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Krzysztof kuczera

Brent L Lee, Krzysztof Kuczera, C Russell Middaugh, Gouri S Jas
No abstract text is available yet for this article.
August 7, 2016: Journal of Chemical Physics
Brent L Lee, Krzysztof Kuczera, C Russell Middaugh, Gouri S Jas
The time-resolved parallel artificial membrane permeability assay with fluorescence detection and comprehensive computer simulations are used to study the passive permeation of three aromatic dipeptides-N-acetyl-phenylalanineamide (NAFA), N-acetyltyrosineamide (NAYA), and N-acetyl-tryptophanamide (NATA) through a 1,2-dioleoyl-sn-glycero-3-phospocholine (DOPC) lipid bilayer. Measured permeation times and permeability coefficients show fastest translocation for NAFA, slowest for NAYA, and intermediate for NATA under physiological temperature and pH...
June 28, 2016: Journal of Chemical Physics
Gouri S Jas, C Russell Middaugh, Krzysztof Kuczera
Chaotropes like urea and guanidinium chloride (GdmCl) tend to destabilize, and kosmotropes like proline tend to stabilize folded structures of peptides and proteins. Here, we combine fluorescence anisotropy decay measurements and molecular dynamics simulations to gain a microscopic understanding of the molecular mechanism for shifting conformational preferences in aqueous, GdmCl, urea, and proline solutions of a simple model dipeptide, N-acetyl-tryptophan-amide (NATA). Measured anisotropy decay of NATA as a function of temperature, pH, and cosolvent concentrations showed reorientations moderately slower in GdmCl and urea and substantially slower in proline compared to those of aqueous environment...
July 21, 2016: Journal of Physical Chemistry. B
Gouri S Jas, Eric C Rentchler, Agnieszka M Słowicka, John R Hermansen, Carey K Johnson, C Russell Middaugh, Krzysztof Kuczera
Fluorescence anisotropy decay measurements and all atom molecular dynamics simulations are used to characterize the orientational motion and preferential interaction of a peptide, N-acetyl-tryptophan-amide (NATA) containing two peptide bonds, in aqueous, urea, guanidinium chloride (GdmCl), and proline solution. Anisotropy decay measurements as a function of temperature and concentration showed moderate slowing of reorientations in urea and GdmCl and very strong slowing in proline solution, relative to water...
March 31, 2016: Journal of Physical Chemistry. B
Wojciech Domaradzki, Krzysztof Sanetra, Bartosz Skwarna, Marek Król, Małgorzata Kuczera, Marek Cisowski
We present a case of a 64-year-old man with coronary artery disease, who underwent a percutaneous coronary intervention of the circumflex artery. As the guidewire was being withdrawn from the target vessel, it became entrapped by the structure of the previously implanted stent. Attempts to retrieve the foreign body were unsuccessful. Changes in electrocardiogram were observed during the procedure, and the level of cardiac biomarkers increased within the next 24-hours. The patient was admitted to the Cardiac Surgery Department...
September 2015: Kardiochirurgia i Torakochirurgia Polska, Polish Journal of Cardio-Thoracic Surgery
Krzysztof Kuczera
This article presents a review of the field of molecular modeling of peptides. The main focus is on atomistic modeling with molecular mechanics potentials. The description of peptide conformations and solvation through potentials is discussed. Several important computer simulation methods are briefly introduced, including molecular dynamics, accelerated sampling approaches such as replica-exchange and metadynamics, free energy simulations and kinetic network models like Milestoning. Examples of recent applications for predictions of structure, kinetics, and interactions of peptides with complex environments are described...
2015: Methods in Molecular Biology
Gouri S Jas, Wendy A Hegefeld, C Russell Middaugh, Carey K Johnson, Krzysztof Kuczera
We present a combined experimental and computational study of unfolding pathways of a model 21-residue α-helical heteropeptide (W1H5-21) and a 16-residue β-hairpin (GB41-56). Experimentally, we measured fluorescence energy transfer efficiency as a function of temperature, employing natural tryptophans as donors and dansylated lysines as acceptors. Secondary structural analysis was performed with circular dichroism and Fourier transform infrared spectroscopy. Our studies present markedly different unfolding pathways of the two elementary secondary structural elements...
July 3, 2014: Journal of Physical Chemistry. B
Nicoleta Ploscariu, Krzysztof Kuczera, Katarzyna E Malek, Magdalena Wawrzyniuk, Ashim Dey, Robert Szoszkiewicz
Notch signaling in metazoans is responsible for key cellular processes related to embryonic development and tissue homeostasis. Proteolitic cleavage of the S2 site within an extracellular NRR domain of Notch is a key early event in Notch signaling. We use single molecule force-extension (FX) atomic force microscopy (AFM) to study force-induced exposure of the S2 site in the NRR domain from mouse Notch 1. Our FX AFM measurements yield a histogram of N-to-C termini lengths, which we relate to conformational transitions within the NRR domain...
May 8, 2014: Journal of Physical Chemistry. B
Gouri S Jas, C Russell Middaugh, Krzysztof Kuczera
We have performed a combined experimental and computational study of the folding of a 21-residue α-helix-forming heteropeptide (WH21). Temperature jump kinetics with improved dynamic range at several temperatures revealed non-exponential relaxation that could be well described with two time constants of 20 and 300 ns at 298 K. In the computational part, we performed multi-microsecond molecular dynamics simulations of WH21 in explicit water, using the AMBER03 and OPLS/AA potentials. The simulations were in good agreement with available experimental data on helix content and relaxation times...
January 16, 2014: Journal of Physical Chemistry. B
Krzysztof Kuczera
No abstract text is available yet for this article.
August 20, 2013: Biophysical Journal
Krzysztof Kuczera, Petri Kursula
We have studied the interactions between calmodulin (CaM) and three target peptides from the death-associated protein kinase (DAPK) protein family using both experimental and modeling methods, aimed at determining the details of the underlying biological regulation mechanisms. Experimentally, calorimetric binding free energies were determined for the complexes of CaM with peptides representing the DAPK2 wild-type and S308D mutant, as well as DAPK1. The observed affinity of CaM was very similar for all three studied peptides...
2012: Journal of Biomolecular Structure & Dynamics
Kristi Y Deleon, Achal P Patel, Krzysztof Kuczera, Carey K Johnson, Gouri S Jas
We present a study of structural analysis and reorientational dynamics of Angiotensin I (AngI) and Angiotensin II (AngII) in aqueous solution. AngI is a decapeptide that acts as a precursor to the octapeptide AngII in the Renin-Angiotensin-Aldosterone system for blood pressure regulation. Experimental structural characterization of these peptides, carried out with circular dichroism and infrared spectroscopy, showed that the angiotensins are mostly disordered but exhibit a measurable population of ordered structures at room temperature...
2012: Journal of Biomolecular Structure & Dynamics
Gouri S Jas, Wendy A Hegefeld, Peter Májek, Krzysztof Kuczera, Ron Elber
We investigate the kinetics and thermodynamics of a helical turn formation in the peptide Ac-WAAAH-NH(2). NMR measurements indicate that this peptide has significant tendency to form a structure of a helical turn, while temperature dependent CD establishes the helix fraction at different temperatures. Molecular dynamics and milestoning simulations agree with experimental observables and suggest an atomically detailed picture for the turn formation. Using a network representation, two alternative mechanisms of folding are identified: (i) a direct co-operative mechanism from the unfolded to the folded state without intermediate formation of hydrogen bonds and (ii) an indirect mechanism with structural intermediates with two residues in a helical conformation...
June 14, 2012: Journal of Physical Chemistry. B
Alfredo E Cardenas, Gouri S Jas, Kristine Y DeLeon, Wendy A Hegefeld, Krzysztof Kuczera, Ron Elber
Cellular transport machinery, such as channels and pumps, is working against the background of unassisted material transport through membranes. The permeation of a blocked tryptophan through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane is investigated to probe unassisted or physical transport. The transport rate is measured experimentally and modeled computationally. The time scale measured by parallel artificial membrane permeation assay (PAMPA) experiments is ~8 h. Simulations with the milestoning algorithm suggest mean first passage time (MFPT) of ~4 h and the presence of a large barrier at the center of the bilayer...
March 8, 2012: Journal of Physical Chemistry. B
Sudharsan Parthasarathy, Adriana Altuve, Simon Terzyan, Xuejun Zhang, Krzysztof Kuczera, Mario Rivera, David R Benson
Mammalian type B (mitochondrial) b(5) cytochromes exhibit greater amino acid sequence diversity than their type A (microsomal) counterparts, as exemplified by the type B proteins from human (hCYB5B) and rat (rCYB5B). The comparison of X-ray crystal structures of hCYB5B and rCYB5B reported herein reveals a striking difference in packing involving the five-strand β-sheet, which can be attributed to fully buried residue 21 in strand β4. The greater bulk of Leu21 in hCYB5B in comparison to that of Thr21 in rCYB5B results in a substantial displacement of the first two residues in β5, and consequent loss of two of the three hydrogen bonds between β5 and β4...
June 21, 2011: Biochemistry
Kyung-Hoon Lee, Krzysztof Kuczera, Mark M Banaszak Holl
We have carried out stochastic boundary molecular dynamics simulations to estimate free energy changes for substitutions of Gly with Val, Arg and Trp residues in a collagen-like peptide. The relative free energy change differences of mutants containing a Val, an Arg and a Trp relative to the wild type are 5.7, 8.1 and 9.5 kcal/mol, respectively. The corresponding free energy change differences of mutants containing two mutated residues are on average 7.6, 10.5 and 14.7 kcal/mol, respectively. We show that the free energy change differences are correlated with the severity of OI from statistical analysis and mechanical properties of the individual tropocollagen molecules...
July 2011: Biophysical Chemistry
Kevin C Song, Philip W Livanec, Jeffery B Klauda, Krzysztof Kuczera, Robert C Dunn, Wonpil Im
Single-molecule fluorescence measurements have been used to characterize membrane properties, and recently showed a linear evolution of the fluorescent lipid analogue BODIPY-PC toward small tilt angles in Langmuir-Blodgett monolayers as the lateral surface pressure is increased. In this work, we have performed comparative molecular dynamics (MD) simulations of BODIPY-PC in DPPC (dipalmitoylphosphatidylcholine) monolayers and bilayers at three surface pressures (3, 10, and 40 mN/m) to explore (1) the microscopic correspondence between monolayer and bilayer structures, (2) the fluorophore's position within the membrane, and (3) the microscopic driving forces governing the fluorophore's tilting...
May 19, 2011: Journal of Physical Chemistry. B
Wendy A Hegefeld, Krzysztof Kuczera, Gouri S Jas
We have employed a combination of experiment and simulation to characterize the ensemble of structures sampled by human Peptide YY (hPYY), an important member of the neuropeptide Y family. Experimental structural characterization carried out with far UV circular dichroism spectroscopy and Fourier Transform-Infrared measurements confirmed that the major feature of the secondary structure of hPYY is the α-helix, encompassing about half the peptide residues, with smaller contributions from turn and β-sheet like structures...
July 2011: Biopolymers
Wendy A Hegefeld, Shen-En Chen, Kristine Y DeLeon, Krzysztof Kuczera, Gouri S Jas
We used a combined approach of experiment and simulation to determine the helical population and folding pathway of a small helix forming blocked pentapeptide, Ac-(Ala)(5)-NH(2). Experimental structural characterization of this blocked peptide was carried out with far UV circular dichroism spectroscopy, FTIR, and NMR measurements. These measurements confirm the presence of the α-helical state in a buffer solution. Direct molecular dynamics and replica-exchange simulations of the pentapeptide were performed using several popular force fields with explicit solvent...
December 2, 2010: Journal of Physical Chemistry. A
Kyung-Hoon Lee, Krzysztof Kuczera, Mark M Banaszak Holl
Molecular dynamics simulations were carried out to calculate free energy differences between the folded and unfolded states of wild type and mutant collagen model peptides. The calculated stability of the collagen models was compared with the severity of osteogenesis imperfecta. Free energy differences of Gly → Xaa (Xaa: Ser, Cys, Glu, and Asp) mutations between the wild type and the mutants at position 15 of the model peptide were 3.8, 4.2, 5.6, and 8.8 kcal/mol, respectively. The corresponding free energy differences of a second Gly mutation at the same position in different chains were, on average, 1...
March 2011: Biopolymers
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