the review manuscripts submitted to our journal. Typically, refereeing a review manuscript takes longer than refereeing a research report and this can lead to some frustration for authors who are waiting for a decision on acceptance of their manuscript. In addition, I want to thank the staff of Bentham Science Publishing for their efforts over the past ten years to help me manage the publishing process. Specifically, Mr. Muhammad Ilyas has been a great friend and colleague in this effort. He has recently been joined by Nazia Kamran, who has been tireless in her efforts to help manage the journal. A new development in the process of dealing with manuscripts is the Content Management System developed by Bentham Science Publishing. Starting in summer of 2009, we have been using this system exclusively for manuscript submission, peer review, and all decision making with respect to new submissions. This system can be accessed at www.bentham-editorial.org. From that portal, authors can register and submit manuscripts and then check back later to get information on the peer review process. With lots of fine tuning, we expect this system to speed processing of manuscripts in the future.

Cooperative interactions within biological macromolecules are of fundamental physiological relevance and have been studied in great detail. Yet, even in the best investigated case of oxygen binding by hemoglobin, our understanding of the structural and thermodynamic bases of cooperativity is far from satisfactory. Several theoretical models have been proposed to explain cooperative O2 binding to hemoglobin, among which the two-state model by Monod, Wyman and Changeux, has been the most successful and the most thoroughly tested. This model explains the functional properties of hemoglobin as resulting from the equilibrium of two quaternary conformations, named R and T, characterized by different ligand affinity, and is capable of very accurate (but not always exact) predictions. This review focuses on the experiments carried out to test the models of cooperativity, and especially the two-state model, and identifies two major deviations, or groups of deviations, between the predictions of this model and the actual experimental results, namely (i) the changes in the behaviour of the T- and R-state due to solvent components; (ii) the appearance of R-like reactivity under experimental conditions in which the T-state should be largely prevalent. Modern models of cooperativity, devised to account for these discrepancies while maintaining the basic two-state hypothesis of Monod, Wyman and Changeux, are also reviewed.

The intent of this article is to review recent literature on ribosome inactivating proteins (RIPs) including isolation and characterization of new RIPs, studies on the crystal structures and mechanisms of actions of RIPs, the use of saporin-based neurotoxins to selectively lesion cholinergic neurons in neuroscience research, and the use of RIP-based conjugates and immunotoxins in anticancer therapy.

Amyloid-β (Aβ) peptide is commonly found in human Alzheimer's disease (AD) brain and is the main component of Alzheimer amyloid plaques. The predominant forms of Aβ in the human brain are Aβ(1-40) and Aβ(1-42), but Aβ(25-35) fragment, physiologically present in elderly people, is the more toxic region and has been recently found to play a relevant role in AD, due to its peculiar aggregation properties. In this work, we review the current understanding on the conformations and biological activity of Aβ(25-35) exploring aggregation, cytotoxic and neurodegenerative properties of this fundamental Aβ fragment, in order to provide an effective starting point to better approach a pathology spread and problematic as AD.

Lysosomal enzymes undergo phosphorylation on their mannose residues in the Golgi apparatus and are recognized by two distinct type I transmembrane glycoproteins designated as the mannose 6-phosphate receptors; MPR300, (Mr 300 kDa) and MPR46, (Mr 46 kDa) that internally transport them to the lysosomes. In humans, absence of this recognition system leads to severe lysosomal storage disease, emphasizing their essential role in the biogenesis of lysosomes. Among the two receptors only MPR46 shows an absolute requirement for divalent metal ions. Only MPR300 is known to be a multifunctional protein that also binds many other ligands such as the human IGF-II, thyroglobulin, retinoic acid, granzyme A and B. In mammals, the extracytoplasmic domain of MPR300 protein is comprised of 15 repetitive cassettes which share significant similarity with each other and also with the single cassette that constitutes the extracytoplasmic domain of MPR46. Therefore it became necessary to understand the evolution of these receptors. Homologous proteins were affinity purified from different non-mammalian vertebrates such as birds, reptiles, amphibians, fish and also from the invertebrates, echinodermates (starfish) and molluscs (unio). Cloning and sequencing of both receptors from different mammals, chicken, fish and MPR46 from starfish revealed that these proteins exhibit similar structural domains as the mammalian receptors. α-fucosidase characterized from the molluscs exhibits specific interaction with the putative MPR300 protein from the same species. Available evidence suggests evolutionary conservation of both receptors from molluscs, as below these species no receptors that bind phosphomannan have been identified.

Random mutagenesis is a powerful tool for generating enzymes, proteins, entire metabolic pathways, or even entire genomes with desired or improved properties. This technology is used to evolve genes in vitro through an iterative process consisting of recombinant generation. Coupled with the development of powerful high-throughput screening or selection methods, this technique has been successfully used to solve problems in protein engineering. There are many methods to generate genetic diversity by random mutagenesis and to create combinatorial libraries. This can be achieved by treating DNA or whole bacteria with various chemical mutagens, by passing cloned genes through mutator strains, by “error-prone” PCR mutagenesis, by rolling circle error-prone PCR, or by saturation mutagenesis. The next sections of this review article focus on recent advances in techniques and methods used for in vitro directed evolution of enzymes using random mutagenesis. Selected examples, highlighting successful applications of these methods, are also presented and discussed.