6^th International Conference on Structural Biology August 22-23, 2016 New Orleans, Louisiana, USA

Ihosvany Camps holds a Bachelor degree in Physics from the Faculty of Physics, University of Havana (Cuba, 1995), Master degree in Physics from the Faculty of Physics, University of Havana (Cuba, 1996) and a PhD in Physics from the Institute of Physics, Federal Fluminense University (Brazil, 2001). Has experience in Condensed Matter Physics and Computational Modelling. Currently, has as main research lines the study of electronic properties of nanostructures and the molecular modelling of organic and inorganic systems including the modelling of drugs (rational drug design, fragment-based drug design, and de novo design), molecular docking, and studies on polymorphism of pharmaceutical solids.

In this work we made use of the fragment-based drug design (FBDD) and de novo design to obtain more powerful acetylcholinesterase (AChe) inhibitors. The acetylcholinesterase is associated to the Alzheimer’s Disease (AD). It was found that the cholinergic pathways in the cerebral cortex is compromised in AD and the accompanying cholinergic deficiency contributes to the cognitive deterioration of AD patients. In the FBDD approach, fragments are docked into the active site of the protein. As fragments are molecular groups with low number of atoms, it is possible to study they interaction with localized amino acids. Once the interactions are measured, the fragments are organized by affinity and then linked between them to form new molecules with high degree of interaction with the active site. In the other approach, we used the de novo design technique starting from reference drugs used in the AD treatment. These drugs were break into fragments (seeds). In the growing strategy, fragments were add to each seed growing new molecules. In the linking strategy, two or more separated seeds are linked with different fragments. Both strategies produced a library of more than 2M compounds. This library was filtered using ADME properties. The resulting library with around 6k compound was filtered again. In this case, structures with Tanimoto coefficient greater than 0.85 were discarded. The final library with 1.5k compounds was submitted to docking studies. As a result, 10 compounds with better interaction energy than the reference drugs were obtained. We acknowledge financial support of FAPEMIG.

Chan-Shing Lin has completed his PhD at University of California, Irvine, in 1992. He has published more than 65 papers in reputed journals and has been serving as an Editorial Board Member of Archive of Virology and Frontier journals. He has also consulted biotechnology companies in building the cGMP processes for manufacturing vaccines and bio-medicals.

The virus-like particle (VLP) assembled from capsid subunits of the dragon grouper nervous necrosis virus (DGNNV) is very similar to its native T=3 virion, in addition that the VLPs can enter fish cells with macropinocytosis way. Furthermore, the disulfide bounds are not essential for the VLP formation, whereas cations are involved in the VLP stability in vitro. At pH 8.0, the VLPs can be precipitated with EDTA at room temperature. In weak basic condition, cryoEM model of the capsid protein (52-213th amino acids) at 3.56 Ã… resolution reveals calcium-ion bridges and unique cation-Ï€ interactions. Submersion of VLP crystals in cations provide sharper diffraction intensity than control and enhanced the radiation damage. All together supports that cations stabilize the viral particle by holding three subunits in an asymmetric unit of trimer.

Takeshi Hasegawa is currently a graduate student of Ritsumeikan University at Department of Bioinformatics of College of Life Sciences.

To seek the drug candidate molecules, it is necessary to assess the binding affinity of a protein with its inhibitors. A large number of computational methods for estimation the binding free energy have been proposed. MD simulation is a powerful method for computationally estimating the physical quantity including the binding free energy. Although the estimation of the physical quantity of the system which has a huge amount of the degree of the freedom requires enormous computational cost, we sometimes cannot explore the enough structural space to evaluate an accurate value. On the other hand, 3D-RISM theory, a statistical theory for the molecular liquid, can estimate the solvation free energy in a reasonable computational cost by analytically calculating configuration integral of the solvent. In this regards, the combination of the 3D-RISM theory and MD simulation can escape the insufficient sampling. However, the quantitative capability of the MM/3D-RISM method has been ambiguous so far since this is a somehow novel method and has been applied to few systems. We apply this method to estimate binding free energy between Pim1 kinase and its inhibitors. Pim1 kinase is a famous target protein for treating hematopoietic malignancies, such as leukemia, lymphoma and prostate cancer. As a result, we get an approximately R=0.7 of the correlation coefficient between experimental and calculated values. Furthermore, we suggest a way of possible a lead optimization procedure by means of the 3D-RISM theory and MM/3D-RISM method.

Jessica Richard has completed her PhD in Biochemistry and Molecular Biology at Louisiana State University Health Sciences Center in New Orleans, LA in May 2016. She is currently a Post-doctoral fellow in the laboratory of Dr. Sunyoung Kim. She is investigating the evolution of sequence-structure-function relationships in kinesin motor proteins.

There is a growing appreciation for the importance of correlated motions within β-sheets of enzymatic proteins. Case in point, kinesin ATPases have α/β organization with a central β-sheet that physically separates the two ligand-binding sites: The active and microtubule (MT)-binding sites. Meta-analysis of existing kinesin X-ray structures revealed that a change in motor function is correlated with a change in β-sheet twist. We hypothesized that the change in twist was due to key sequence differences that occurred within the central β-sheet during the evolution of the kinesin nanomotor. We first identified three β-sheet motifs in which sequence changes correlate with different kinesin functional outputs. These motifs were structurally and functionally validated. X-ray structures of both β-sheet substitution and an active site surface loop substitution were generated. We show that single-site substitution of the central β-sheet results in loss of β-strand and changes in twist that are propagated across the β-sheet. Our functional assays provide evidence that these substitutions alter communication between the enzyme’s active and MT-binding sites. While correlated motions in β-sheets are predominately studied in terms of backbone interactions, we show that side chain identity contributes to these motions. We conclude that β-sheet sequence changes promote enzyme specialization and are likely a universal design principle in NTPases.

Mohammed A. Mansour has completed his PhD at the age of 28 years from Nagoya University graduate school of Medicine, Japan in the field of Biochemistry of cancer and cell signaling. He has been assigned the position of lecturer of Biochemistry and Cancer Biology in Tanta University faculty of Science, Egypt since October 2015. He has published up to 10 papers in highly reputed journals including oncotarget, FEBS J, Exp Cell Res and Tumor Biol. He is interested in understanding the molecular pathogenesis of human solid, hard -to-cure cancers. During his PhD project, he focused on the identification of alterations of tumor suppressor genes and oncogenes in colon cancer, followed by elucidation of their detailed biological and biochemical functions. This detailed work resulted in 3 first author publications, and two co-author papers from collaborative studies. His research thus focuses on taking clinically relevant targets, understanding their molecular function, and determining how to modulate them in the laboratory and in in vivo models.

Invadopodia are specialized actin-based microdomains of the plasma membrane that combine adhesive properties with matrix degrading activities. Proper functioning of the bone, immune, and vascular systems depend on these organelles, and their relevance in cancer cells is linked to tumor metastasis. The elucidation of the mechanisms driving invadopodia formation is a prerequisite to understanding their role and ultimately to controlling their functions. Special AT-rich sequence-binding protein 2 (SATB2) was reported to suppress tumor cell migration and metastasis. However, the mechanism of action of SATB2 is unknown. Here, we show that SATB2 inhibits invadopodia formation in HCT116 cells and that the molecular scaffold palladin is inhibited by exogenous expression of SATB2. To confirm this association, we elucidated the function of palladin in HCT116 using a knock down strategy. Palladin knock down reduced cell migration and invasion and inhibited invadopodia formation. This phenotype was confirmed by a rescue experiment. We then demonstrated that palladin expression in SATB2-expressing cells restored invasion and invadopodia formation. Our results showed that SATB2 action is mediated by palladin inhibition and the SATB2/palladin pathway is associated with invadopodia formation in colorectal cancer cells.

Rebecca S Buckley has completed her PhD in 2016 from Louisiana State University Medical School & Health Sciences Center. She is currently a Postdoctoral fellow in the lab of Sunyoung Kim where she is continuing her work on the functional characterization of a surface-exposed, drug-binding loop and its role in kinesin mechanochemistry and oligomerization.

In kinesins, loop-5 is implicated in mechanochemistry and widely noted for its allosteric druggability. Yet, its native role has been obscured by its sequence variability and irregular conformations: No signature sequence in function or ligand-binding has been defined. Here we hypothesize that the loop-5 protein backbone is shaped by small spatial motifs in a catalytically-dependent manner. Mining of small motifs, <5 residues in length and based on amide hydrogen-bonding and phi/psi angles showed that loop-5 of two different processive kinesin motor proteins have variable and conserved ordered structures that are not dependent on amino acid identity. Mutation of conserved, inter-linked loop-5 niches is shown to selectively deregulate mechanical output and catalysis of both motors. Analysis of 55 reported substitutions in 6 kinesins complemented our experiments; disruption of mechanochemical coupling is correlated with mutation in small motifs and not within classical secondary structures. Thus, loop-5 has a conserved function as a kinesin transducer but we redefine it as a series of variable and conserved 3D motif switches that can encode a spectrum of mechanocoupling strategies. Modular organization of a series of small spatial motifs is extendable to other loops in motor proteins specifically and NTPases more broadly.

Nakashima is a second year graduate student of Ritsumeikan University, Collage of life sciences, Department of Bioinformatics.

It is well known that the 3-D structure in lysozyme-like fold show wide variety but partially common topology. The aim of our research is to discuss whether common folding unit and common folding mechanism exist by analyzing c(chicken)-type lysozyme family which has folding mechanisms that have been investigated extensively, and its superfamily proteins i(invertabrate)-type, g(goose)-type, l(lambda-phage)-type lysozyme family. In order to achieve it, we mainly used Average Distance Map(ADM) analysis which predicts distribution of folding unit and F-value analysis which predicts the contact frequency of each residue. These methods are based on inter-residue average distance calculation with known 3-D structures. First we conducted BLAST search to get homologous proteins of each family. Then we got rid of the sequence of one of the pair which indicate more than 90% identity and sequence which causes large alignment gap on secondary structure. Finally we used 73 c-type, 52 i-type, 53 g-type and 100 l-type lysozyme proteins as objective proteins. Next we conducted the MAFFT alignment program and combined with our result of ADM analysis. As a result, we found that strongly conserved folding units exist in each family. Furthermore, we made use of combinatorial extension (CE) structural alignment program. As a result, the distribution of conserved units on 3-D structure within a family is partially conserved beyond family. These conserved regions included residues which indicate high contact frequency. That is, we can suggest the common folding mechanism among lysozyme superfamily.