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Tytuł:
Preferential solvation of amides by methanol - a comparison of molecular dynamics calculations with the experimental data
Autorzy:
Zielkiewicz, J.
Powiązania:
https://bibliotekanauki.pl/articles/1965827.pdf
Data publikacji:
2001
Wydawca:
Politechnika Gdańska
Tematy:
amides
alcohols
preferential solvation
Kirkwood-Buff integrals
molecular dynamics simulations
Opis:
Using the Kirkwood-Buff theory of solutions, the preferential solvation of the N-methylacet-amide (NMA), N-methylformamide, (NMF), and N,N-dimethylformamide, (DMF), molecule has been investigated in the binary {amide+methanol} mixtures at 313.15 K. Moreover, for the {amide+methanol} mixtures, where amide = NMF, DMF, and NMA, the molecular dynamics calculations at xamide=0.518 were performed. From the obtained molecule-molecule radial distribution functions, (rdf), and atom-atom rdf, it was possible to estimate the local mole fractions around the amide molecule, the orientation effects of molecules within the solvation shell, and a possibility of the formation of complexes. The general picture obtained from analysis of the molecular dynamics results is consistent with the deductions derived from thermodynamic data.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2001, 5, 3; 317-329
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
15N magnetic relaxation study of backbone dynamics of the ribosome-associated cold shock response protein Yfia of Escherichia coli
Autorzy:
Zhukov, Igor
Bayer, Peter
Schölermann, Beate
Ejchart, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1040866.pdf
Data publikacji:
2007
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
anisotropic overall molecular diffusion
model-free approach
15N NMR spectroscopy
stress adaptation
disordered polypetide chain motion
protein Y
Opis:
In the solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli in the free state two structural segments can be distinguished: a well structured, rigid N-terminal part displaying a βαβββα topology and a flexible C-terminal tail comprising last 20 amino-acid residues. The backbone dynamics of Yfia protein was studied by 15N nuclear magnetic relaxation at three magnetic fields and analyzed using model-free approach. The overall diffusional tumbling of the N-terminal part is strongly anisotropic with a number of short stretches showing increased mobility either on a subnanosecond time scale, or a micro- to millisecond time scale, or both. In contrast, the unstructured polypeptide chain of the C-terminal part, which cannot be regarded as a rigid structure, shows the predominance of fast local motions over slower ones, both becoming faster closer to the C-terminus.
Źródło:
Acta Biochimica Polonica; 2007, 54, 4; 769-775
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular dynamics simulation of histone H3 and H4 N-terminal tail conformation in the presence and absence of nucleosome core
Autorzy:
Zhang, R.
Erler, J.
Langowski, J.
Powiązania:
https://bibliotekanauki.pl/articles/1954427.pdf
Data publikacji:
2014
Wydawca:
Politechnika Gdańska
Tematy:
histone tail
REMD
H4K 16 acetylation
nucleosome
Opis:
Histone N (C)-terminal tails play an important role in chromatin remodeling and gene regulation. Posttranslational modifications (PTMs) of histone tails are known to be correlated to distinct states of gene activity, but the molecular mechanism of these processes is largely unknown. PTMs alter the electrostatic environment and conformation of histone tails, as w ell as their interaction with other components. Here we performed extensive Replica Exchange Molecular Dynamics (REMD) simulations for the H4 and H3 tails, isolated and with inclusion of a nucleosome. Our results agree with the predictions of previous the teoretical studies for the secondary structure of isolated tails, but show strong dependence on the force field used. In the presence of the nucleosome, the secondary structure of histone tails is destabilized. Furthermore, H4K16 is found to insert into the DNA minor groove, whereas the acetylated H4K16 stays on the surface of DNA .
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2014, 18, 3; 281--288
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Nitrosubstituted analogs of isoxazolines and isoxazolidines: a surprising estimation of their biological activity via molecular docking
Autorzy:
Zawadzińska, Karolina
Gostyński, Bartłomiej
Powiązania:
https://bibliotekanauki.pl/articles/35126576.pdf
Data publikacji:
2023
Wydawca:
Radomskie Towarzystwo Naukowe
Tematy:
isoxazolines
isoxazolidines
molecular docking
molecular dynamics
biological activity
izoksazoliny
izoksazolidyny
dokowanie molekularne
dynamika molekularna
aktywność biologiczna
Opis:
The biological activities in the field of antimicrobial application of trihalomethylated isoxazolines and isoxazolidines were investigated by means of molecular docking. In our work, we compared these two groups of heterocyclic compounds due to their strength of non-covalent binding affinity with several exemplary proteins that are known to partake in various biological processes. The obtained results show that the investigated compounds possess higher binding affinities to selected proteins than many hitherto known and applied compounds.
Źródło:
Scientiae Radices; 2023, 2, 1; 25-46
2956-4808
Pojawia się w:
Scientiae Radices
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Protein-protein docking refinement using restraint molecular dynamics simulations
Autorzy:
Zacharias, M.
Powiązania:
https://bibliotekanauki.pl/articles/1938618.pdf
Data publikacji:
2016
Wydawca:
Politechnika Gdańska
Tematy:
protein-protein complex
docking prediction
force field modeling
implicit solvent modeling
Opis:
A realistic prediction of the structure of protein-protein complexes is of major importance to obtain three-dimensional models for the interaction of proteins to form complexes and assemblies. In addition to the systematic search for putative binding sites on the surface of two binding partners, the second step of a docking effort, the refinement of docked complexes, is a major bottleneck to obtain realistic interaction geometries. Typically, the first initial systematic search employs rigid partner structures or few flexible degrees of freedom, whereas the refinement step involves fully flexible partner structures. The possibility to refine docked complexes using restraint MD simulations combined with an implicit solvent (Generalized Born) mode l was explored on three example test complexes starting from unbound partner structures. Significant improvement, both in scoring and agreement with the native complex structure after refinement was observed for two test cases. No improvement was found for a test case of a complex with lower binding affinity. The method can be easily applied to any docked protein-protein complex, however, more general applicability requires further improvements in the scoring function.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2016, 20, 4; 353-360
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Structure and dynamics of water adsorbed on the lignite surface: Molecular dynamics simulation
Autorzy:
You, Xiaofang
He, Meng
Cao, Xiaoqiang
Lyu, Xianjun
Li, Lin
Powiązania:
https://bibliotekanauki.pl/articles/109688.pdf
Data publikacji:
2019
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
low rank coal
water molecule
oxygen-containing functional groups
molecular dynamics
Opis:
The effects of oxygen-containing functional groups on the structure and dynamic properties of water molecules near a lignite surface were investigated through molecular dynamics (MD) simulations. Because of its complex composition and structure, a graphite surface containing hydroxyl, carboxyl, and carbonyl groups was used to represent the lignite surface model. According to X-ray photoelectron spectroscopic (XPS) results, the composing proportion of hydroxyl, carbonyl and carboxyl is 21:13:6. The density profiles of oxygen and hydrogen atoms indicate that the brown coal surface characteristics influence the structural and dynamic properties of water molecules. The interfacial water is much more ordered than bulk water. The results of the radial distribution functions, mean square displacements, and local self-diffusion coefficients for the water molecules in the vicinity of three oxygen-containing functional groups confirmed that carboxyl groups are the preferential adsorption sites.
Źródło:
Physicochemical Problems of Mineral Processing; 2019, 55, 1; 10-20
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers.
Autorzy:
Woźniak-Celmer, Edyta
Ołdziej, Stanisław
Ciarkowski, Jerzy
Powiązania:
https://bibliotekanauki.pl/articles/1044161.pdf
Data publikacji:
2001
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
protein phosphatase inhibitors
constrained simulated annealing
protein phosphatase 1A and 2B
molecular dynamics
homology modeling
Opis:
The oligomeric metalloenzymes protein phosphatases dephosphorylate OH groups of Ser/Thr or Tyr residues of proteins whose actions depend on the phosphorus signal. The catalytic units of Ser/Thr protein phosphatases 1, 2A and 2B (PP1c, PP2Ac and PP2Bc, respectively), which exhibit about 45% sequence similarity, have their active centers practically identical. This feature strongly suggests that the unknown structure of PP2Ac could be successfully homology-modeled from the known structures of PP1c and/or PP2Bc. Initially, a theoretical model of PP1c was built, including a phosphate and a metal dication in its catalytic site. The latter was modeled, together with a structural hydroxyl anion, as a triangular pseudo-molecule (Zno or Mno), composed of two metal cations (double Zn2+ or Mn2+, respectively) and the OH- group. To the free PP1c two inhibitor sequences R29RRRPpTPAMLFR40 of DARPP-32 and R30RRRPpTPATLVLT42 of Inhibitor-1, and two putative substrate sequences LRRApSVA and QRRQRKpRRTI were subsequently docked. In the next step, a free PP2Ac model was built via homology re-modeling of the PP1c template and the same four sequences were docked to it. Thus, together, 20 starting model complexes were built, allowing for combination of the Zno and Mno pseudo-molecules, free enzymes and the peptide ligands docked in the catalytic sites of PP1c and PP2Ac. All models were subsequently subjected to 250-300 ps molecular dynamics using the AMBER 5.0 program. The equilibrated trajectories of the final 50 ps were taken for further analyses. The theoretical models of PP1c complexes, irrespective of the dication type, exhibited increased mobilities in the following residue ranges: 195-200, 273-278, 287-209 for the inhibitor sequences and 21-25, 194-200, 222-227, 261, 299-302 for the substrate sequences. Paradoxically, the analogous PP2Ac models appeared much more stable in similar simulations, since only their "prosegment" residues 6-10 and 14-18 exhibited an increased mobility in the inhibitor complexes while no areas of increased mobility were found in the substrate complexes. Another general observation was that the complexes with Mn dications were more stable than those with Zn dications for both PP1c and PP2Ac units.
Źródło:
Acta Biochimica Polonica; 2001, 48, 1; 35-52
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Dyskretne metody symulacji zjawisk przepływowych w gazach i cieczach
Discrete Methods of Simulation of Flow Phenomena in Gases and Liquids
Autorzy:
Wolszakiewicz, T.
Walenta, Z. A.
Powiązania:
https://bibliotekanauki.pl/articles/403663.pdf
Data publikacji:
2013
Wydawca:
Wojskowa Akademia Techniczna im. Jarosława Dąbrowskiego
Tematy:
metody numeryczne
Bezpośrednia Symulacja Monte Carlo
dynamika molekularna
simulation methods
direct simulation Monte Carlo
molecular dynamics
Opis:
W pracy rozpatrzone zostały dwie metody numerycznej symulacji zjawisk przepływowych w ośrodkach gazowych i ciekłych, oparte na molekularnym opisie ośrodka: metoda Bezpośredniej Symulacji Monte Carlo oraz metoda Dynamiki Molekularnej. Metody te pozwalają na modelowanie w sposób bezpośredni przebiegu reakcji chemicznych, oddziaływania ośrodka ze ściankami ich zaletą jest także względna łatwość dostosowania się do skomplikowanej geometrii. Wadą są długie czasy obliczeń, co jednak może być przezwyciężone przez wykorzystanie coraz powszechniej dostępnych komputerów o dużej szybkości obliczeń.
The paper presents two methods of simulation of flow phenomena in gases and liquids based on molecular description of the medium: the Direct Simulation Monte Carlo method and the Molecular Dynamics method. These methods offer the possibility of direct modelling of chemical reactions and interactions of the medium with solid walls. Apart from that they have the advantage of relatively easy adaptation to complex geometries. Their main disadvantage is the long computing time, which, however, may be overcome with the use of the modern, fast computers presently available.
Źródło:
Problemy Mechatroniki : uzbrojenie, lotnictwo, inżynieria bezpieczeństwa; 2013, 4, 4 (14); 67-76
2081-5891
Pojawia się w:
Problemy Mechatroniki : uzbrojenie, lotnictwo, inżynieria bezpieczeństwa
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Application of the Lennard-Jones potential in modelling robot motion
Zastosowanie potencjału Lennard-Jonesa do modelowania ruchu robotów
Autorzy:
Wójcicki, Piotr
Zientarski, Tomasz
Powiązania:
https://bibliotekanauki.pl/articles/408380.pdf
Data publikacji:
2019
Wydawca:
Politechnika Lubelska. Wydawnictwo Politechniki Lubelskiej
Tematy:
swarm
Lennard-Jones potential
molecular dynamics simulation
rój
potencjał Lennard-Jones
symulacja metodą dynamiki molekularnej
Opis:
The article proposes a method of controlling the movement of a group of robots with a model used to describe the interatomic interactions. Molecular dynamics simulations were carried out in a system consisting of a moving groups of robots and fixed obstacles. Both the obstacles and the group of robots consisted of uniform spherical objects. Interactions between the objects are described using the Lennard-Jones potential. During the simulation, an ordered group of robots was released at a constant initial velocity towards the obstacles. The objects’ mutual behaviour was modelled only by changing the value of the interaction strength of the potential. The computer simulations showed that it is possible to find the optimal value of the potential impact parameters that enable the implementation of the assumed robotic behaviour scenarios. Three possible variants of behaviour were obtained: stopping, dispersing and avoiding an obstacle by a group of robots.
W artykule zaproponowano metodę kontrolowania ruchu grupy robotów za pomocą modelu stosowanego do opisu oddziaływań międzyatomowych. Przeprowadzono symulacje metodą dynamiki molekularnej w układzie składającym się z ruchomych grup robotów oraz nieruchomych przeszkód. Zarówno przeszkody, jak i roboty składały się z jednolitych sferycznych obiektów. Oddziaływania między obiektami opisano za pomocą potencjału Lennard-Jonesa. Podczas symulacji, początkowo uporządkowana grupa robotów poruszała się ze stałą prędkością w kierunku przeszkód. Wzajemne zachowanie obiektów modelowano tylko poprzez zmianę wartości parametrów potencjału oddziaływań. Symulacje komputerowe wykazały, że możliwe jest znalezienie optymalnych wartości parametrów oddziaływania, które umożliwiają uzyskanie pożądanego zachowania robotów. W trakcie symulacji uzyskano trzy możliwe warianty zachowania: zatrzymywanie, rozpraszanie i omijanie przeszkód przez grupę robotów.
Źródło:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska; 2019, 9, 4; 14-17
2083-0157
2391-6761
Pojawia się w:
Informatyka, Automatyka, Pomiary w Gospodarce i Ochronie Środowiska
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A molecular dynamics study of the influence of chemical reduction on the structure of amorphous Germania
Autorzy:
Witkowska, A.
Murawski, L.
Bergmański, G.
Powiązania:
https://bibliotekanauki.pl/articles/1963001.pdf
Data publikacji:
2002
Wydawca:
Politechnika Gdańska
Tematy:
oxide glasses
hydrogen reduction
molecular dynamics
structural modelling
Opis:
The contribution is dedicated to the molecular dynamics (MD) study of the structure of reduced germania glass of composition 1Ge 1GeO2. The work is inspired by a recent report on the formation of Ge clusters in hydrogen reduced germanate glasses containing oxides of heavy metals. The MD simulations have been performed in the microcanonical (NVE) ensemble, using a simple two-body Born-Mayer-Huggins interaction potential. A tendency of germanium atoms to agglomeration into clusters, observed in the present calculations, is compared with an analogous tendency of Bi and Pb atoms, observed previously in the xBi (1-x)GeO2 and xPb (1-x)GeO2 systems. The differences in the short and medium-range order in GeO2 system between the 1Ge 1GeO2 and GeO2 glasses are discussed.
Źródło:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk; 2002, 6, 2; 273-281
1428-6394
Pojawia się w:
TASK Quarterly. Scientific Bulletin of Academic Computer Centre in Gdansk
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular Dynamics in Biological Systems Observed by NMR Relaxation in a Rotating Frame
Autorzy:
Wierzuchowska, D.
Skórski, L.
Blicharska, B.
Powiązania:
https://bibliotekanauki.pl/articles/1490095.pdf
Data publikacji:
2012-02
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
76.60.-k
76.90.+d
Opis:
NMR relaxation provides powerful tools for obtaining information on three-dimensional structures, dynamic properties and intermolecular interactions of biological macromolecules. One of these methods, called dispersion profile, is based on measuring the field dependence of spin-relaxation rates in the rotating frame, $R_{1ρ} = 1//T_{1ρ}$, in the presence of a low magnetic field $B_1$. In the presented study we use this method for investigation of molecular dynamics in protein samples. Dispersion profiles can be predicted theoretically and using two models, assuming either dipolar interaction between protons or power law dispersion, we have evaluated some molecular dynamic parameters of water adsorbed on protein surface. Our researches are focused on the connections of obtained parameters of molecular dynamics with conformation changes of protein. We have calculated the correlation times and power parameters for samples of lyophilized powder of albumins (egg white and bovine and rabbit blood serum) and lysozyme, as well as its aqueous solutions. Analysis of these parameters yields valuable information on the molecular nature of investigated biological systems. We also used this method to analyze experimental data of $T_{1ρ}$ obtained by other authors for bovine serum albumin and we have found good accordance with their conclusions concerning molecular dynamics of proteins.
Źródło:
Acta Physica Polonica A; 2012, 121, 2; 434-438
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular Dynamics of Proteins Investigated by NMR Relaxation Methods
Autorzy:
Wierzuchowska, D.
Blicharska, B.
Powiązania:
https://bibliotekanauki.pl/articles/1360657.pdf
Data publikacji:
2014-04
Wydawca:
Polska Akademia Nauk. Instytut Fizyki PAN
Tematy:
76.60.-k
76.90.+d
Opis:
The nuclear magnetic resonance relaxation times of solvent water nuclei are known to decrease upon addition of diamagnetic solute protein. For this reason NMR relaxation methods are able to provide information on molecular dynamics changes of water protons and their interaction with macromolecules' surfaces. We present results of measurements of relaxation rates $R_1$ = 1/$T_1$, $R_2$ = 1/$T_2$ and $R_{1ρ}$ = 1/$T_{1ρ}$ in the rotating frame for three proteins: chicken egg white lysozyme, egg white albumin, and bovine serum albumin, obtained at proton resonant frequency of 60 MHz. Besides the relaxation rates dependences on concentration in the 4-23% (g/100 g solution) range, the analysis of the Carr-Purcell-Meiboom-Gill CPMG multi-echo $T_2$ experiments with variable pulse rate τ was performed. The dependences of relaxation rates on protein concentration are linear at low concentration. When protein concentration increases the slope of the straight line rapidly changes at so-called "critical" concentration which depends on MW of the diluted protein. Investigated dispersion of $T_2$, obtained using the CPMG method with a variable pulse rate, for concentrations higher and lower than the "critical" one, exhibits unequal behavior. At high concentration one-exponential curves and at low concentration two-exponential curves correspond closely with experimental data. The obtained parameters of exponents allow an estimation of the ratio of the amount of water with the determined motion freedom, that is free and bounded water, in solution. We showed that the CPMG dispersion method applied to aqueous protein solutions may widen the current understanding of the nature of molecular dynamics of hydrated water protons in non-perturbed environment.
Źródło:
Acta Physica Polonica A; 2014, 125, 4; 907-910
0587-4246
1898-794X
Pojawia się w:
Acta Physica Polonica A
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Effect of the oxygen-containing functional group on the adsorption of hydrocarbon oily collectors on coal surfaces
Autorzy:
Wan, He
Hu, Xianglin
Luukkanen, Saija
Qu, Juanping
Zhang, Chonghui
Xue, Jiwei
Li, Hui
Yang, Wei
Yang, Shenghong
Bu, Xianzhong
Powiązania:
https://bibliotekanauki.pl/articles/2146920.pdf
Data publikacji:
2022
Wydawca:
Politechnika Wrocławska. Oficyna Wydawnicza Politechniki Wrocławskiej
Tematy:
oxygen-containing functional groups
hydrocarbon oily collectors
molecular dynamics simulation
coal surfaces
adsorption
Opis:
The oxygen-containing functional groups (OCFG) on the coal surface affect the adsorption effect of hydrocarbon oily collectors (HOC). An investigation of the interaction between the HOC and OCFG in the absence and presence of water is conducive to understanding the effect of OCFG type on the adsorption of HOC on the coal surface. In this paper, FTIR analysis was used to analyze the OCFG type of coal surface. The adsorption behavior of HOC on different OCFG surfaces was investigated using molecular dynamics simulation. The results indicated the presence of OCFG such as -OH, -COOH, -C=O, and -COCH3 on the coal surface. In conditions without water, the effect of OCFG on HOC adsorption capability follows the order -COOH > -C=O > -OH > -COCH3. In an aqueous solution, the effect of OCFG on HOC adsorption capability follows the order -C=O>-COCH3>-OH>-COOH. Moreover, the hydrophilicity of OCFG is the key factor that affects the adsorption effect of HOC. In other words, the adsorption effect of HOC on the coal surface in an aqueous solution does not depend on the strength of the interaction between the OCFG and HOC in the absence of water, but on the hydrophilicity of the OCFG. The -COOH and -OH on the coal surface are not conducive to the adsorption of HOC onto the coal surface. Masking the -COOH and -OH of the coal surface is beneficial in improving the coal flotation performance with HOC as a collector.
Źródło:
Physicochemical Problems of Mineral Processing; 2022, 58, 4; art. no. 149937
1643-1049
2084-4735
Pojawia się w:
Physicochemical Problems of Mineral Processing
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Molecular modelling techniques in environmental research
Autorzy:
Urniaż, R. D.
Rutkowska, E.
Jastrzębski, J. P.
Książek, P.
Rudnicka, K.
Powiązania:
https://bibliotekanauki.pl/articles/363208.pdf
Data publikacji:
2013
Wydawca:
Uniwersytet Warmińsko-Mazurski w Olsztynie
Tematy:
molecular dynamics
molecular modeling
pharmacokinetics
pharmacophore modeling
QSAR
dynamika molekularna
modelowanie molekularne
farmakokinetyka
modelowanie farmakoforowe
Opis:
Over the last few decades significant increase in computational methods (in silico) was annotated. Novel methods have been developed and applied for hypothesis improvement and testing in regions of industrial, pharmaceutical and environmental research. The term in silico methods include variety of approaches. Considerable attention has been attracted to databases, data analysis tools, quantitative structure-activity relationships (QSAR), pharmacophore models, molecular docking and dynamics, pharmacokinetics and other molecular modelling techniques. In silico methods are often accompanied by experimental data, both to create the model and to test it. Such models are frequently used in the discovery and optimization of novel molecules with expected affinity to a target, the estimation of absorption, distribution, metabolism, excretion and toxicity properties as well as physicochemical characterization. The review summarizes briefly the applications of most common molecular modelling techniques and evaluates their application in environmental research. Additionally, this study considers computer aided methods as potential and complex tools that may serve as valuable partnership with wet-lab experiments and may provide a rational aid to minimize the cost and time of research.
Źródło:
Environmental Biotechnology; 2013, 9, 2; 39-51
1734-4964
Pojawia się w:
Environmental Biotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Badanie struktury i dynamiki N-terminalnych sekwencji dermorfiny i ich analogów z wykorzystaniem spektroskopii NMR w ciele stałym i rentgenografii
Studies on the structure and dynamics of N-terminal sequences of dermorphin and their analogs by means of solid state NMR spectroscopy and XRD
Autorzy:
Trzeciak-Karlikowska, K.
Powiązania:
https://bibliotekanauki.pl/articles/171648.pdf
Data publikacji:
2012
Wydawca:
Polskie Towarzystwo Chemiczne
Tematy:
peptydy opioidowe
oddziaływania CH-pi
dynamika molekularna
oddziaływanie peptyd–fosfolipid
spektroskopia NMR
1H Ultra Fast MAS NMR
PISEMA MAS
PILGRIM
XRD
opioid peptides
CH-pi interactions
molecular dynamics
peptide–phospholipid interaction
NMR spectroscopy
Opis:
Deltorphin I (Tyr-d-Ala-Phe-Asp-Val-Val-Gly-NH_2) and dermorphin (Tyr-d-Ala-Phe- -Gly-Tyr-Pro-Ser-NH_2) are natural opioid peptides that have been isolated from the skin of South American frogs [1]. The presence of d-amino acid is crucial for their biological activity. The synthetic analogs of given heptapeptides containing l-alanine are not analgesics [2]. Analysis of the influence of stereochemistry on molecular packing, dynamics and biological functions of neuropeptides is still important for receptor studies and practical applications (e.g. design of new selective pain killers). Presented research is focused on the structure and dynamics of two N-terminal sequences of dermorphin: tripeptide Tyr-d-Ala-Phe 1, tetrapeptide Tyr-D-Ala-Phe-Gly 2, and their analogs with l-alanine: Tyr-Ala-Phe 3 and Tyr-Ala-Phe-Gly 4, using solid state NMR and X-ray diffraction. This study clearly demonstrates that 1 and 2 crystallized under different conditions to form exclusively one structure [3, 4]. In contrast, tripeptide and tetrapeptide with l-Ala in the sequence very easily form different crystal modifications. Tyr-Ala-Phe 3 crystallizes into two forms: 3a and 3b [5], while Tyr-Ala-Phe-Gly 4 gives three modifications: 4a, 4b and 4c [4]. It seems that one of the factors, which can be important in the preorganization mechanism anticipating the formation of crystals, is the intramolecular CH-đ interaction between aromatic rings of tyrosine and/or phenylalanine and the methyl group of alanine. Such interaction is possible only for d-Ala residue. For l-Ala in the peptide sequence, the methyl group is aligned on the opposite side with respect at least to one of the aromatic groups. It can be further speculated that such internal CH-π contacts can also occur during the interaction of ligand–receptor, making the message sequence of opioid peptides more rigid and finally selective. By employing different NMR experiments (e.g. PISEMA MAS and PILGRIM) it was proven that the main skeleton of analyzed peptides is rigid, whereas significant differences in the molecular motion of the aromatic residues were observed [4, 6]. Solid state 2H NMR spectroscopy of samples with deuterium labeled aromatic rings: Tyrd4-d-Ala-Phe 5, Tyr-d-Ala-Phed5 6, Tyrd4-Ala-Phe 7, Tyr-Ala-Phe^d5 8 was used to analyze the geometry and time scale of the molecular motion. At ambient temperature, the tyrosine ring of sample 5 is rigid and in the sample 6 the phenylalanine ring undergoes a "π -flip". The tyrosine rings of form I of 7 and 8 are static, while the phenylalanine rings of form II of 7 and 8 undergo a fast regime exchange [6]. Variable temperature 2H measurements proved that the tyrosine and phenylalanine rings of two forms of compounds 7 and 8 became more mobile with increasing temperature. In contrast, the aromatic rings of samples 5 and 6 preserve their dynamics regime (static tyrosine and "π -flip" phenylalanine) in a large range of temperatures [6]. The analysis of 13C, 15N labeled tetrapeptide Tyr-D-Ala-Phe-Gly 2’-phospholipid membrane interactions suggests that peptide 2’ is aligned on the surface of the membrane (RFDR MAS) and the sandwich-like π -CH_3-π arrangement of the pharmacophore is preserved (DARR) [7].
Źródło:
Wiadomości Chemiczne; 2012, 66, 9-10; 867-891
0043-5104
2300-0295
Pojawia się w:
Wiadomości Chemiczne
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 144

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