The mechanism of cis-trans isomerization of prolyl peptides by cyclophilin

The mechanism of cis-trans isomerization of prolyl peptides catalyzed by cyclophilin (CyP) was studied computationally via molecular dynamics (MD) simulations of the transition state (TS) and the cis and trans forms of the ground state (GS), when bound to CyP and when free in aqueous solution. The MD simulations include four enzyme-bound species of tetrapeptide (Suc-Ala-XC([double bond]O)-NPro-Phe-pNA; X = Gly, Trp, Ala, and Leu). In water, the prolyl amide bond is favorably planar with the presence of conformers exhibiting +/-20 degrees twist of the C-N dihedral. In the active site a hydrogen bond between the cis-prolyl amide carbonyl O and the backbone amide N-H of Asn102 retains the 20 degrees twist of the C-N dihedral. The TS structure is characterized by a 90 degrees twist of the amide C-N bond and a more favorable interaction with Asn102 due to the shorter distance between Asn102(HN) and the amide carbonyl O. The conformational change of cis --> TS also involves pyramidalization of the amide N, which results in the formation of a hydrogen bond between the amide N and the guanidino group of Arg55. Both Asn102 and Arg55 are held in the same position in CyP.cis-isomer as in CyP.TS. In the ligand-free CyP the Arg55 guanidino group is highly disorganized and Asn102 is displaced 1 A from the position in the ligand-bound CyP. Thus, the organization of Arg55 and Asn102 occurs upon substrate binding. The geometrical complimentarity of the organized enzyme structure to the TS structure is a result of preferential binding of the proline N and the amide carbonyl of the TS compared to that of GS. However, the N-terminal part (Suc-Ala) becomes repositioned in the TS such that two hydrogen bonds disappear, one hydrogen bond appears and two other hydrogen bonds becomes weaker on the conversion of CyP.cis to CyP.TS. During this conversion, total hydrophobic contact between enzyme and the peptide is preserved. Thus, the interaction energies of GS and TS with enzyme are, as a whole, much alike. This does not support the contention that TS is bound more tightly than GS by K(m)/K(TS) = 10(6) in the cis --> trans reaction. Repositioning of the N-terminal part of the peptide on CyP.TS formation becomes more pronounced when the substrate X residue is changed from Gly < Trp < Ala < Leu. We propose that the larger turning of the N-terminus is responsible for the larger value of the experimentally observed Delta S(++) and Delta H(++), which sum up to little change in Delta G(++). The positioning of the Arg55 and the degree of 20 degrees twist of the amide C-N bond are considered as criteria for Near Attack Conformers (NACs) in cis-trans isomerization. NACs account for approximately 30% of the total GS populations of the cis-isomer. Similar NAC populations were observed with four different substrates. This is consistent with the insensitivity of enzymatic activity to the nature of the X residue. Also, the NAC population in CyP.trans-AAPF was comparable to that in CyP.cis-AAPF, in accord with similar experimentally measured rates of the cis --> trans and trans --> cis reaction in CyP. These NACs, found in CyP.cis and CyP.trans, resemble only one of the four possible TS configurations in the water reaction. The identity of this TS structure (syn/exo) is in accord with experimentally determined KIE values in the enzymatic reaction. However, the geometry of the active site was also complementary to another TS structure (anti/exo) that was not detected in the active site by the same KIE measurements, implying that the geometrical fitness of the TS cannot be a single determining factor for enzymatic reactions.     

Selectivity in platinum-catalyzed cis-trans carbon-carbon double-bond isomerization

The isomerization of trans-2-butene to its cis conformer was found to be easier on Pt111 surfaces than the opposite cis to trans conversion. This kinetic trend, which is opposite to what would be expected on thermodynamic grounds, is explained by an increased stability of the cis isomer upon adsorption. A model where adsorption energies are affected by steric interactions between the side moieties of the olefin and the surface suggests that selectivity toward cis versus trans formation may be manipulated by controlling the structure of the surface of the catalyst.     

Isothermal cis-trans isomerization behavior of polyacetylene films

Isothermal cis-trans isomerization behavior was studied by differential scanning calorimetry for conventional Shirakawa polyacetylene (S-PA) film and highly stretchable polyacetylene (hs-x) films synthesized using catalysts aged at high temperature. The rate of isomerization is slower for S-PA than for hs-x. Kinetic results of isomerization are analyzed by a stretched exponential function with exponent n (0 < n < 1), which is different from the previously assumed single exponential function. An activation energy of 31 kcal/mol was obtained for all the samples. © 1995 John Wiley & Sons, Inc.     

Conformational preferences and cis-trans isomerization of azaproline residue

The conformational study of N-acetyl-N'-methylamide of azaproline (Ac-azPro-NHMe, the azPro dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the effects of the replacement of the backbone CHalpha group by the nitrogen atom on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). The incorporation of the Nalpha atom into the prolyl ring results in the different puckering, backbone population, and barriers to prolyl cis-trans isomerization from those of Ac-Pro-NHMe (the Pro dipeptide). In particular, the azPro dipeptide has a dominant backbone conformation D (beta2) with the cis peptide bond preceding the azPro residue in both the gas phase and solution. This may be ascribed to the favorable electrostatic interaction or intramolecular hydrogen bond between the prolyl nitrogen and the amide hydrogen following the azPro residue and to the absence of the unfavorable interactions between electron lone pairs of the acetyl carbonyl oxygen and the prolyl Nalpha. This calculated higher population of the cis peptide bond is consistent with the results from X-ray and NMR experiments. As the solvent polarity increases, the conformations B and B* with the trans peptide bond become more populated and the cis population decreases more, which is opposite to the results for the Pro dipeptide. The conformation B lies between conformations D and A (alpha) and conformation B* is a mirror image of the conformation B on the phi-psi map. The barriers to prolyl cis-trans isomerization for the azPro dipeptide increase with the increase of solvent polarity, and the cis-trans isomerization proceeds through only the clockwise rotation with omega' approximately +120 degrees about the prolyl peptide bond for the azPro dipeptide in the gas phase and in solution, as seen for the Pro dipeptide. The pertinent distance d(N...H-NNHMe) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure and the lower rotational barriers for the azPro dipeptide than those for the Pro dipeptide in the gas phase and in solution.     

Kinetic analysis of cis-trans thermal isomerization of polyacetylene

A single broad exothermic peak due to cis-trans isomerization appears near 140°C in the differential scanning calorimetry (DSC) curve of polyacetylene (PA) films, polymerized by a nonsolvent method using a high-temperature-aged catalyst. This exothermic peakis described by a two-state model, in which population probabilities for cis and trans states are assumed to change through the forward and backward reactions. The enthalpy difference between the two states is 1.69 kcal/mol, which was derived from the slope of the plot of heat of isomerization versus cis content. The activation energy was determined experimentally from the heating-rate dependence of the peak temperature. A single activated process with an activation energy of 28 kcal/mol was observed for the PA film. Other parameters such as the preexponential factor were estimated by comparing theoretical and experimental DSC curves.     

Microcantilever sensing and actuation with end-grafted stimulus-responsive elastin-like polypeptides

Stimulus-responsive elastin-like polypeptides (ELPs) grafted onto surfaces are of significant technical interest because they can be exploited for force generation, in sensing applications, or as molecular switches with tunable properties. Changes in the conformational state of grafted ELPs, induced by a phase transition or changes in osmotic pressure, lead to significant changes in the surface stress in the ELP graft layer and translate into detectable changes in microcantilever deflection. In this study, we investigate the conformational mechanics of ELPs in response to changes in solution pH and ionic strength using atomic force microscopy (AFM) microcantilever deflection and quartz crystal microbalance (QCM) measurements. We show that the use of genetically encoded, surface-grafted ELPs is exciting for cantilever actuation and sensing because commonly available microfabricated cantilever springs offer a simple and nonintrusive way to detect changes in solvent type, temperature, and pH, promising great potential for sensing applications in microfluidic devices.     

二硅烯化合物顺反异构化过渡态动力学参数的计算

本文介绍了过渡态理论对双键取代物顺反异构化过程的处理方法. 计算了1,2-二叔丁基-1,2-二(2,4,6-三甲苯基)二硅烯、1,2-二[二(三甲硅基)]-氨基-1,2-二(2,4,6-三甲苯基)二硅烯和1,2-二甲基-1,2-二苯基二硅烯等化合物的顺反异构化的活化熵变和相应过程的Arrhenius A因子. 前两个化合物的计算结果与West的实验值符合得很好. 后一个化合物, 尚未见到动力学实验结果的报道. 本文指出了这类化合物构型熵贡献的重要性.     

Conformational preferences and cis-trans isomerization of L-lactic acid residue

The conformational study on N-acetyl- N'-methylamide of l-lactic acid (Ac-Lac-NHMe, the Lac dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore its backbone conformational preferences and cis-trans isomerization for the depsipeptide with an ester bond in the gas phase and in solution. In the gas phase and in chloroform, the conformation tB with a trans depsipeptide bond is most preferred for the Lac dipeptide, whose backbone torsion angles are phi approximately -150 degrees and psi approximately -5 degrees , juxtaposed to those of the 3 10-helical structure. The larger shift in phi is brought to reduce the repulsion between the two carbonyl carbons of the acetyl and NHMe groups. However, the polyproline II-like tF conformation becomes more populated and the relative stability of conformation tB decreases significantly as the solvent polarity increases. This may be ascribed to weakening a C(5) hydrogen bond between the depsipeptidyl oxygen and the carboxyl amide hydrogen that plays a role in stabilizing the conformation tB in the gas phase and in chloroform. The cis populations about the depsipeptide bond are nearly negligible in the gas phase and in solution. The rotational barriers to the cis-trans isomerization of the depsipeptide bond for the Lac dipeptide are calculated to be about 11 kcal/mol, which is about half of those for the Ala dipeptide, although they increase somewhat with the increase of solvent polarity. The cis-trans isomerization of the depsipeptide bond proceeds through either clockwise or anticlockwise rotations with torsion angles of about +90 degrees or -90 degrees , respectively, in the gas phase and in solution, whereas it has been known that the isomerization proceeds through only the clockwise rotation for alanyl and prolyl peptide bonds. The pertinent distances between the depsipeptidyl oxygen and the carboxyl amide hydrogen can describe the role of this hydrogen bond in stabilizing the transition state structures in the gas phase and in solution.     

Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides

We investigated the effect of temperature, ionic strength, solvent polarity, and type of guest residue on the force-extension behavior of single, end-tethered elastin-like polypeptides (ELPs), using single molecule force spectroscopy (SMFS). ELPs are stimulus-responsive polypeptides that contain repeats of the five amino acids Val-Pro-Gly-Xaa-Gly (VPGXG), where Xaa is a guest residue that can be any amino acid with the exception of proline. We fitted the force-extension data with a freely jointed chain (FJC) model which allowed us to resolve small differences in the effective Kuhn segment length distributions that largely arise from differences in the hydrophobic hydration behavior of ELP. Our results agree qualitatively with predictions from recent molecular dynamics simulations and demonstrate that hydrophobic hydration modulates the molecular elasticity for ELPs. Furthermore, our results show that SMFS, when combined with our approach for data analysis, can be used to study the subtleties of polypeptide-water interactions and thus provides a basis for the study of hydrophobic hydration in intrinsically unstructured biomacromolecules.     

Volume-demanding cis-trans isomerization of 1,2-diaryl olefins in the solid state

Volume-demanding cis-trans photoisomerization of the aromatic substituted alkenes 1-3 in the solid state at room temperature and at 50 degrees C is presented. Alkene 3 did not undergo the cis-trans isomerization in the solid state either at room temperature or at 50 degrees C. The importance of the presence of void space near the reaction center to facilitate the large volume change during cis-trans photoisomerization is discussed.     

The infrared-driven cis-trans isomerization of HONO. II: Vibrational relaxation and slow isomerization channel

In a recent paper [R. Schanz et al., J. Chem. Phys. 122, 044509 (2005)], we investigated the IR-driven cis-trans isomerization of HONO in a Kr matrix with the help of femtosecond IR spectroscopy. We found that isomerization occurs on a 20 ps time scale, however, with a cis-->trans quantum yield of only 10% that is significantly below the value reported in the literature (close to 100%). At the same time, we concluded that vibrational energy has not completely dissipated out of the molecule at the maximum delay time we reached in this study (500 ps). In order to verify whether additional, slower reaction channels exist, we extend the study here to delay times up to 100 ns. At a temperature of 32 K, we indeed find an additional isomerization channel on a 2 ns timescale, which increases the total cis-->trans quantum yield to approximately 30%. The trans-->cis quantum yield is approximately 7%. There is still a discrepancy between the quantum yields we observe and the literature values, however, we provide experimental evidence that this discrepancy is due to the different temperatures of our study. Vibrational cooling occurs on a 20 ns time scale, and cascades in a highly nonstatistical manner through one single normal mode (most likely the ONO bending mode nu(5)). Intermolecular energy dissipation into the rare gas matrix is more efficient than intramolecular vibrational energy redistribution and the matrix environment can certainly not be considered a weak perturbation.     

Effects of Hofmeister anions on the phase transition temperature of elastin-like polypeptides

The modulation of the lower critical solution temperature (LCST) of two elastin-like polypeptides (ELPs) was investigated in the presence of 11 sodium salts that span the Hofmeister series for anions. It was found that the hydrophobic collapse/aggregation of these ELPs generally followed the series. Specifically, kosmotropic anions decreased the LCST by polarizing interfacial water molecules involved in hydrating amide groups on the ELPs. On the other hand, chaotropic anions lowered the LCST through a surface tension effect. Additionally, chaotropic anions showed salting-in properties at low salt concentrations that were related to the saturation binding of anions with the biopolymers. These overall mechanistic effects were similar to those previously found for the hydrophobic collapse and aggregation of poly(N-isopropylacrylamide), PNIPAM. There is, however, a crucial difference between PNIPAM and ELPs. Namely, PNIPAM undergoes a two-step collapse process as a function of temperature in the presence of sufficient concentrations of kosmotropic salts. By contrast, ELPs undergo collapse in a single step in all cases studied herein. This suggests that the removal of water molecules from around the amide moieties triggers the removal of hydrophobic hydration waters in a highly coupled process. There are also some key differences between the LCST behavior of the two ELPs. Specifically, the more hydrophilic ELP V5A2G(3)-120 construct displays collapse/aggregation behavior that is consistent with a higher concentration of anions partitioning to polymer/aqueous interface as compared to the more hydrophobic ELP V(5)-120. It was also found that larger anions could bind with ELP V5A2G(3)-120 more readily in comparison with ELP V(5)-120. These latter results were interpreted in terms of relative binding site accessibility of the anion for the ELP.     

Quantum yields of the mercury photosensitized cis-trans isomerization of 1,3-pentadiene

The quantum yields of thecis trans andtrans cis Hg 6(³P₁) photosensitized isomerizations of 1,3-pentadiene at 100 Torr and 22°C are 0.54±0.02 and 0.42±0.02, respectively. The steady state ratio ([trans]/[cis])_ss is 1.27±0.05 which is almost identical with the ratio of the quantum yields, (ct)/(tc)=1.29±0.10. Thecistrans isomerization is suggested as a useful actinometer for mercury sensitized reactions.

---

Hg 6(³P₁) 1,3- 100 22°C 0,54±0,02 0,42±0,02, . ([]/[]) 1,27±0,05, ( )/( )=1,29±0,10. , .

     

Study of the cis-trans isomerization of enalapril by reversed-phase liquid chromatography

Enalapril is a dipeptidic angiotensin converting enzyme inhibitor. It exists as a mixture of two conformers in solution with respect to the peptide bond involving the proline amino group. The RPLC of such products may yield peak splitting or multiple peaks as a result of the slow kinetics of the conformation change. In this study, the influence of the flow-rate, pH, temperature, organic modifier and counter ion on the peak shape and the separation of the cis and trans conformers are examined qualitatively by HPLC. It appears that decrease of relaxation time for isomerization with concomitant improvement in peak shape is favoured by a decrease in pH and flow-rate, increase of temperature, choice of organic solvent (nature, amount) and cationic counter ion concentration in the mobile phase. The elution order of the isomers was dependent on the nature of the organic modifier whereas the separation selectivity was improved by an increase of pH or the addition of a negatively charged counter ion. In addition, an NMR investigation on enalapril is described.