The ability of arginine-rich peptides to cross the lipid bilayer and enter cytoplasm, unlike their lysine-based analogues, is intensively studied in the context of cell-penetrating peptides. Although the experiments have not yet reconstructed their internalization mechanism, the computational studies have shown that the type or charge of lipid polar groups is one of the crucial factors in their translocation. In order to gain more detailed insight into the interaction of guanidinium (Gdm+) and ammonium (NH4+) cations, as important building blocks in arginine and lysine amino acids, with lipid bilayers, we conducted the experimental and computational study that tackles this phenomenon. The adsorption of Gdm+ and NH4+ on lipid bilayers prepared from a zwitterionic (DPPC) and an anionic (DPPS) lipid was examined by thermoanalytic and spectroscopic techniques. Using temperature-dependent UV-Vis spectroscopy and DSC calorimetry we determined the impact of Gdm+ and NH4+ on the thermotropic properties of lipid bilayers. FTIR data, along with molecular dynamics simulations, unraveled the molecular-level details on the nature of their interactions, showing the proton transfer between NH4+ and DPPS, but not between Gdm+ and DPPS. The findings originated from this work imply that Gdm+ and NH4+ form qualitatively different interactions with lipids of different charge which is reflected in the physico-chemical interactions that arginine-and lysine-based peptides establish at a complex and chemically heterogeneous environment such as the biological membrane.

• Klíčová slova
• 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-Dipalmitoyl-sn-glycero-3-phosphoserine (DPPS), Guanidinium (Gdm(+)) and ammonium (NH(4)(+)) cations, Molecular dynamics (MD) simulations, Spectroscopic (UV–Vis, FTIR) and calorimetric (DSC) study,
• MeSH
• arginin MeSH
• fosfatidylseriny chemie   MeSH
• guanidin MeSH
• kalorimetrie MeSH
• kationty MeSH
• lecitiny MeSH
• lipidové dvojvrstvy * chemie   MeSH
• lysin MeSH
• penetrační peptidy * MeSH
• simulace molekulární dynamiky MeSH
• spektrální analýza MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• arginin MeSH
• fosfatidylseriny MeSH
• guanidin MeSH
• kationty MeSH
• lecitiny MeSH
• lipidové dvojvrstvy * MeSH
• lysin MeSH
• penetrační peptidy * MeSH

A combination of Fourier transform infrared and phase transition measurements as well as molecular computer simulations, and thermodynamic modeling were performed to probe the mechanisms by which guanidinium (Gnd+) salts influence the stability of the collapsed versus uncollapsed state of an elastin-like polypeptide (ELP), an uncharged thermoresponsive polymer. We found that the cation's action was highly dependent upon the counteranion with which it was paired. Specifically, Gnd+ was depleted from the ELP/water interface and was found to stabilize the collapsed state of the macromolecule when paired with well-hydrated anions such as SO42-. Stabilization in this case occurred via an excluded volume (or depletion) effect, whereby SO42- was strongly partitioned away from the ELP/water interface. Intriguingly, at low salt concentrations, Gnd+ was also found to stabilize the collapsed state of the ELP when paired with SCN-, which is a strong binder for the ELP. In this case, the anion and cation were both found to be enriched in the collapsed state of the polymer. The collapsed state was favored because the Gnd+ cross-linked the polymer chains together. Moreover, the anion helped partition Gnd+ to the polymer surface. At higher salt concentrations (>1.5 M), GndSCN switched to stabilizing the uncollapsed state because a sufficient amount of Gnd+ and SCN- partitioned to the polymer surface to prevent cross-linking from occurring. Finally, in a third case, it was found that salts which interacted in an intermediate fashion with the polymer (e.g., GndCl) favored the uncollapsed conformation at all salt concentrations. These results provide a detailed, molecular-level, mechanistic picture of how Gnd+ influences the stability of polypeptides in three distinct physical regimes by varying the anion. It also helps explain the circumstances under which guanidinium salts can act as powerful and versatile protein denaturants.

• MeSH
• guanidin chemie   MeSH
• hydrofobní a hydrofilní interakce MeSH
• kationty MeSH
• peptidy chemie   MeSH
• spektroskopie infračervená s Fourierovou transformací MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• guanidin MeSH
• kationty MeSH
• peptidy MeSH

Gating charges in voltage-sensing domains (VSD) of voltage-sensitive ion channels and enzymes are carried on arginine side chains rather than lysine. This arginine preference may result from the unique hydration properties of the side chain guanidinium group which facilitates its movement through a hydrophobic plug that seals the center of the VSD, as suggested by molecular dynamics simulations. To test for side chain interactions implicit in this model we inspected interactions of the side chains of arginine and lysine with each of the 19 non-glycine amino acids in proteins in the protein data bank. The arginine guanidinium interacts with non-polar aromatic and aliphatic side chains above and below the guanidinium plane while hydrogen bonding with polar side chains is restricted to in-plane positions. In contrast, non-polar side chains interact largely with the aliphatic part of the lysine side chain. The hydration properties of arginine and lysine are strongly reflected in their respective interactions with non-polar and polar side chains as observed in protein structures and in molecular dynamics simulations, and likely underlie the preference for arginine as a mobile charge carrier in VSD.

• MeSH
• arginin chemie   MeSH
• databáze proteinů MeSH
• draslíkový kanál ERG1 chemie   MeSH
• gating iontového kanálu MeSH
• guanidin chemie   MeSH
• hydrofobní a hydrofilní interakce MeSH
• lidé MeSH
• lysin chemie   MeSH
• protein - isoformy chemie   MeSH
• sekvence aminokyselin MeSH
• simulace molekulární dynamiky * MeSH
• statická elektřina MeSH
• strukturní homologie proteinů MeSH
• voda chemie   MeSH
• vodíková vazba MeSH
• vztahy mezi strukturou a aktivitou MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• arginin MeSH
• draslíkový kanál ERG1 MeSH
• guanidin MeSH
• KCNH2 protein, human MeSH Prohlížeč
• lysin MeSH
• protein - isoformy MeSH
• voda MeSH

Ab initio free energy calculations of guanidinium pairing in aqueous solution confirm the counterintuitive conjecture that the like-charge ion pair is thermodynamically stable. Transferring the guanidinium pair to the inside of a POPC lipid bilayer, like-charge ion pairing is found to occur also inside the membrane defect. It is found to contribute to the nonadditivity of ion transfer, thereby facilitating the presence of ions inside the bilayer. The effect is quantified by free energy decomposition and comparison with ammonium ions, which do not form a stable pair. The presence of two charges inside the center of the bilayer leads to the formation of a pore. Potential consequences for cell penetrating peptides and ion conduction are drawn.

• MeSH
• fosfatidylcholiny chemie   MeSH
• guanidin chemie   MeSH
• kvantová teorie MeSH
• lipidové dvojvrstvy chemie   MeSH
• simulace molekulární dynamiky MeSH
• termodynamika MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 1-palmitoyl-2-oleoylphosphatidylcholine MeSH Prohlížeč
• fosfatidylcholiny MeSH
• guanidin MeSH
• lipidové dvojvrstvy MeSH
• voda MeSH

A series of 2,9-substituted 6-guanidinopurines, structurally related to the cyclin-dependent kinase (CDK) inhibitors olomoucine and roscovitine, has been synthesized and characterized. A new copper-catalyzed method for the synthesis of 2-substituted 6-guanidino-9-isopropylpurines under mild reaction conditions has been developed. All prepared compounds were screened for their CDK1 and CDK2 inhibitory activities, cytotoxicity and antiproliferative effects in the breast cancer-derived cell line MCF7. The most active derivative 16g possessed an identical side chain in the C2 position to roscovitine; this compound displayed approximately five fold higher inhibitory activity towards CDK2/cyclin E and more than ten fold increase in cytotoxicity in MCF7 cells. Interestingly and in contrast to previously described findings, (S)-6-guanidinopurine derivatives were generally more active than their (R)-counterparts. Kinase selectivity profiling of (R)- and (S)-enantiomers 16e and 16g, respectively, revealed that introduction of a guanidino group at the C6 position of the purine moiety decreased selectivity towards protein kinases compared to roscovitine. Nevertheless, increased inhibitory activity and decreased selectivity offer a good starting point for further development of new protein kinase inhibitors.

• MeSH
• buněčný cyklus účinky léků   MeSH
• cyklin-dependentní kinasa 2 antagonisté a inhibitory   metabolismus   MeSH
• guanidin analogy a deriváty   chemická syntéza   farmakologie   MeSH
• inhibitory proteinkinas chemická syntéza   chemie   farmakologie   MeSH
• lidé MeSH
• MFC-7 buňky MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• proliferace buněk účinky léků   MeSH
• proteinkinasa CDC2 antagonisté a inhibitory   metabolismus   MeSH
• protinádorové látky chemická syntéza   chemie   farmakologie   MeSH
• puriny chemická syntéza   chemie   farmakologie   MeSH
• screeningové testy protinádorových léčiv MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• CDK2 protein, human MeSH Prohlížeč
• cyklin-dependentní kinasa 2 MeSH
• guanidin MeSH
• inhibitory proteinkinas MeSH
• proteinkinasa CDC2 MeSH
• protinádorové látky MeSH
• puriny MeSH

Guanidinium carbonate was used in this study as a simple proxy for the biologically relevant arginine-carbonate interactions in water. Molecular dynamics (MD) simulations of guanidinium carbonate were performed with nonpolarizible water using two implementations of the ion force fields. In the first, the ions had full charges, while in the second, the ions had reduced charges in order to effectively account for electronic polarization effects of water. The results from the simulations were then compared to data from previous neutron scattering experiments. It was found that there were significant discrepancies between the full charge force field MD simulations and the experimental results due to excessive ion pairing and clustering in the former. In contrast, reducing the ionic charges yields a more regular solution with a simulated structure, which fits well the experimental data.

• MeSH
• guanidin chemie   MeSH
• ionty chemie   MeSH
• maloúhlový rozptyl MeSH
• neutronová difrakce MeSH
• proteiny chemie   metabolismus   MeSH
• simulace molekulární dynamiky * MeSH
• uhličitany chemie   MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• guanidin MeSH
• ionty MeSH
• proteiny MeSH
• uhličitany MeSH
• voda MeSH

The behavior of guanidinium chloride at the surface of aqueous solutions is investigated using classical molecular dynamics (MD) simulations. It is found that the population of guanidinium ions oriented parallel to the interface is greater in the surface region than in bulk. The opposite is true for ions in other orientations. Overall, guanidinium chloride is depleted in the surface region, in agreement with the fact that the addition of guanidinium chloride increases the surface tension of water. The orientational dependence of the surface affinity of the guanidinium cation is related to its anisotropic hydration. To bring the ion to the surface in the parallel orientation does not require hydrogen bonds to be broken, in contrast to other orientations. The surface enrichment of parallel-oriented guanidinium indicates that its solvation is more favorable near the surface than in bulk solution for this orientation. The dependence of the bulk and surface properties of guanidinium on the force field parameters is also investigated. Despite significant quantitative differences between the force fields, the surface behavior is qualitatively robust. The implications for the orientations of the guanidinium groups of arginine side chains on protein surfaces are also outlined.

• MeSH
• guanidin chemie   MeSH
• ionty chemie   MeSH
• povrchové napětí MeSH
• simulace molekulární dynamiky MeSH
• voda chemie   MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• guanidin MeSH
• ionty MeSH
• voda MeSH

Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.

• MeSH
• guanidin chemie   MeSH
• oligopeptidy chemie   MeSH
• simulace molekulární dynamiky * MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• guanidin MeSH
• oligopeptidy MeSH
• voda MeSH

Using a combination of experimental techniques (circular dichroism, differential scanning calorimetry, and NMR) and molecular dynamics simulations, we performed an extensive study of denaturation of the Trp-cage miniprotein by urea and guanidinium. The experiments, despite their different sensitivities to various aspects of the denaturation process, consistently point to simple, two-state unfolding process. Microsecond molecular dynamics simulations with a femtosecond time resolution allow us to unravel the detailed molecular mechanism of Trp-cage unfolding. The process starts with a destabilizing proline shift in the hydrophobic core of the miniprotein, followed by a gradual destruction of the hydrophobic loop and the α-helix. Despite differences in interactions of urea vs guanidinium with various peptide moieties, the overall destabilizing action of these two denaturants on Trp-cage is very similar.

• MeSH
• cirkulární dichroismus MeSH
• denaturace proteinů MeSH
• diferenciální skenovací kalorimetrie MeSH
• guanidin chemie   MeSH
• magnetická rezonanční spektroskopie MeSH
• močovina chemie   MeSH
• molekulární modely MeSH
• tryptofan chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• guanidin MeSH
• močovina MeSH
• tryptofan MeSH

Domains rich in cationic amino acids are ubiquitous in peptides with the ability to cross cell membranes, which is likely related to the binding of such polypeptides to anionic groups on the membrane surface. To shed more light on these interactions, we investigated specific interactions between basic amino acids and oligopeptides thereof and anions by means of electrophoretic experiments and molecular dynamics simulations. To this end, we measured the electrophoretic mobilities of arginine, lysine, tetraarginine, and tetralysine in sodium chloride and sodium sulfate electrolytes as a function of ionic strength. The mobility was found to be consistently lower in sodium sulfate than in sodium chloride at the same ionic strength. The decrease in mobility in sodium sulfate was greater for tetraarginine than for tetralysine and was larger for tetrapeptides compared to the corresponding free amino acids. On the basis of molecular dynamics simulations and Bjerrum theory, we rationalize these results in terms of enhanced association between the amino acid side chains and sulfate. Simulations also predict a greater affinity of sulfate to the guanidinium side chain groups of arginine than to the ammonium groups of lysine, as the planar guanidinium geometry allows simultaneous strong hydrogen bonding to two sulfate oxygens. We show that the sulfate binding to arginine, but not to lysine, is cooperative. These results are consistent with the greater decrease in the mobility of arginine compared to that of lysine upon addition of sulfate salt. The nonspecific mobility retardation by sulfate is ascribed to its electrostatic interaction with the cationic amino acid side chain groups.

• MeSH
• chlorid sodný chemie   MeSH
• elektroforéza metody   MeSH
• guanidin chemie   MeSH
• ionty chemie   MeSH
• molekulární modely MeSH
• osmolární koncentrace MeSH
• peptidy chemie   genetika   MeSH
• polylysin chemie   MeSH
• simulace molekulární dynamiky * MeSH
• sírany chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chlorid sodný MeSH
• guanidin MeSH
• ionty MeSH
• peptidy MeSH
• polyarginine MeSH Prohlížeč
• polylysin MeSH
• sírany MeSH
• sodium sulfate MeSH Prohlížeč