Solvent Effects on the Energetics of Prolyl Peptide Bond Isomerization

Racemic Ac-Gly-[β,δ-(13)C]Pro-OMe was synthesized, and the kinetics and thermodynamics of the isomerization of its prolyl peptide bond were determined in nine solvents by using NMR and IR spectroscopy. The free energy of activation is 1.3 kcal/mol larger in water than in aprotic solvents, and correlates with the ability of a solvent to donate a hydrogen bond but not with solvent polarity. These results are consistent with conventional pictures of amide resonance, which require transfer of charge between oxygen and nitrogen during isomerization. Similar medium effects may modulate the stability of planar peptide bonds in the active site of peptidyl-prolyl cis-trans isomerases (PPIases) and during the folding, function, or lysis of proteins.     

Inductive Effects on the Energetics of Prolyl Peptide Bond Isomerization: Implications for Collagen Folding and Stability

The hydroxylation of proline residues in collagen enhances the stability of the collagen triple helix. Previous X-ray diffraction analyses had demonstrated that the presence of an electron-withdrawing substituent on the pyrrolidine ring of proline residues has significant structural consequences [Panasik, N., Jr.; Eberhardt, E. S.; Edison, A. S.; Powell, D. R.; Raines, R. T. Int. J. Pept. Protein Res.1994, 44, 262-269]. Here, NMR and FTIR spectroscopy were used to ascertain kinetic and thermodynamic properties of N-acetyl-[β,γ-(13)C]D,L-proline methylester (1); N-acetyl-4(R)-hydroxy-L-proline [(13)C]methylester (2); and N-acetyl-4(R)-fluoro-L-proline methylester (3). The pK(a)'s of the nitrogen atom in the parent amino acids decrease in the order: proline (10.8) > 4(R)-hydroxy-L-proline (9.68) > 4(R)-fluoro-L-proline (9.23). In water or dioxane, amide I vibrational modes decrease in the order: 1 > 2 > 3. At 37 °C in dioxane, the rate constants for amide bond isomerization are greater for 3 than 1. Each of these results is consistent with the traditional picture of amide resonance coupled with an inductive effect that results in a higher bond order in the amide C=O bond and a lower bond order in the amide C-N bond. Further, at 37 °C in water or dioxane equilibrium concentrations of the trans isomer increase in the order: 1 < 2 < 3. Inductive effects may therefore have a significant impact on the folding and stability of collagen, which has a preponderance of hydroxyproline residues, all with peptide bonds in the trans conformation.     

Hydrogen‐Bond Cooperativity in Formamide2–Water: A Model for Water‐Mediated Interactions

The rotational spectrum of formamide₂–H₂O formed in a supersonic jet has been characterized by Fourier‐transform microwave spectroscopy. This adduct provides a simple model of water‐mediated interaction involving the amide linkages, as occur in protein folding or amide‐association processes, showing the interplay between self‐association and solvation. Mono‐substituted ¹³C, ¹⁵N, ¹⁸O, and ²H isotopologues have been observed and their data used to investigate the structure. The adduct forms an almost planar three‐body sequential cycle. The two formamide molecules link on one side through an N?H???O hydrogen bond and on the other side through a water‐mediated interaction with the formation of C=O???H?O and O???H?N hydrogen bonds. The analysis of the quadrupole coupling effects of two ¹⁴N‐nuclei reveals the subtle inductive forces associated to cooperative hydrogen bonding. These forces are involved in the changes in the C=O and C?N bond lengths with respect to pure formamide.     

Toward assessing the position-dependent contributions of backbone hydrogen bonding to beta-sheet folding thermodynamics employing amide-to-ester perturbations

An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.     

Combined use of Overhauser spectroscopy and NMR diffusion experiments for mapping the hydration structure of nucleosides: structure and dynamics of uridine in water

Complementary results from 13C intermolecular nuclear Overhauser effects (NOE), 1H-13C heteronuclear Overhauser spectroscopy (HOSEY) and 1H-NMR diffusion measurements were used for probing the structure of the first solvation shell of uridine in water. It is demonstrated that a cyclic dihydrate is formed. The two water molecules produce two hydrogen bonds with the two oxygen atoms from the pyrimidine ring and accept only one hydrogen bond from the amide proton. The dihydrate has only a short lifetime as compared with the rotational correlation time of the free nucleoside. The chemical exchange constant of the amide proton with water is then estimated by diffusion experiments. The results are consistent with previous data obtained for uracil in water and provide interesting information about water accessibility in nucleic acid bases.     

Peptide bond isosteres: ester or (E)-alkene in the backbone of the collagen triple helix

[structure: see text] Collagen is the most abundant protein in animals. Interstrand N-H...O=C hydrogen bonds between backbone amide groups form a ladder in the middle of the collagen triple helix. Isosteric replacement of the hydrogen-bond-donating amide with an ester or (E)-alkene markedly decreases the conformational stability of the triple helix. Thus, this recurring hydrogen bond is critical to the structural integrity of collagen. In this context, an ester isostere confers more stability than does an (E)-alkene.     

The effect of a trans-locked Gly-Pro alkene isostere on collagen triple helix stability

An alkene isostere of Gly-trans-Pro was synthesized and incorporated into a host Ac-(Gly-Pro-Hyp)8-Gly-Gly-Tyr-NH2 peptide to investigate the effect of locking a proline amide bond. Proline amide bond isomerization is the slow step in collagen folding. By locking the amide, we hypothesized an increase in stability of the collagen triple helix. The substitution instead destabilized the collagen host peptide. The Tm value of the host control peptide was 50.0 degrees C, while the peptide containing the isostere, Ac-(Gly-Pro-Hyp)3-Gly-psi[(E)CH C]-Pro-Hyp-(Gly-Pro-Hyp)4-Gly-Gly-Tyr-NH2, had a Tm value of 28.3 degrees C. There are clearly factors that contribute to collagen stability and folding that we do not yet understand.     

Direct UV Raman monitoring of 3(10)-helix and pi-bulge premelting during alpha-helix unfolding

We used UV resonance Raman (UVRR) spectroscopy exciting at approximately 200 nm within the peptide bond pi --> pi* transitions to selectively study the amide vibrations of peptide bonds during alpha-helix melting. The dependence of the amide frequencies on their Psi Ramachandran angles and hydrogen bonding enables us, for the first time, to experimentally determine the temperature dependence of the peptide bond Psi Ramachandran angle population distribution of a 21-residue mainly alanine peptide. These Psi distributions allow us to easily discriminate between alpha-helix, 3(10)-helix and pi-helix/bulge conformations, obtain their individual melting curves, and estimate the corresponding Zimm and Bragg parameters. A striking finding is that alpha-helix melting is more cooperative and shows a higher melting temperature than previously erroneously observed. These Psi distributions also enable the experimental determination of the Gibbs free energy landscape along the Psi reaction coordinate, which further allows us to estimate the free energy barriers along the AP melting pathway. These results will serve as a benchmark for the numerous untested theoretical studies of protein and peptide folding.     

C[bond]H- - -O hydrogen bonds in beta-sheetlike networks: combined X-ray crystallography and high-pressure infrared study

Close interactions of the C(alpha)[bond]H- - -O type have been analyzed via X-ray crystallography and high-pressure infrared spectroscopy. The results demonstrate that the C(alpha)[bond]H- - -O interactions can offer an additional stability to the beta-sheet formation. X-ray structural data suggest that while 1-acetamido-3-(2-pyrimidinyl)-imidazolium bromide exhibits a bilayer stacking, the PF(6)(-) salt reveals a beta-sheetlike pattern. The appearance of the free-NH infrared absorption indicates that the conventional N[bond]H- - -O or N[bond]H- - -N hydrogen bonds do not fully dominate the packing for the PF(6)(-) salt. The high-pressure infrared study suggests that the C(alpha)[bond]H- - -O hydrogen bonds are the important determinants for the stability of the PF(6)(-) salt. This study also verifies that the imidazolium C[bond]H stretching frequency shifts to a longer wavelength upon the formation of the C[bond]H- - -O hydrogen bonds.     

Monitoring Backbone Hydrogen‐Bond Formation in β‐Barrel Membrane Protein Folding

β‐barrel membrane proteins are key components of the outer membrane of bacteria, mitochondria and chloroplasts. Their three‐dimensional structure is defined by a network of backbone hydrogen bonds between adjacent β‐strands. Here, we employ hydrogen–deuterium (H/D) exchange in combination with NMR spectroscopy and mass spectrometry to monitor backbone hydrogen bond formation during folding of the outer membrane protein X (OmpX) from E. coli in detergent micelles. Residue‐specific kinetics of interstrand hydrogen‐bond formation were found to be uniform in the entire β‐barrel and synchronized to formation of the tertiary structure. OmpX folding thus propagates via a long‐lived conformational ensemble state in which all backbone amide protons exchange with the solvent and engage in hydrogen bonds only transiently. Stable formation of the entire OmpX hydrogen bond network occurs downhill of the rate‐limiting transition state and thus appears cooperative on the overall folding time scale.     

Correlated hydrogen bonding fluctuations and vibrational cross peaks in N-methyl acetamide: simulation based on a complete electrostatic density functional theory map

The coherent nonlinear response of the entire amide line shapes of N-methyl acetamide to three infrared pulses is simulated using an electrostatic density functional theory map. Positive and negative cross peaks contain signatures of correlations between the fundamentals and the combination state. The amide I-A and I-III cross-peak line shapes indicate positive correlation and anticorrelation of frequency fluctuations, respectively. These can be ascribed to correlated hydrogen bonding at C[double bond]O and N-H sites. The amide I frequency is negatively correlated with the hydrogen bond on carbonyl C[double bond]O, whereas the amide A and III are negatively and positively correlated, respectively, with the hydrogen bond on amide N-H.     

Impact of four (13)C-proline isotope labels on the infrared spectra of ribonuclease T1

Ribonuclease T1 was biosynthesized, with all four prolines (13)C-labeled in the peptide C[double bond]O bond, using a proline auxotrophic yeast strain of Saccharomyces cerevisiae. The (13)C- and (12)C-proline isotopomers of ribonuclease T1 were investigated by infrared spectroscopy in the thermally unfolded and natively folded state at 80 and 20 degrees C, respectively. In the thermally unfolded state, both proteins established almost indistinguishable spectral features in the secondary structure sensitive amide I region. In contrast, the spectra measured at 20 degrees C revealed substantial qualitative and quantitative differences, though parallel analysis by circular dichroism suggested identical native folds for both isotopomers. Major spectral differences in the infrared spectra were detected at 1626 and 1679 cm(-1), which are diagnostic marker bands for antiparallel beta-sheets in ribonuclease T1 and at 1645 cm(-1), a region that is characteristic for the infrared absorption of irregular structures. Starting with the known three-dimensional structure of ribonuclease T1, the observed effects of the isotope labeling are discussed on the basis of transition dipole coupling between the (12)C[double bond]O and (13)C[double bond]O groups. The experimental results were confirmed by transition dipole coupling calculations of the amide I manifold of the labeled and unlabeled variant.     

Peptide secondary structure folding reaction coordinate: correlation between uv raman amide III frequency, Psi Ramachandran angle, and hydrogen bonding

We used UV resonance Raman (UVRR) spectroscopy to quantitatively correlate the peptide bond AmIII3 frequency to its Psi Ramachandran angle and to the number and types of amide hydrogen bonds at different temperatures. This information allows us to develop a family of relationships to directly estimate the Psi Ramachandran angle from measured UVRR AmIII3 frequencies for peptide bonds (PBs) with known hydrogen bonding (HB). These relationships ignore the more modest Phi Ramachandran angle dependence and allow determination of the Psi angle with a standard error of +/-8 degrees , if the HB state of a PB is known. This is normally the case if a known secondary structure motif is studied. Further, if the HB state of a PB in water is unknown, the extreme alterations in such a state could additionally bias the Psi angle by +/-6 degrees . The resulting ability to measure Psi spectroscopically will enable new incisive protein conformational studies, especially in the field of protein folding. This is because any attempt to understand reaction mechanisms requires elucidation of the relevant reaction coordinate(s). The Psi angle is precisely the reaction coordinate that determines secondary structure changes. As shown elsewhere (Mikhonin et al. J. Am. Chem. Soc. 2005, 127, 7712), this correlation can be used to determine portions of the energy landscape along the Psi reaction coordinate.     

Magnitudes and chemical consequences of R(3)N(+)-C-H...O[double bond]C hydrogen bonding

The magnitude of the stabilizing interaction between an aliphatic C[bond]H bond attached to an ammonium nitrogen and a carbonyl oxygen was evaluated by ab initio calculations at the MP2/6-311++G** level of theory. Attractive R(3)N(+)-C-H...O[double bond]C interactions play an important role in supramolecular recognition and various types of stereoselective catalysis. Our calculations show that R(3)N(+)-C-H...O[double bond]C is the strongest hydrogen bond of the C-H...O type known to date. Such hydrogen bonds remain as stabilizing interactions even in water for amide acceptors.     

Conformational Stability of Bovine Serum Albumin in Aqueous Amides: A Further Insight into the Mechanism of Urea Acting on the Protein

The binding distances of fluorescein to bovine serum albumin (BSA) in formamide‐water and N,N‐dimethyl‐ formamide‐water mixtures were determined by fluorescence quenching method and compared with the values in urea‐water mixtures in our previous work. The results, together with the analysis of fluorescence spectra, were utilized to probe the conformational stability of protein in aqueous amides, providing a further insight into the mechanism of urea acting on protein. The spectral properties of BSA showed significant difference in the aqueous solutions of the three kinds of amide and indicated that both NH₂ group and C=O group could form hydrogen bond with the protein, serving as donor and acceptor, respectively. However, the results revealed that the multiple hydrogen bonds of NH₂ group with back bond and hydrophilic side chains of the protein played a key role in the nonspecific urea‐mediated network of intramolecular interaction due to its higher hydrogen bonding capability compared to C=O group.     

Coupling of intramolecular hydrogen bonding to the cis-to-trans isomerization of a proline imide bond of small model peptides

A relationship between intramolecular hydrogen bonding and the cis-trans isomerization of a proline imide bond for proline-containing short peptides were studied by proton NMR and infrared spectroscopy using DMSO-d6/CDCl3 mixed solvents. The percentage of the trans form increases with increasing fraction of CDCl3 in the mixed solvents except for compounds without possibility of intramolecular hydrogen bonding. Chemical shift variations of amide protons with solvent mixing ratios were found to be useful for judging whether the amide protons take part in the intramolecular hydrogen bonding to a considerable degree or not. These results and infrared spectra were used to specify intramolecularly hydrogen bonded structures of the peptides. Formation of the 10-membered or 13-membered hydrogen bonded ring which includes the carbonyl group precedent to the prolyl residue facilitates the cis-to-trans isomerization and these hydrogen bonded rings are strong enough to restrict the proline imide bond to the trans form in CDCl3 solution. On the other hand, a 7-membered hydrogen bonded ring is not so effective in restricting the proline imide bond.     

Synthesis and characterization of a family of biodegradable poly(ester amide)s derived from glycine

A series of aliphatic poly(ester amide)s derived from 1,6-hexanediol, glycine, and diacids with a variable number of methylenes (from 2 to 8) have been synthesized and characterized. Infrared spectroscopy shows that the studied polymers present a unique kind of hydrogen bond that is established between their amide groups. Thermal properties as melting, glass transition, and decomposition temperatures are reported. The data indicate that all the polymers are highly crystalline. Thus, different kinds of spherulites (positive and/or negative) were obtained depending on the preparation conditions and on the polymer samples. Moreover, all the polymers crystallized from dilute diol solutions as ribbonlike crystals where a regular folding habit and a single hydrogen bond direction could be deduced. A test of enzymatic hydrolysis was employed to assess the potential biodegradability of these polymers. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 1271–1282, 1998     

蛋白折叠中的暂态结构与表面水分子慢尺度动力学

蛋白表面水的慢尺度动力学行为往往被认为与蛋白的结构稳定性、功能以及折叠过程有关, 但在分子水平上, 还不清楚水分子的慢尺度动力学如何参与蛋白折叠过程. 以Trp-cage蛋白作为个案, 本文利用40条100 ns(总长4 μs)的全原子分子动力学轨迹,分析了蛋白折叠过程中蛋白表面水分子的停留行为,并探究影响蛋白表面水分子慢尺度行为的微观因素. 结果发现, 即使在蛋白折叠过程中蛋白拓扑结构变化很大, 残基之间也会形成稳定的局部暂态结构. 这些结构为水分子提供饱和、稳定的氢键, 通过与水分子之间的极性相互作用, 以及凹形的几何结构, 约束水分子长时停留, 我们称之为“停留中心”. 停留中心的形成是引起水分子慢尺度行为的重要因素. 另外, 停留中心的分布与蛋白折叠的进程有密切关系, 特别地, 在折叠轨迹中, 疏水核周围的残基组成了一个主要的停留中心. 研究结果不但有助于解释水分子慢尺度特征行为的来源, 还可以为实验中通过研究水分子在蛋白附近的慢尺度行为, 揭示蛋白折叠过程中的关键步骤提供一些启发.     

Contribution of intramolecular C=O...H-N hydrogen bonding to the solvent-induced reentrant phase separation of poly(N-isopropylacrylamide)

Changes in the local environment around amide groups of poly(N-isopropylacrylamide) (PNiPA) during a solvent-induced reentrant phase separation have been investigated by infrared spectroscopy combined with quantum chemical calculations. The addition of methanol or tetrahydrofuran as a cosolvent to an aqueous solution of PNiPA causes spectral changes in the amide I regions. By preparing a dimer model compound for PNiPA, we can establish the assignment of the amide I bands for the polymer in solutions. Hydrogen-deuterium exchange experiments of the amide protons of PNiPA and its dimer models have revealed that the amide groups of PNiPA form an intramolecular C=O...H-N hydrogen bond even in a good solvent. The result has suggested that the change in the amide I envelope of PNiPA observed during the solvent-induced phase transition reflects the modification of the intramolecular C=O...H-N hydrogen bond of PNiPA as well as the variation in solvation state of the amide groups. On the basis of the assignment, we have discussed contributions of the intramolecular C=O...H-N hydrogen bond to the phase behavior of PNiPA.     

N[bond]C(alpha) bond dissociation energies and kinetics in amide and peptide radicals. Is the dissociation a non-ergodic process?

Dissociations of aminoketyl radicals and cation radicals derived from beta-alanine N-methylamide, N-acetyl-1,2-diaminoethane, N(alpha)-acetyl lysine amide, and N(alpha)-glycyl glycine amide are investigated by combined density functional theory and M?ller-Plesset perturbational calculations with the goal of elucidating the mechanism of electron capture dissociation (ECD) of larger peptide and protein ions. The activation energies for dissociations of N[bond]C bonds in aminoketyl radicals decrease in the series N[bond]CH(3) > N-CH(2)CH(2)NH(2) > N[bond]CH(2)CONH(2) approximately N[bond]CH(CONH(2))(CH(2))(4)NH(2). Transition state theory rate constants for dissociations of N[bond]C(alpha) bonds in aminoketyl radicals and cation-radicals indicate an extremely facile reaction that occurs with unimolecular rate constants >10(5) s(-1) in species thermalized at 298 K in the gas phase. In neutral aminoketyl radicals the N[bond]C(alpha) bond cleavage results in fast dissociation. In contrast, N[bond]C(alpha) bond cleavage in aminoketyl cation-radicals results in isomerization to ion-molecule complexes that are held together by strong hydrogen bonds. The facile N[bond]C(alpha) bond dissociation in thermalized ions indicates that it is unnecessary to invoke the hypothesis of non-ergodic behavior for ECD intermediates.