Wyniki wyszukiwania - BazTech

1

New UNRES force field package with Fortan 90

Lubecka E. A., Liwo A.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

|

2016

|

Vol. 20, No 4

399--408

EN

UNRES is a coarse-grained model of polypeptide chains. Until now, each version of UNRES (UNRESPACK v.3.2 and earlier ones) has been written in Fortran 77. Due to the fact that Fortran 77 enables us to use only static arrays, the Fortran 77 version has significant memory problems, and consequently, UNRESPACK has had to be split into many programs. Our recent work was focused on creating a new UNRES package with Fortran 90 (UNRESPACK v.4.0), based on the previous Fortran 77 versions. Fortran 90 provides dynamic memory allocation, user defined data types, and structuring the code into modules which encompass subroutines, functions, and variables. Moreover, Fortran 90 adds internal functions and subroutines, providing greater flexibility. The whole code of UNRES with Fortran 90 has been restructured, so that it now consists of modules that can be assembled to create the main simulation program and companion programs. This approach enabled us to eliminate the redundancy of the code, while keeping all functions of the package.

2

Preliminary studies of interaction between nanotubes and toll-like receptors

Mozolewska M. A., Krupa P., Rasulev B., Liwo A., Leszczyński J.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

|

2014

|

Vol. 18, No 4

351--355

EN

Toll-like receptors ( TLR s) are a group of proteins which play a crucial role in the innate immune system. The main function of TLR s 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 direc tly with the source of the problem. Carbon nanostructures, particularly nanotubes, are one of the car rier molecules of the future. However, there is still no knowledge about the exact mechani sms of toxicity and possible interactions with macromolecules, such as proteins. In our study we tr ied to determine, if the nanotubes could interfere with the innate immune system by interac ting with TLR s. For this purpose, we used the following TLR structures downloaded from the RCSB Protein Data Bank: TLR 2 (3 A 7 C ), TLR 4/ MD (3 FXI ), TLR 5 (3 V 47), TLR 3 (2 A 0 Z ), and the complexes of TLR 1/ TLR 2 (2 Z 7 X ) and TLR 2/ TLR 6 (3 A 79). 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. TLR 2), which results in their binding to these sites without subst antial use of the external force.

3

The Study of Conformational Equilibrium of c[Gln-Trp-Phe-Gly-Leu-Met], a NK-2 Tachykinin Antagonist

Brzozowski K., Łęgowska A., Rodziewicz-Motowidło S., Liwo A., Rolka K.

Polish Journal of Chemistry

|

2002

|

Vol. 76 / nr 6

807-814

EN

Conformational studies of NK-2 tachykinin antagonist c[Gln-Trp-Phe-Gly-Leu-Met] were performed using a combination of two-dimensional NMR spectroscopy and theoretical methods. The three dimensional structure of the peptide studied was determined by global conformational search, using the EDMC method with the ECEPP/3 force field and subsequent calculation of statistical weights of the obtained conformations by fitting the theoretical NOESY spectra and vicinal coupling constants 3JNHH_ to the experimental ones. Using this approach, a set of six conformations with statistical weights higher than 3% was obtained. The first two ones with the values of statistical weights over 30% can be considered as dominant ones. The structure of the most populated conformation is stabilized by type IV _-turn around Trp7-Phe8 and a _-turn centered at Trp7. In the second one, two _ turns were found: II and III_ around Met11-Gln6 and Gln6-Trp7, respectively. In both conformations, the aromatic groups of Trp7 and Phe8 are almost perpendicularly oriented to the peptide backbone. The results obtained correlate well with those published for the peptide studied by three other groups. In contrast to the results obtained by other groups, which used interproton distances as constrains, the approach described here enables to determine the conformational equilibrium of the peptide studied.

4

A Fluorescence, 1H NMR spectroscopy and molecular dynamics study of the influence of rotamer population on fluorescence decay of tyrosine, phenylalanine and their derivatives

Ganzynkowicz R., Liwo A., Wiczk W.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

|

2001

|

Vol. 5, No 3

311-316

EN

Molecular dynamics simulations were carried out on tyrosine and phenylalanine and their derivatives with various terminal groups to determine the populations of side-chain rotamers. The obtained populations were compared with those calculated from fluorescence-decay lifetime distributions and NMR studies. It was found that theoretically calculated populations do not match the experimental ones, which suggests that the static rotamer model is inadequate to explain the dynamics of tyrosine and phenylalanine side chain in fluorescence and NMR experiments.

5

A Comparison of Solution Conformations of Scyliorhinin I and Its Analogue with N-Methyl-L-phenylalanine in Position 7

Klaudel L., Rodziewicz-Motowidło S., Liwo A., Rolka K.

Polish Journal of Chemistry

|

2000

|

Vol. 74, nr 8

1091-1099

EN

Their solution structures are characterized by families consisting of 7 and 8 conformers, respectively, with statistical weights higher than 2%. The 3D structure of Scyl is rather flexible, whereas the presence of a local constrait in position 7 significantly rigidifies the whole molecule.

6

The ECEPP package for conformational analysis of polypeptides

Ripoll D. R., Liwo A., Czaplewski C.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

|

1999

|

Vol. 3, No 3

313-331

EN

We present here the ECEPPAK (developed in the laboratory of prof. H.A. Scheraga, Cornell University) and ANALYZE packages for the conformational search of polypeptides that is based on the ECEPP/3 force field. The functions of the program include energy calculation and minimization and global conformational search using the Electrostatically Driven Monte Carlo (EDMC) method. The search can be constrained using experimental information e.g., the distance constraints from NMR measurements. The sister program, ANALYZE, allows the user to classify the conformations by means of cluster analysis and fit the statistical weights of the conformations to best fit the experimental observables. The package is extensively parallelized, which allows the user to carry out the conformational search even of comparatively large polypeptides in real time.

7

Cyclic Analogues of Proline-Rich Protein Fragments : Part II : Conformational Studies Using NMR Spectroscopy and Theoretical Conformational Analysis

Rodziewicz S., Wirkus-Romanowska I., Ciurak M., Miecznikowska H., Kupryszewski G., Czaplewski C., Liwo A., Rolka K.

Polish Journal of Chemistry

|

1999

|

Vol. 73, nr 10

1697-1710

EN

These peptides were designed based on the immunoregulatory activity of linear peptides obtained after chymotrypsin digestion of PRP. Despite the fact that the structures of both analogues cannot be interpreted in terms of a single conformation, the superposition of the most populated conformations of the cyclic peptides studied revealed a similar geometry for the Tyr-Val-pro-Leu-Phe-Pro fragment (RMSD=1.6 A) in both peptides and therefore might be considered to be responsible for the biological activity.

8

A user-friendly interface to computer programs for the determination of the characteristics of equilibrium systems from physicochemical data

Arłukowicz P., Arłukowicz E., Kira J., Liwo A.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

|

1998

|

Vol. 2, No 1

55-72

EN

A graphical user interface to programs for the determination of equilibrium parameters from physicochemical data (GOLEM) has been developed. The program converts input data written in a common chemical language into the algebraic form required by the programs that do actual computations. This includes translation of chemical equations into algebraic form and building up the history of the preparation of solutions. The program works on PC/DOS platforms and in the current version prepares the data for the program STOICHIO (J. Kostrowicki, A. Liwo, see Comput. Chem., vol.11, no.3, p.195, 1987) which determines the stoichiometry and equilibrium constants from physicochemical measurements.