Molecular BioSystems

doi: 10.1039/c6mb90044epmid: N/A

doi: 10.1039/c6mb90045cpmid: N/A

Lokhande, Sonali; Patra, Biranchi N.; Ray, Animesh

doi: 10.1039/c6mb00598epmid: 27714015

Huntington's disease is a rare neurodegenerative disorder whose complex pathophysiology exhibits system-wide changes in the body, with striking and debilitating clinical features targeting the central nervous system. Among the various molecular functions affected in this disease, mitochondrial dysfunction and transcriptional dysregulation are some of the most studied aspects of this disease. However, there is evidence of the involvement of a mutant Huntingtin protein in the processes of DNA damage, chromosome condensation and DNA repair. This review attempts to briefly recapitulate the clinical features, model systems used to study the disease, major molecular processes affected, and, more importantly, examines recent evidence for the involvement of the mutant Huntingtin protein in the processes regulating chromosome condensation, leading to DNA damage response and neuronal death.

Oldrati, Vera; Arrell, Miriam; Violette, Aude; Perret, Frédéric; Sprüngli, Xavier; Wolfender, Jean-Luc; Stöcklin, Reto

doi: 10.1039/c6mb00516kpmid: 27787525

The term “venomics” was coined to describe the global study of venom and venom glands, targeting comprehensive characterization of the whole toxin profile of a venomous animal by means of proteomics, transcriptomics, genomics and bioinformatics studies. This integrative approach is supported by the rapid evolution of protein, RNA and DNA sequencing techniques, as well as databases, knowledge-bases and biocomputing algorithms. The aim of this review is to illustrate advances in the field of venomics during the last decade, addressing each step of the procedure, from sample collection to data treatment. A special focus is made on new perspectives for a better understanding of the venomous function and for fostering the discovery of new venom-derived drug candidates.

Hu, Rui; Yap, Hong-Kin; Fung, Yik-Hong; Wang, Yong; Cheong, Wing-Lam; So, Lok-Yan; Tsang, Chui-Shan; Lee, Lawrence Yoon Suk; Lo, Warrick Ken Cheung; Yuan, Jian; Sun, Ning; Leung, Yun-Chung; Yang, Guoqiang; Wong, Kwok-Yin

Xu, Jianhua; Han, Kun; Liu, Dongdong; Lin, Li; Miao, Peng

doi: 10.1039/c6mb00659kpmid: 27785510

MiRNAs are a fascinating kind of biomolecule due to their vital functions in gene regulation and potential value as biomarkers for serious diseases including cancers. Exploiting convenient and sensitive methods for miRNA expression assays is imperative. In this study, we employ an exonuclease (RecJf) and a nicking endonuclease (Nt.BbvCI) to catalyse isothermal reactions for the amplified detection of miRNA. The degree of cyclical enzymatic amplification depends on the initial target miRNA level, which can determine the density of DNA probes bound on the electrode surface. Since DNA probes with an amino group at the 3′ end are able to locate silver nanoparticles on the electrode, which provide intense stripping responses, the sensitive quantification of miRNA can be achieved. The proposed method has a limit of detection as low as 35 aM, with remarkable specificity, which offers a new approach for investigating miRNA networks and for clinical diagnosis applications.

Timofeeva, Anna M.; Buneva, Valentina N.; Nevinsky, Georgy A.

doi: 10.1039/c6mb00573jpmid: 27782255

It was shown previously that approximately 30% ± 5% of antibodies against myelin basic protein (MBP) and the DNA of patients with systemic lupus erythematosus (SLE) and multiple sclerosis (MS) possess catalytic activities that play an important negative role in the pathogenesis of MS and SLE. An immunoglobulin light chain phagemid library derived from peripheral blood lymphocytes of patients with SLE was used. The small pools of phage particles displaying light chains with different affinity for MBP were isolated by affinity chromatography on MBP-Sepharose, and the fraction eluted with 0.5 M NaCl was used for preparation of individual monoclonal light chains (MLChs, 26–27 kDa). The clones were expressed in E. coli in a soluble form. MLChs were purified by metal chelating chromatography followed by FPLC-gel filtration. The activity of one MLCh (NGTA1-Me-pro) was inhibited only by EDTA, and it efficiently hydrolyzed MBP (but not other proteins) and four different oligopeptides corresponding to four known immunodominant sequences containing cleavage sites of MBP only in the presence of several different metal ions. An unexpected result was obtained: NGTA1-Me-pro demonstrated two pH optima, two optimal concentrations of Me2+ ions, and two Km values for MBP. The protein sequence of NGTA1-Me-pro, having two metalloprotease active centers, has homology with several mammalian metalloproteases. Recently, it was shown that one other MLCh possesses serine-like and metalloprotease activity. The principal possibility of the existence of MLChs with several different active centers is unexpected, but very important for the further understanding of unknown possibilities for immune systems and the biological functions of antibodies.

Ferreira, Luisa A.; Uversky, Vladimir N.; Zaslavsky, Boris Y.

doi: 10.1039/c6mb00608fpmid: 27714063

Partition coefficients of non-ionic essentially nonpolar compounds between air and rat biological tissues and between blood and other tissues were examined and found to be linearly interrelated according to the previously established equation for partition coefficients of solutes in aqueous two-phase systems: log Kblood–tissue-1 = k0 + k1 log Kblood–tissue-2 + k2 log Kblood–tissue-3, where k0, k1, and k2 are constants. Analysis of partition coefficients of amphiphilic and ionizable drugs between blood and different tissues in rats in vivo showed that the above relationship holds for the blood–tissue partition coefficients of these compounds as well. The data obtained indicate that distribution of organic compounds between different biological tissues may be considered in the framework of solute partitioning in aqueous two-phase systems, and imply that aqueous media in different tissues have different solvent properties, and compound–water interactions in these media may respond to different environments governed by the tissue composition.

Ebrahimi, Kourosh Honarmand; Bill, Eckhard; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

doi: 10.1039/c6mb00235hpmid: 27722502

Ferritin is a nanocage protein made of 24 subunits. Its major role is to manage intracellular concentrations of free Fe(ii) and Fe(iii) ions, which is pivotal for iron homeostasis across all domains of life. This function of the protein is regulated by a conserved di-iron catalytic center and has been the subject of extensive studies over the past 50 years. Yet, it has not been fully understood how Fe(ii) is oxidized in the di-iron catalytic center and it is not known why eukaryotic and microbial ferritins oxidize Fe(ii) with different kinetics. In an attempt to obtain a new insight into the mechanism of Fe(ii) oxidation and understand the origin of the observed differences in the catalysis of Fe(ii) oxidation among ferritins we studied and compared the mechanism of Fe(ii) oxidation in the eukaryotic human H-type ferritin (HuHF) and the archaeal ferritin from Pyrococcus furiosus (PfFtn). The results show that the spectroscopic characteristics of the intermediate of Fe(ii) oxidation and the Fe(iii)-products are the same in these two ferritins supporting the proposal of unity in the mechanism of Fe(ii) oxidation among eukaryotic and microbial ferritins. Moreover, we observed that a site in the di-iron catalytic center controls the distribution of Fe(ii) among subunits of HuHF and PfFtn differently. This observation explains the reported differences between HuHF and PfFtn in the kinetics of Fe(ii) oxidation and the amount of O2 consumed per Fe(ii) oxidized. These results provide a fresh understanding of the mechanism of Fe(ii) oxidation by ferritins.

Różycki, Bartosz; Cieplak, Marek

doi: 10.1039/c6mb00606jpmid: 27714009

Cellulosomes are complex multi-enzyme machineries which efficiently degrade plant cell-wall polysaccharides. The multiple domains of the cellulosome proteins are often tethered together by intrinsically disordered regions. The properties and functions of these disordered linkers are not well understood. In this work, we study endoglucanase Cel8A, which is a relevant enzymatic component of the cellulosomes of Clostridium thermocellum. We use both all-atom and coarse-grained simulations to investigate how the conformations of the catalytic domain of Cel8A are affected by the disordered linker at its C terminus. We find that when the endoglucanase is bound to its substrate, the effective stiffness of the linker can influence the distances between groups of amino-acid residues throughout the entire enzymatic domain. In particular, variations in the linker stiffness can lead to small changes in the geometry of the active-site cleft. We suggest that such geometrical changes may have an effect on the catalytic activity of the enzyme.