Volume 2, Issue 1-2

Akt/PKB kinases are central mediators of cell homeostasis. There are three highly homologous Akt isoforms, Akt1/PKBα, Akt2/PKBβ and Akt3/PKBγ. Hyperactivation of Akt signaling is a key node in the progression of a variety of human cancer, by modulating tumor growth, chemoresistance and cancer cell migration, invasion and metastasis. It is now clear that, to understand the mechanisms on how Akt affects specific cancer cells, it is necessary to consider the relative importance of each of the three Akt isoforms in the altered cells. Akt1 is involved in tumor growth, cancer cell invasion and chemoresistance and is the predominant altered isoform found in various carcinomas. Akt2 is related to cancer cell invasion, metastasis and survival more than tumor induction. Most of the Akt2 alterations are observed in breast, ovarian, pancreatic and colorectal carcinomas. As Akt3 expression is limited to some tissues, its implication in tumor growth and resistance to drugs mostly occurs in melanomas, gliomas and some breast carcinomas. To explain how Akt isoforms can play different or even opposed roles, three mechanisms have been proposed: tissue-specificity expression/activation of Akt isoforms, distinct effect on same substrate as well as specific localization through the cyto-skeleton network. It is becoming clear that to develop an effective anticancer Akt inhibitor drug, it is necessary to target the specific Akt isoform which promotes the progression of the specific tumor.

Embryonic stem cells have the ability to differentiate into nearly all cell types. However, the molecular mechanism of its pluripotency is still unclear. Oct3/4, Sox2 and Nanog are important factors of pluripotency. Oct3/4 (hereafter referred to as Oct4), in particular, has been an irreplaceable factor in the induction of pluripotency in adult cells. Proteins interacting with Oct4 and Nanog have been identified via affinity purification and mass spectrometry. These data, together with iterative purifications of interacting proteins allowed a protein interaction network to be constructed. The network currently includes 77 transcription factors, all of which are interconnected in one network. In-depth studies of some of these transcription factors show that they all recruit the NuRD complex. Hence, transcription factor clustering and chromosomal remodeling are key mechanism used by embryonic stem cells. Studies using RNA interference suggest that more pluripotency genes are yet to be discovered via protein-protein interactions. More work is required to complete and curate the embryonic stem cell protein interaction network. Analysis of a saturated protein interaction network by system biology tools can greatly aid in the understanding of the embryonic stem cell pluripotency network.

Increased prevalence of multi-drug resistance in pathogens has encouraged researchers to focus on finding novel forms of anti-infective agents. Antimicrobial peptides (AMPs) found in animal secretions are components of host innate immune response and have survived eons of pathogen evolution. Thus, they are likely to be active against pathogens and even those that are resistant to conventional drugs. Many peptides have been isolated and shown to be effective against multi-drug resistant pathogens. More than 500 AMPs have been identified from amphibians. The abundance of AMPs in frog skin is remarkable and constitutes a rich source for design of novel pharmaceutical molecules. Expression and post-translational modifications, discovery, activities and probable therapeutic application prospects of amphibian AMPs will be discussed in this article.

Mitogen activated protein kinases (MAPKs) play important roles in the development of eukaryotic organisms through the regulation of signal transduction pathways stimulated by external signals. MAPK signaling pathways have been associated with the regulation of cell growth, differentiation, and chemotaxis, indicating that MAPKs contribute to a diverse set of developmental processes. In most eukaryotes, the diversity of external signals is likely to far exceed the diversity of MAPKs, suggesting that multiple signaling pathways might share MAPKs. Do different signaling pathways converge before MAPK function or can MAPKs maintain signaling specificity through interactions with specific proteins? The genetic and biochemical analysis of MAPK pathways in simple eukaryotes such as Dictyostelium offers opportunities to investigate functional specificity of MAPKs in G-protein-mediated signal transduction pathways. This review considers the regulation and specificity of MAPK function in pathways that control Dictyostelium growth and development.

Carboxyltransferase is one component of the multifunctional enzyme acetyl-CoA carboxylase which catalyzes the first committed step in fatty acid biosynthesis. Carboxyltransferase is an α 2 β 2 heterotetramer and possesses two distinct but integrated functions. One function catalyzes the transfer of carbon dioxide from biotin to acetyl-CoA, whereas the other involves binding to the mRNA encoding both subunits. When carboxyltransferase binds to the mRNA both enzymatic activity and translation of the mRNA are inhibited. However, the substrate acetyl-CoA competes with mRNA for binding. Thus, mRNA binding by carboxyltransferase provides an effective mechanism for regulating enzymatic activity and gene expression. This conceptual review takes the position that regulation of enzymatic activity and gene expression of carboxyltransferase by binding to its own mRNA is at its most fundamental level the result of the symmetry in the chemical reaction catalyzed by the enzyme. The chemical reaction is symmetrical in that both substrates generate enolate anions during the course of catalysis. The chemical symmetry led to a structural symmetry in the enzyme where both the α and β subunits contain oxyanion holes that stabilize the enolate anions. Then the region of the mRNA that codes for the oxyanion holes provided the binding sites for carboxyltransferase. Thus, the symmetry of the chemical reaction formed the foundation for the evolution of the mechanism for regulation of carboxyltransferase.

Periplasmic binding proteins (PBPs) are a crucial part of ATP-binding cassette import systems in Gram-negative bacteria. Central to their function is the ability to undergo a large-scale conformational rearrangement from open-unliganded to closed-liganded, which signals the presence of substrate and starts its translocation. Over the years, PBPs have been extensively studied not only owing to their essential role in nutrient uptake but also because they serve as excellent models for both practical applications (e.g., biosensor technology) and basic research (e.g., allosteric mechanisms). Although much of our knowledge at atomic level has been inferred from the detailed, static pictures afforded by crystallographic studies, nuclear magnetic resonance (NMR) has been able to fill certain gaps in such body of work, particularly with regard to dynamic processes. Here, we review NMR studies on PBPs, and their unique insights on conformation, dynamics, energetics, substrate binding, and interactions with related transport proteins. Based on the analysis of recent paramagnetic NMR results, as well as crystallographic and functional observations, we propose a mechanism that could explain the ability of certain PBPs to achieve a closed conformation in absence of ligand while others seem to remain open until ligand-mediated closure.

Despite the fact that cyclosporin A (CsA) and tacrolimus (FK506) are very potent drugs in the treatment of serious autoimmune diseases and in the prevention of graft vs. host reactions or tissue rejections after allo- or xenotransplantations, modern transplantation medicine attempts to develop alternative medication regimes without these calcineurin inhibitors. The primary motivation for this endeavor is the high incidence of dramatic side effects upon immunosuppressive therapy. CsA and FK506 target not only the calcineurin/NFAT pathway, but they also bind and inhibit members of distinct peptidyl-prolyl cis/trans isomerase families, which are involved in numerous important signal transduction pathways. Therefore, the development of a potent calcineurin inhibitor that discriminates between calcineurin and other protein phosphatases and peptidyl-prolyl cis/trans isomerases, respectively, should improve the drug safety in clinical use and represent a valuable tool in basic research to investigate calcineurin modulated pathways. This review gives a current overview about novel calcineurin inhibitors, which were identified by screening of compound libraries and in natural materials or were derived from known inhibitors in the past decades. Thereby, we focus on their structure, properties and biological effects.

The ubiquitously expressed natural polyamines putrescine, spermidine, and spermine are small, flexible cationic compounds that exert pleiotropic actions on various regulatory systems and, accordingly, are essentially involved in diverse life functions. These roles of polyamines result from their capability to interact with negatively charged regions of all major classes of biomolecules, which might act in response by changing their structures and functions. The present review deals with polyamine-protein interactions, thereby focusing on mammalian proteins. We discuss the various modes in which polyamines can interact with proteins, describe major types of affected functions illustrated by representative examples of involved proteins, and support information with respective structural evidence from elucidated three-dimensional structures. A specific focus is put on polyamine interactions at protein surfaces that can modulate the aggregation of proteins to organized structural networks as well as to toxic aggregates and, moreover, can play a role in important transient protein-protein interactions.

Cystatins are small proteins, typically composed of 100–120 amino acids, which together with similar proteins devoid of inhibitory properties, belong to a cystatin ‘superfamily’. Cystatins can do more than just inhibit proteases: two important aspects described here are aggregation properties linked to misfolding diseases and the unique ability of monellin, a plant cystatin, to elicit sweet taste. The explanation of the puzzling phenomenon of ‘sweet proteins’ required an in-depth structural study of monellin, also regarding the causes of the high thermal stability of its single chain structure. The detailed mechanisms by which cystatins aggregate could be relevant in the study of misfolding diseases involving cystatins. They are reviewed here with emphasis on 3D domain swapping, typical of aggregating cystatins. While studying monellin, we noticed that it aggregates in a conventional way, probably through the cross-β spine mechanism. However, several cystatins derived from oryzacystatin_I to emulate the taste behavior of monellin aggregate via different mechanisms.

In the past years aldose reductase (AKR1B1; AR) is thought to be involved in the pathogenesis of secondary diabetic complications such as retinopathy, neuropathy, nephropathy and cataractogenesis. Subsequently, several AR inhibitors have been developed and tested for diabetic complications. Although these inhibitors have found to be safe for human use, they have not been successful in clinical studies because of limited efficacy. Recently, the potential physiological role of AR has been reassessed from a different point of view. Diverse groups suggested that AR, in addition to reducing glucose, also efficiently reduces oxidative stress-generated lipid peroxidation-derived aldehydes and their glutathione conjugates. Because lipid aldehydes alter cellular signals by regulating the activation of transcription factors such as NF-κB and AP1, inhibition of AR could inhibit such events. Indeed, a wide array of recent experimental evidence indicates that the inhibition of AR prevents oxidative stress-induced activation of NF-κB and AP1 signals that lead to cell death or growth. Furthermore, AR inhibitors have been shown to prevent inflammatory complications such as sepsis, asthma, colon cancer and uveitis in rodent animal models. The new experimental in vitro and in vivo data has provided a basis for investigating the clinical efficacy of AR inhibitors in preventing other inflammatory complications than diabetes. This review describes how recent studies have identified novel plethoric physiological and pathophysiological significance of AR in mediating inflammatory complications, and how the discovery of such new insights for this old enzyme could have considerable importance in envisioning potential new therapeutic strategies for the prevention or treatment of inflammatory diseases.

The aldo-keto reductase (AKR) superfamily consists of over 150 protein members sharing similar structure and enzymatic activities. To date, 13 human AKRs have been identified, and they participate in xenobiotic detoxification, biosynthesis and metabolism. Increasing evidence suggests the involvement of human AKR proteins in cancer development, progression and treatment. Some proteins demonstrate multiple functional features in addition to being a reductase for carbonyl groups. This review article discusses the most recent progress made in the study of humans AKRs.