TASK Quarterly   Scientific Bulletin of the Centre of Informatics - Tricity Academic Supercomputer & networK   ISSN 1428-6394

## Volume 18, Number 4, 2014 From Computational Biology to System Biology

### Contents:

• Joanna Makowska, Dorota Uber, Wioletta Żmudzińska and Lech Chmurzyński Conformational Analysis of Fragment of Human Pin1 WW Domain: Influence of Charged Amino-Acid Residues on β-hairpin Structure - abstract | full text | doi:10.17466/tq2014/18.4/e
• Mutharasu Gnanavel, Olli Yli-Harja and Meenakshisundaram Kandhavelu Protein-Protein Interaction and Coarse Grained Simulation Study of Glioblastoma Multiforme Reveals Novel Pathways of GPR17 - abstract | full text | doi:10.17466/tq2014/18.4/g
• Helen W. German, Manikanthan Bhavaraju, Sahin Uyaver and Ulrich H. E. Hansmann Computational Insights into the Self-Assembly of Phenylalanine-Based Molecules - abstract | full text | doi:10.17466/tq2014/18.4/k
• Paweł Krupa, Magdalena A. Mozolewska, Bakhtiyor Rasulev, Cezary Czaplewski and Jerzy Leszczynski Towards Mechanisms of Nanotoxicity – Interaction of Gold Nanoparticles with Proteins and DNA - abstract | full text | doi:10.17466/tq2014/18.4/l
• Magdalena A. Mozolewska, Paweł Krupa, Bakhtiyor Rasulev, Adam Liwo and Jerzy Leszczynski Preliminary Studies of Interaction between Nanotubes and Toll-Like Receptors - abstract | full text | doi:10.17466/tq2014/18.4/m
• Erik J. Alred, Emily G. Scheele, Workalemahu M. Berhanu and Ulrich H. E. Hansmann Comparative stability analysis of D23N mutated A$\beta$ - abstract | full text | doi:10.17466/tq2014/18.4/n
• Przemysław Jurczak and Martyna Maszota-Zieleniak NMR Studies of Human Cystatin C – Stable Isotope Labeling of Human Cystatin C - abstract | full text | doi:10.17466/tq2014/18.4/o
• Agnieszka Karczyńska, Bartłomiej Zaborowski and Magdalena /Slusarz Investigation of Interactions between Dermorphin Analogs and $\mu$-Opioid Receptor - abstract | full text | doi:10.17466/tq2014/18.4/p
• Maksim Kouza, Michal Jamroz, Dominik Gront, Sebastian Kmiecik and Andrzej Kolinski Mechanical Unfolding of DDFLN4 Studied by Coarse-Grained Knowledge-Based CABS Model - abstract | full text | doi:10.17466/tq2014/18.4/r
• M. Strumillo, A. E. Dawid, A. Szczasiuk and Dominik Gront Implementation and Evaluation of New Protocol for Comparative Modeling of Protein Structures - abstract | full text | doi:10.17466/tq2014/18.4/s
• Jacek Biesiada, Marc Sudman, Michael Wagner, Andrew Rupert, Jill Hollenbach, Johannes-Peter Haas, Jarek Meller and Susan D. Thompson Analysis of Susceptibility Loci for Juvenile Idiopathic Arthritis in the Extended MHC Region Using High Resolution SNP and HLA Allele Typing - abstract | full text | doi:10.17466/tq2014/18.4/a

### Abstracts:

• Joanna Makowska, Dorota Uber, Wioletta Żmudzińska and Lech Chmurzyński Conformational Analysis of Fragment of Human Pin1 WW Domain: Influence of Charged Amino-Acid Residues on β-hairpin Structure

We examined the effect of like-charged residues on the conformation of an original nine amino-acid-residue fragment of the human Pin1 WW domain (hPin1) with the following sequence: Ac-Arg-Met-Ser-Arg-Ser-Ser-Gly-Arg-Val-NH2 (U9). This was facilitated by CD and NMR spectroscopic measurements, and molecular dynamics calculations. Our earlier studies suggested that the presence of like-charged residues at the end of a short polypeptide chain composed of nonpolar residues could induce a chain reversal. For the U9 peptide, canonical MD simulations with NMR-derived restraints demonstrated the presence of ensembles of structures with a tendency to form a β-chain reversal. Additionally, thermal stabilities of the peptide under study were measured using differential scanning calorimetry (DSC). The estimated well defined phase transition point showed that conformational equilibria in the U9 peptide were strongly dependent on temperature.

• Mutharasu Gnanavel, Olli Yli-Harja and Meenakshisundaram Kandhavelu Protein-Protein Interaction and Coarse Grained Simulation Study of Glioblastoma Multiforme Reveals Novel Pathways of GPR17

Studies of receptor mediated signaling networks in neuronal cells provide a unique opportunity to uncover the basis of many diseases. Receptor signaling cascades proceed from the cell surface, where extra cellular factors interact with their specific receptors e.g. G-Protein Coupled Receptors (GPR). Recent studies have shown that the activation or suppression of GPR17 in diseased neuronal cells has potential impact in altering the tumor conditions. We identified many hundred times expressions of GPR17 in Glioblastoma Multiforme (GBM) from the RNA-Seq data. We also observed many other genes having similar expression patterns with GPR17, indicating possible connections of this receptor with diverse gene products. We performed a coarse-grained simulation of ~ 500 proteins inside a cytoplasm like a box with solvent water molecules. The summarized protein interaction networks resulted from a coarsegrained simulation and large scale protein-protein docking reveals novel molecular connections and pathways.

• Helen W. German, Manikanthan Bhavaraju, Sahin Uyaver and Ulrich H. E. Hansmann Computational Insights into the Self-Assembly of Phenylalanine-Based Molecules

In a recent paper “Self-Assembly of Phenylalanine-Based Molecules”, we have studied the formation and stability of phenylalanine and diphenylalanine constructs. In the case of diphenylalanine we observe nanotubes, however, phenylalanine molecules aggregate in layers of four, not six, molecules. In the preset paper, we extend this previous work and compare the energetics of all experimentally observed structures, simulated structures, and designed structures, by way of single point Density Functional Theory (DFT) calculations. We take a detailed look at water content, pore size and dipole moments inside our phenylalaninecontaining tubes and analyze stabilizing factors in the nanostructures.

• Paweł Krupa, Magdalena A. Mozolewska, Bakhtiyor Rasulev, Cezary Czaplewski and Jerzy Leszczynski Towards Mechanisms of Nanotoxicity – Interaction of Gold Nanoparticles with Proteins and DNA

Even though most of the existing studies of gold nanoparticles indicate that they are safe to use, some researchers show that specific forms of nanoparticles (e.g. nanorods) are able to destroy the cell membrane and very small nanoparticles (below 37 nm in diameter) in high concentration have been deadly for mice. We used the Amber12 package to perform a series of molecular dynamics (MD) simulations of gold nanoparticles with various small proteins important for the human body and a DNA molecule to determine the interactions and consequently the possible toxicity of gold clusters. Lennard-Jones interactions were used to simulate the behavior of gold nanoparticles with biomacromolecules in water with an optimal set of parameters (selected based on a comparison of MD structures and structures computed by DFT). Gold nanoparticle structures were obtained as a result of MD simulations from an initial structure, where gold atoms were at a distance of 10 ˚ from one another. A predicted BDNA structure of a palindromic sequence A 'CGCATGAGTACGC' and a 2JYK molecule were used as representatives of the DNA molecule. The preliminary results show that, in particular small gold nanoparticles, interact strongly with proteins and DNA by creating stable complexes, which can then cause harmful reactions to the human body when present in high concentration.

• Magdalena A. Mozolewska, Paweł Krupa, Bakhtiyor Rasulev, Adam Liwo and Jerzy Leszczynski Preliminary Studies of Interaction between Nanotubes and Toll-Like Receptors

Toll-like receptors (TLRs) are a group of proteins which play a crucial role in the innate immune system. The main function of TLRs is to recognize structurally conserved molecules, which are inserted to the organism of the host by microbes, and then to activate the immune response. Current development of drugs is often connected not only with the drug itself, but also with the way it is delivered into the human body to interact directly with the source of the problem. Carbon nanostructures, particularly nanotubes, are one of the carrier molecules of the future. However, there is still no knowledge about the exact mechanisms of toxicity and possible interactions with macromolecules, such as proteins. In our study we tried to determine, if the nanotubes could interfere with the innate immune system by interacting with TLRs. For this purpose, we used the following TLR structures downloaded from the RCSB Protein Data Bank: TLR2 (3A7C), TLR4/MD (3FXI), TLR5 (3V47), TLR3 (2A0Z), and the complexes of TLR1/TLR2 (2Z7X) and TLR2/TLR6 (3A79). The preliminary results of our Steered Molecular Dynamics (SMD) simulations have shown that nanotubes interact very strongly with the binding pockets of some receptors (e.g. TLR2), which results in their binding to these sites without substantial use of the external force.

• Erik J. Alred, Emily G. Scheele, Workalemahu M. Berhanu and Ulrich H. E. Hansmann Comparative stability analysis of D23N mutated A$\beta$

Amyloid β (Aβ) is the subject of numerous studies due to its link to the devastating Alzheimer's disease and it exists in a parallel structure in fibril aggregate. The Iowa mutant (D23 N) Aβ posses a unique antiparallel fibril aggregate structure and can also form parallel structure. This structural difference, coupled with the fact that occurrence of the Iowa mutant is correlated with early onset Alzheimer's, suggests to use these peptides as candidates for computational studies of the structural determinants of the toxicity of Alzheimer's disease. In order to compare the two observed Aβ structural motifs, we designed a computational study to probe the factors that affect the stability of parallel and antiparallel aggregates. Since the structural changes may occur on a timescale beyond that sampled in traditional molecular dynamics (MD), we employed a techniques of scaling the mass to reduce the solution's viscosity and compared the results to regular molecular dynamics. The knowledge gained from this study could provide insight into the mechanism of selection for antiparallel and parallel two fold structures.

• Przemysław Jurczak and Martyna Maszota-Zieleniak NMR Studies of Human Cystatin C – Stable Isotope Labeling of Human Cystatin C

The objective of this study was to obtain a double and triple labeled human cystatin C (hCC). Another objective was to record sets of 2D and 3D NMR spectra of the hCC dimer (in a solution) using a 700 MHz spectrometer. The data obtained during attempts to determine the NMR structure should provide useful information about chemical shifts of amino acid residues. They will certainly accelerate solving the human cystatin C NMR structure. In this paper the main focus is put on triple isotopic labeling, protein overproduction and NMR analysis of hCC. The first two processes lead to obtaining hCC labeled with stable isotopes of carbon (13 C), nitrogen (15 N) and hydrogen (2 H) (double labeled hCC was obtained with a similar method). The obtained protein was later used for the purpose of NMR spectra.

• Agnieszka Karczyńska, Bartłomiej Zaborowski and Magdalena /Slusarz Investigation of Interactions between Dermorphin Analogs and $\mu$-Opioid Receptor

Opioid receptors play the pain control function in the body. Most of the research is carried out to find the most effective analgesic. The earliest analgesic is morphine, however, unfortunately it has many side effects [Mizoguchi H et al. 2003 J. Pharmacol Sci. 93 423]. At a later time dermorphin was discovered as another potent analgesic [Montecucchi P C et al. 1981 Int. J. Pept. Protein Res. 17 275]. Unfortunately, this peptide is not resistant to enzymatic metabolism [Kisara K et al. 1986 Br. J. Pharmacol. 87 183; Sasaki Y et al. 1985 Neuropeptides 5 391]. The objective of this study is to search for new opioid analgesics by investigation of interactions between dermorphin analogs and the µ-opioid receptor using molecular modeling methods. MOPR (µ-Opioid Peptide Receptor) complexes with several ligands (with known biological activity) were modeled to explain how the structure of the complex was related to the biological activity. The investigated dermorphin analogs containing [DMT1 , D-Arg2 ] (especially tetrapeptides) may become a good alternative for the currently used analgesics.

• Maksim Kouza, Michal Jamroz, Dominik Gront, Sebastian Kmiecik and Andrzej Kolinski Mechanical Unfolding of DDFLN4 Studied by Coarse-Grained Knowledge-Based CABS Model

Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied using a CABS – coarse-grained knowledge-based protein model. Our study demonstrates that CABS is capable of reproducing the unfolding free energy landscape of protein unfolding and highlights an important role of non-native interactions in the protein unfolding process. The obtained three peaks in the force-extension profile suggest a four-state picture of DDFLN4 protein unfolding and correspond reasonably to the results of the all-atom simulation in explicit solvent.

• M. Strumillo, A. E. Dawid, A. Szczasiuk and Dominik Gront Implementation and Evaluation of New Protocol for Comparative Modeling of Protein Structures

Template-based modeling (termed also Comparative or Homology Modeling) of a protein structure is one of ubiquitous tasks of structural bioinformatics. The method can deliver model structures important for testing biological hypotheses, virtual docking and drug design. The performance of these methods is evaluated every two years during a Critical Assessment of Protein Structure Prediction (CASP) experiment. In this contribution we present a new automated protocol for template-based modeling, which combines computational tools recently developed in our laboratory: the database of protein domain structures (BDDB) with one dimensional and three dimensional threading applications. The protocol was tested during a CASP11 experiment.

• Jacek Biesiada, Marc Sudman, Michael Wagner, Andrew Rupert, Jill Hollenbach, Johannes-Peter Haas, Jarek Meller and Susan D. Thompson Analysis of Susceptibility Loci for Juvenile Idiopathic Arthritis in the Extended MHC Region Using High Resolution SNP and HLA Allele Typing

Juvenile idiopathic arthritis (JIA) spans several pediatric arthropathies that involve autoimmune responses. Primary genetic risk factors for JIA have been mapped to Major Histocompatibility Complex (MHC) class I and class II genes. Recent genome-wide association studies using SNP arrays have shown that the non-HLA genetic component of JIA involves multiple low-risk loci, reinforcing the notion that JIA is a complex genetic trait with a strong HLA component. In this work, with the goal of detailed mapping and analysis of linkage disequilibrium (LD) patterns and associations with JIA in the extended MHC (xMHC) region, we combined SNP data from Aﬀymetrix SNP Array 6.0 and Immunochip (IC) platforms with high resolution typing of 8 classical HLA genes. A cohort of about 800 affected individuals and about 500 ethnically matched controls from the Cincinnati region, as well as secondary validation cohorts of affected individuals and matched controls from Germany were used to perform the analysis, and to assess reproducibility of the results across different platforms and populations. Accurate high resolution maps of linkage with classical HLA genes and association with individual HLA alleles were generated. High concordance of results obtained using Aﬀymetrix SNP Array 6.0 and IC was observed, with an additional resolution and improved mapping of associations provided by the latter in some regions. Several new peaks of statistically significant and reproducible association with JIA outside the regions of strong LD with classical HLA genes were observed, including one peak in the class III region, and one in the telomeric end of xMHC. Conditional analysis provided further evidence that these associations appear to be independent of classical HLA genes studied here. The results and observed association patterns are further discussed in the context of other recent studies on autoimmune diseases, including the role of HLA-DRB1 in adult Rheumatoid Arthritis.