Wyniki wyszukiwania - Biblioteka Nauki

1

Monte Carlo simulations of protein-like heteropolymers.

100%

Sikorski A. , Romiszowski P.

Acta Biochimica Polonica

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2001

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tom 48

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nr 1

77-81

EN

Properties of a simple model of polypeptide chains were studied by the means of the Monte Carlo method. The chains were built on the (310) hybrid lattice. The residues interacted with long-range potential. There were two kinds of residues: hydrophobic and hydrophilic forming a typical helical pattern -HHPPHPP-. Short range potential was used to prefer helical conformations of the chain. It was found that at low temperatures the model chain formes dense and partially ordered structures (non-unique). The presence of the local potential led to an increase of helicity. The effect of the interplay between the two potentials was studied. After the collapse of the chain further annealing caused rearrangement of helical structures. Dynamic properties of the chain at low temperature depended strongly on the local chain ordering.

2

Monte Carlo simulations of protein-like heteropolymers

86%

Sikorski A. , Romiszowski P.

Acta Biochimica Polonica

|

2001

|

tom 48

|

nr 1

EN

Properties of a simple model of polypeptide chains were studied by the means of the Monte Carlo method. The chains were built on the (310) hybrid lattice. The residues interacted with long-range potential. There were two kinds of residues: hydrophobic and hy- drophilic forming a typical helical pattern -HHPPHPP-. Short range potential was used to prefer helical conformations of the chain. It was found that at low temperatures the model chain formes dense and partially ordered structures (non-unique). The presence of the local potential led to an increase of helicity. The effect of the interplay between the two potentials was studied. After the collapse of the chain further annealing caused rearrangement of helical structures. Dynamic properties of the chain at low temperature depended strongly on the local chain ordering.

3

Factors improving the accuracy of determination of 15N relaxation parameters in proteins

86%

Zhukov I. , Ejchart A.

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tom 46

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nr 3

EN

A number of factors at all stages of data processing which affect the accuracy of determination of 15N relaxation parameters in 15N-labeled proteins is discussed. Methods which allow to improve accuracy of the determined parameters are presented using data obtained for Cucurbita maxima trypsin inhibitor.

4

Coarse-grained modeling of protein structure, dynamics and protein-protein interactions

72%

Koliński A. , Kmiecik S. , Jamróz M. , Błaszczyk M. , Kouza M. , Kurciński M.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2014

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tom Vol. 18, No 3

219--229

EN

Theoretical prediction of protein structures and dynamics is essent ial for understanding the molecular basis of drug action, metabolic and signaling pathway s in living cells, designing new technologies in the life science and material sciences . We developed and validated a novel multiscale methodology for the study of protein folding proces ses including flexible docking of proteins and peptides. The new modeling technique starts fr om coarse-grained large-scale simulations, followed by selection of the most plausible final structu res and intermediates and, finally, by an all-atom rectification of the obtained structures. Except f or the most basic bioinformatics tools, the entire computational methodology is based on the models an d algorithms developed in our lab. The coarse-grained simulations are based on a high-resol ution lattice representation of protein structures, a knowledge based statistical for ce field and efficient Monte Carlo dynamics schemes, including Replica Exchange algorithms. This p aper focuses on the description of the coarse-grained CABS model and its selected applications.

5

Insight into protein dynamics from nuclear magnetic relaxation studies

72%

Ejchart A.

Polimery

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2007

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tom T. 52, nr 10

745-751

EN

In the review (63 references) the nuclear magnetic relaxation which is a unique experimental method giving insight into dynamic processes existing in proteins and covering a broad range of time scales was presented. This method, however, is demanding experimentally and theoretically. Exprimental methods limited to 15N nuclei are briefly presented and their limitations discussed. Analysis of experimental relaxation data for proteins can be done in the frame of model-free approach or applying spectral density mapping. Both those approaches are difficult for the physical interpretation of results. Besides motional parameters, some structural parameters influence relaxation rates and have to be estimated or determined. Hopefully, many problems connected with the analysis of relaxation data in proteins can be overcome with relaxation measurements at multiple magnetic fields for different isotopes like 15N, 13C, and 2H.

PL

W artykule przeglądowym (63 poz. lit.) przedstawiono wykorzystanie magnetycznej relaksacji jądrowej do badania dynamiki cząsteczkowej w białkach. Ograniczając dyskusję do najczęściej w przypadku białek badanego izotopu 15N, omówiono najważniejsze aspekty doświadczalne pomiarów prędkości relaksacji oraz metody ich interpretacji i powiązania z dynamiką cząsteczkową. W przypadku jąder 15N dominują dwa mechanizmy relaksacji, dipolowy i wywoływany przez anizotropię ekranowania. W równaniach opisujących prędkości relaksacji dotyczące tych mechanizmów pojawiają się gęstości spektralne, których postać analityczna zależy od przyjętego modelu ruchu. Ponieważ ruchy wektorów N-H w białkach są złożone, więc do ich opisu stosuje się model ogólny (model-free approach) lub wyznacza się bezpośrednio zależność gęstości spektralnych od częstości. Odrębnym problemem jest wyznaczenie parametrów strukturalnych, takich jak uśredniona wibracyjnie długość wiązania N-H czy wartości własne tensora ekranowania, które mogą zmieniać się w zależności od reszty aminokwasowej. Pomiary prędkości relaksacji własnej i prędkości interferencji dotyczące szeregu jąder występujących w białkach (15N, 13C, 2H) w wielu polach magnetycznych pozwalają na otrzymanie szczegółowych informacji o dynamice cząsteczek białek.

6

High coordination lattice models of protein structure, dynamics and thermodynamics

72%

Kolinski A. , Skolnick J.

Acta Biochimica Polonica

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1997

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tom 44

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nr 3

EN

A high coordination lattice discretization of protein conformational space is described. The model allows discrete representation of polypeptide chains of globular proteins and small macromolecular assemblies with an accuracy comparable to the accuracy of crystallographic structures. Knowledge based force Held, that consists of sequence specific short range interactions, cooperative model of hydrogen bond network and tertiary one body, two body and multibody interactions, is outlined and discussed. A model of stochastic dynamics for these protein models is also described. The proposed method enables moderate resolution tertiary structure prediction of simple and small globular proteins. Its applicability in structure prediction increases significantly when evolutionary information is exploited or/and when sparse experimental data are available. The model responds correctly to sequence mutations and could be used at early stages of a computer aided protein design and protein redesign. Computational speed, associated with the discrete structure of the model, enables studies of the long time dynamics of polypeptides and proteins and quite detailed theoretical studies of thermodynamics of nontrivial protein models.

7

Importance of intramolecular protein dynamics to kinetics of biochemical processes

72%

Kurzynski M.

Cellular and Molecular Biology Letters

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1999

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tom 04

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nr 1

EN

Several points seem essential for construction of the future statistical theory of biochemical processes. (a) The native proteins involved in these processes reveal a purely stochastic intramolecular dynamics of conformational transitions much slower than the usual vibrational dynamics. At least in the range from 10-11 to 10-7s the relaxation time spectrum of conformational transition dynamics is practically quasi-continuous. (b) The majority of reactions involving proteins are controlled and, presumably, also gated by this stochastic dynamics. (c) Of special importance is the short initial-condition dependent stage of biochemical reactions, neglected in the description of the reaction in terms of the standard kinetics. This stage is directly observed in experiments in which especially prepared initial conformational substates of the protein are confined to the reaction transition state. (d) The initial-condition dependent stage, and not that described by the standard kinetics, is responsible for the coupling of component reactions in the complete catalytic cycles proceeding in the steady-state and more complex processes of biological free energy transduction.