International Conference on Biochemistry October 10-12, 2016 Kuala Lumpur, Malaysia

John Horsley has completed his PhD from the University of Adelaide and currently undertaking Post-doctoral studies from the University of Adelaide, Australia. He is working with the Abell Group focusing on peptide synthesis and has published number of papers in the reputed scientific journals.

Secondary structures in proteins contain motifs which are important in determining protein folding and arrangement. The unique folding pattern creates a well-defined structure of protein which governs the function, as emphasized by the quote structure dictates function. Thus, the ability to control the secondary structure of a protein will enable the regulation of protein activity and function. The main objective of this research is to reversibly control the secondary structure of a cyclic peptide photochemically, using UV and visible light. This is demonstrated by incorporating a cis-trans photoisomerizable azobenzene photo-switch into the naturally occurring antibiotic, gramicidin S, to produce a cyclic peptidomimetic, azobenzene-gramicidin S (Azo-GS). Gramicidin S exists as a cyclic peptide with two antiparallel β-strands, linked by two β-turns. The cis isomer of Azo-GS was found to adopt a β-sheet with a β-turn structure, while the trans isomer exists as a random structure. While gramicidin S is active against both Gram-positive and Gram negative bacteria, our experimental results showed that Azo-GS is only active against Gram positive bacteria. Both isomers of Azo-GS were tested against the Gram positive bacteria, Staphylococcus aureus and the Gram negative bacteria, Escherichia coli, respectively. The cis isomer, containing the more well-defined secondary structure, was found to be active in suppressing the growth of S. aureus, while the trans isomer was found to be inactive. The findings of this research form the basis for photo-switches to function as potential molecular switches to control the secondary structures and ultimately, the activity of peptides.

Wirginia Krzysciak has completed her PhD from Jagiellonian University, Poland. She is an Assistant Professor in the Department of Medical Diagnostics, Faculty of Pharmacy, Medical College, Jagiellonian University in Krakow, Poland. She has published more than 20 papers in peer-review journals on Caries Pathogenesis and Redox Signaling. She is a Lecturer and one of the Instructors of Laboratory Medicine where she teaches Hematology, Laboratory Medicine and Medical Diagnostics. She is also a Founder and the Instructor of Students Association of Laboratory Diagnosticians. She is a Member of Polish Society of Microbiologists and Polish Society of Biochemistry.

Background: Carbohydrate metabolism is one of the key metabolic pathways subject to changes during Streptococcus mutans-mixed biofilm development. Aim: The objective of this study was determination of the role of GCK and PK in S. mutans pathogenicity. Material & Methods: Pyruvate kinase and glucokinase from S. mutans-mixed biofilm species were purified, precipitated and estimated fluorimetrically. The study was performed on type and clinical strains. In total, 21 children with caries were enrolled, (4±1.7 years). As many as 22 individuals without caries (4.12±1.22 years) served as the control group. Phenotyping of isolated bacterial strains was performed, and evaluated by 16S rDNA gene sequencing. Biofilm assay was carried out according to current protocols in microbiology. Results: Out of 100 isolated strains, 74 were classified as S. mutans species. PK and GCK activities were highest after 6 and 12 hours incubation in the mixed biofilm species. PK activity was higher (1.45 mU/mg of protein) in the experimental group compared to the control (1.10 mU/mg of protein). Conclusions: The glycolytic activity increases in the newly formed biofilm after 6 and 12 hours of incubation; however, this activity decreases with dental plaque biofilm aging. It was demonstrated that the amount of synthesized PK in S. mutans-mixed biofilm species grows in the caries group. Inhibition of glycolysis metabolic pathway proteins during mixed-species biofilm of S. mutans development may have an effect on reduction of the development of dental caries in children.

Yui Umekawa is currently pursuing PhD in Biochemistry, Bioenergetics, Molecular Biology at the United Graduate School of Agricultural Sciences, Iwate University, Japan.

Temperature is one of the most important requirements for all living organisms. To survive in severe environments in which temperature changes continuously, some animals have gained the ability to maintain their temperature during the evolutionary process, called homeothermy, which is performed by a complex mechanism involving thermal receptors throughout the body and integration in the hypothalamus that controls shivering and non-shivering thermogenesis. Interestingly, flowers of some plants show a similar homeothermic behavior by inversely controlled respiration to temperature. To clarify the thermoregulatory mechanism in thermogenic plants, we investigated the temperature response of respiration in vivo using modified Arrhenius model using homeothermic spadices of skunk cabbage (Symplocarpus renifolius). Our results clearly showed that overall thermodynamic activation energy exhibits a negative value in the temperature range in which respiration control occurs. Our results suggest that respiratory control in this plant is achieved by a pre-equilibrium chemical reaction in response to temperature. Moreover, citrate-driven respiration analysis using isolated mitochondria from thermogenic spadices further suggests that chemically endothermic reactions, such as NADPH production catalyzed by mitochondrial isocitrate dehydrogenase are involved in our proposed pre-equilibrium reaction. A law of chemical equilibrium known as Le Chatelier's principle may govern the homeothermic control in skunk cabbage.

Md Abu Sayed is currently pursuing his PhD from United Graduate School of Agriculture, Iwate University, Japan. He has been serving as an Assistant Professor in the Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University (HSTU), Dinajpur, Bangladesh since 16 May, 2012.

Skunk cabbage, Symplocarpus renifolius, is known to produce enough heat to melt the snow in early spring. We have isolated a cDNA that encodes a phosphoenolpyruvate carboxylase, termed as SrPEPC from thermogenic florets of skunk cabbage. SrPEPC is a 110.5 kDa protein that contains conserved amino acid regions such as phosphorylation and catalytic domains. Expression of SrPEPC mRNA was highly abundant in the petal and pistil of thermogenic florets. Interestingly, the expression was very low in non-thermogenic tissues including spathe and leaf. Our data suggest that SrPEPC plays a role for tissue-specific heat production in the skunk cabbage.

Kyung Bae Pi has completed his MS from Kyung Hee University. He is a Senior Researcher and Project Leader of Incheon Business Information Technopark. He has published more than 13 papers in reputed journals and has been serving as an Editorial Board Member of repute.

In this study, the antimicrobial activity of recombinant mussel adhesive protein (fp-151) was evaluated against skin flora. The skin flora used for experiments were four Gram-positive bacteria such as Staphylococcus aureus (S. aureus), Streptococcus pyogenes (S. pyogenes), Staphylococcus epidermis (S. epidermis), Propionibacterium acnes (P. acnes) and one Gram-negative bacteria (E. coli). Pour plate assay was applied for determining the antimicrobial effects of recombinant MAP (fp-151). According to the result, recombinant MAP (fp-151) showed 90% of antimicrobial activity and was as good as or even better than penicillin for five skin flora. Also, we aimed to identify key proteomic changes in a HaCaT cell line grown in treated with recombinant MAP (fp-151) peptide, applying proteomic methods using nano-LC and a 4800 Plus MALDI TOF/TOF tandem mass spectrometry device. In a narrowed down and comparative data analysis of both non-treated and treated recombinant MAP (fp-151) peptide groups, differentially expressed proteins were identified as up or down-regulated. Bioinformatic analysis was used to reveal the biological functions and predict its possible mechanism. These results indicate that recombinant MAP (fp-151) has a high antibacterial effect and resistance against bacterial infection and cell damage which therefore, implies that recombinant MAP (fp-151) has its potential use in skin care products.

Geeta Deka joined the Department of Biological Sciences at the Indian Institute of Science as an Integrated PhD student in 2010 and earned her MS degree in 2012. Currently, she is pursuing her PhD under Prof. M.R.N. Murthy. She is attempting to understand the catalytic mechanism of a subset of PLP-dependent enzymes using mutagenesis, X- ray crystallography and enzyme kinetics studies. Apart from her PhD research work, she has gained experience in computational protein design and in the development of rapid diagnostic tools for early detection of malaria. Her curiosity to understand important biological problems motivate her to explore new areas in biology.

Salmonella typhimurium colonizes in the human gastro-intestinal tract due to its ability to withstand high acidic pH (pH<2.5). Its acid tolerance response (ATR) is due to lysine decarboxylase (LDC) and arginine decarboxylase (ADC) systems, which maintains the internal pH of the bacterium close to 4. ADC consumes one proton from the cytoplasm while decarboxylating an arginine to agmatine. The arginine-agmatine antiporter (AdiC) exchanges an internal agmatine with an external arginine. Thus, together, ADC and AdiC reduces the proton concentration within the cell. Here, we present the X-ray crystal structure of the inducible StADC (AdiA) at 3.1 Ã… resolutions. The crystal asymmetric unit contains a decamer (MW ~800 kDa) constitute of five homodimers related by a non-crystallographic five-fold axis of symmetry. The structure represents the apo-form of the enzyme while the earlier reported structure of the E. coli enzyme corresponds to the holo-form. Binding of PLP converts two disordered loops close to the active site into ordered confirmations. These conformational transitions may be important for substrate entry and product release. A large number of acidic residues are found on the surface of StADC. As proposed earlier, low pH may neutralize surface charges in homodimers that are catalytically inactive and promote the formation of functionally active decamers. Comparison of StADC with other members of group III decarboxylases shows that these enzymes are likely to follow similar catalytic mechanisms.

Subashini Mathivanan is a PhD candidate at the Indian Institute of Science, Bangalore, India. Her research expertise is on protein crystallography, emphasized on structural and functional characterization of Salmonella typhimurium propionate kinase and Photorhabdus luminescens oxalate decarboxylase.

Propionate kinase reversibly transfers phosphoryl group from propionyl phosphate to ADP in the final step of non-oxidative catabolism of L-threonine to propionate. There are contrasting views on the phosphoryl transfer mechanism of propionate kinase. Here we report X-ray crystal structures of propionate and nucleotide analog (AMPPNP) bound Salmonella typhimurium propionate kinase at 1.8-2.2 Å resolutions. Although the mode of the nucleotide binding is comparable to those of other members of ASKHA superfamily, propionate is bound at a distinct site, deeper in the hydrophobic pocket defining the active site. The role of Ala88, earlier proposed to be the residue determining substrate specificity, was examined by determining the crystal structures of propionate bound Ala88 mutants A88V and A88G. Kinetic analysis and structural data are consistent with a significant role of Ala88 in substrate specificity determination. In the structure of StTdcD A88V-AMPPNP-Propionate complex, AMPPNP was cleaved to AMP and PNP either due to an unreported catalytic activity of the enzyme or due to radiation damage. The released PNP probably reacted with propionate forming propionyl-pyrophosphate, supporting direct in-line transfer mechanism. Phosphoryl transfer reaction is likely to occur via an associative SN2-like transition state. The proximity of strictly conserved His175 and Arg236 to carboxyl of propionate and γ-phosphate of ATP suggests their involvement in catalysis. Moreover, ligand binding does not induce global domain movement as reported in some other members of ASKHA superfamily. However, the active site pocket defining residues Arg86, Asp143 and Pro116-Leu117-His118 segment are also likely to contribute to substrate specificity.

Turgut Ulutin has completed his PhD from Marmara University, Faculty of Medicine Department of Biochemistry and Post-doctoral studies from Istanbul University, Faculty of Medicine. He is the Head of Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University. He is also the Head of National Society of Medical Biology of Turkey. He has published more than 25 papers in reputed journals.

Whether or not glia derived neurotophic factor (GDNF) has a role in disease mechanism of bipolar disorders has been a matter of debate. Due to their role in regulation of synaptic plasticity in addition to survival and growth of neurons neurotophins are important targets. Recent studies have pointed out that vitamin D can exert protective effects on nervous system by modulating the synthesis of neurotrophins, calcium channels and calcium binding proteins. The expression of neurotrophic factors are regulated via vitamin D in several cell types. Our previous study has showed that vitamin D receptor silencing showed similar effects with beta amyloid treatment and up regulated L type voltage sensitive calcium channels alpha1 C (LVSCC A1C) and nerve growth factor (NGF). These results might indicate the potential role of vitamin D- VDR pathway in neurodegeneration. The aim of this study was to investigate the alterations in the level of GDNF release by 1,25-dihydroxyvitamin D3 treatment in primary cortical neurons. Cerebral cortex dissected from brains of Sprague Dawley rat embryos on the embryonic day 16 and cultured. GDNF levels released to the culture medium were determined by ELISA. Our results showed that vitamin D treatment induced GDNF release to the culture media. These results indicated that the GDNF expression might be regulated by vitamin D in cortical neurons and vitamin D supplementation might be used as a tool for regulating neurotrophic factors in neurodegenerative disorders.