Proline cis-trans isomerization and protein folding

Proline cis-trans isomerization plays a key role in the rate-determining steps of protein folding. The energetic origin of this isomerization process is summarized, and the folding and unfolding of disulfide-intact bovine pancreatic ribonuclease A is used as an example to illustrate the kinetics and structural features of conformational changes from the heterogeneous unfolded state (consisting of cis and trans isomers of X-Pro peptide groups) to the native structure in which only one set of proline isomers is present.     

Prolyl cis-trans isomerization as a molecular timer

Proline is unique in the realm of amino acids in its ability to adopt completely distinct cis and trans conformations, which allows it to act as a backbone switch that is controlled by prolyl cis-trans isomerization. This intrinsically slow interconversion can be catalyzed by the evolutionarily conserved group of peptidyl prolyl cis-trans isomerase enzymes. These enzymes include cyclophilins and FK506-binding proteins, which are well known for their isomerization-independent role as cellular targets for immunosuppressive drugs. The significance of enzyme-catalyzed prolyl cis-trans isomerization as an important regulatory mechanism in human physiology and pathology was not recognized until the discovery of the phosphorylation-specific prolyl isomerase Pin1. Recent studies indicate that both phosphorylation-dependent and phosphorylation-independent prolyl cis-trans isomerization can act as a novel molecular timer to help control the amplitude and duration of a cellular process, and prolyl cis-trans isomerization might be a new target for therapeutic interventions.     

Wavelength dependent cis-trans isomerization in vision.

The primary event in vision is the light-driven cis-trans isomerization of the 11-cis-retinal chromophore in the G-protein coupled receptor rhodopsin. Early measurements showed that this photoisomerization has a reaction quantum yield phi of approximately 0.67 [Dartnall (1936) Proc. R. Soc. A 156, 158-170; Dartnall (1968) Vision Res. 8, 339-358] and suggested that the quantum yield was wavelength independent [Schneider (1939) Proc. Natl. Acad. Sci. U.S.A. 170, 102-112]. Here we more accurately determine phi(500) = 0.65 +/- 0.01 and reveal that phi surprisingly depends on the wavelength of the incident light. Although there is no difference in the quantum yield between 450 and 480 nm, the quantum yield falls significantly as the photon energy is reduced below 20 000 cm(-1) (500 nm). At the reddest wavelength measured (570 nm), the quantum yield is reduced by 5 +/- 1% relative to the 500 nm value. These experiments correct the long-held presumption that the quantum yield in vision is wavelength independent, and support the hypothesis that the 200 fs photoisomerization reaction that initiates vision is dictated by nonstationary excited-state vibrational wave packet dynamics.     

UV-induced cis-trans isomerization of zearalenone in contaminated maize

In the literature, it has been shown that the naturally occurring trans-zearalenone (ZEN) is transformed by ultraviolet irradiation to cis-ZEN. However, the practical relevance of this transformation in animal feeding remains unclear. The aim of the present preliminary investigation was to examine the effect of UV-irradiation on the concentration of trans-ZEN in a natural feed matrix at different dry matter contents to simulate the dry and wet feeding techniques usually applied in pig feeding. Four variants, air dry or wet ZEN-contaminated ground maize either irradiated or not were tested and analysed with conventional HPLC-FLD for trans-ZEN changes, which were further examined for cis-ZEN formation by HPLC-MS/MS. In conclusion, it could be shown that, under the investigated wet feed conditions, naturally occurring trans-ZEN was partially converted by ultraviolet irradiation to its cis counterpart. In contrast, the cis/trans isomerization seemed not to be relevant in dry maize. The consequence of this finding for practical liquid feeding systems for pigs requires further investigation. Additionally, an improvement of the analytical method for cis-ZEN determination is needed.     

Proline cis-trans isomerization controls autoinhibition of a signaling protein

Autoinhibition is being widely used in nature to repress otherwise constitutive protein activities and is typically regulated by extrinsic factors. Here we show that autoinhibition can be controlled by an intrinsic intramolecular switch afforded by prolyl cis-trans isomerization. We find that a proline on the linker tethering the two SH3 domains of the Crk adaptor protein interconverts between the cis and trans conformation. In the cis conformation, the two SH3 domains interact intramolecularly, thereby forming the basis of an autoinhibitory mechanism. Conversely, in the trans conformation Crk exists in an extended, uninhibited conformation that is marginally populated but serves to activate the protein upon ligand binding. Interconversion between the cis and trans, and, hence, of the autoinhibited and activated conformations, is accelerated by the action of peptidyl-prolyl isomerases. Proline isomerization appears to make an ideal switch that can regulate the kinetics of activation, thereby modulating the dynamics of signal response.     

Effects of proline cis-trans isomerization on TB domain secondary structure.

The transforming growth factor beta (TGF-beta) binding protein-like (TB) domain is found principally in proteins localized to extracellular matrix fibrils, including human fibrillin-1, the defective protein in the Marfan syndrome. Analysis of the nuclear magnetic resonance (NMR) data for the sixth TB module from human fibrillin-1 has revealed the existence of two stable conformers that differ in the isomerization states of two proline residues. Unusually, the two isoforms do not readily interconvert and are stable on the time scale of milliseconds. We have computed independent structures of the major and minor conformers of TB6 to assess how the domain fold adjusts to incorporate alternatively cis- or trans-prolines. Based on previous observations, it has been suggested that multiple conformers can only be accommodated in flexible regions of protein structure. In contrast, P22, which exists in trans in the major form and cis in the minor form of TB6, is in a rigid region of the domain, which is confirmed by backbone dynamics measurements. Overall, the structures of the major and minor conformers are similar. However, the secondary structure topologies of the two forms differ as a direct consequence of the changes in proline conformation.     

Mechanism of cis-trans isomerization of unsaturated fatty acids in Pseudomonas putida

We studied the pattern of the cis-trans isomerization of unsaturated fatty acids in cells of Pseudomonas putida S12 grown in a medium supplemented with oleic acid which was deuterated at both of the C atoms of its double bond. Direct evidence that isomerization does not include a transient saturation of the double bond was obtained. In addition, analysis of the amino acid sequences of the seven known Cti proteins identified them as heme-containing proteins of the cytochrome c type.     

Peptidyl-prolyl cis-trans isomerase does not affect the Pro-43 cis-trans isomerization rate in folded calbindin D9k

The calcium-binding protein calbindin D9k has previously been shown to exist in two folded forms only differing in the proline cis-trans isomerism of the Gly-42-Pro-43 amide bond. This bond is located in a flexible loop connecting the two EF-hand Ca2+ sites. Calbindin D9k therefore constitutes a unique test case for investigating if the recently discovered enzyme peptidyl-prolyl cis-trans isomerase (PPIase) can affect the cis-trans exchange rate in a folded protein. The 1H NMR saturation transfer technique has been used to measure the rate of interconversion between the cis and trans forms of calbindin in the presence of PPIase (PPIase:calbindin concentration ratio 1:10) at 35 degrees C. No rate enhancement could be detected.     

Enzyme-like effect of metmyoglobin on the thermal cis-trans isomerization of stilbazolium betaine

cis →trans isomerization. A study of the pH and ionic strength dependence of the isomerization reaction rate of the photochrome associated with metmyoglobin was perfomed. A comparative investigation of the reaction carried out in the presence of three proteins, metmyoglobin, apomyoglobin, and human albumin, indicates a specific influence of the heme pocket environment on the reaction. Possible mechanisms of the reaction acceleration are considered. Received: 8 December 1999 / Accepted: 15 February 2000     

The cis-trans isomerization of aromatic heptaenes catalyzed by sulfur and phosphorus compounds]

It was shown that sulfur and phosphorus compounds (sodium thiosulfate, sodium tripolyphosphate, sodium hexametaphosphate, monosodium phosphate) catalyze cis-trans isomerization of aromatic heptaens. Preparative method of levorin isomerezation at the presence of sodium thiosulfate was elaborated. The isolated product was a fully trans-isomer.     

Dose-effect of dietary oleic acid: oleic acid is conditionally essential for some organs

The minimum dietary intake of oleic acid that is indispensable to maintain a normal content of this fatty acid in several tissues (heart, muscle, kidney and testis) was determined in the rat. For this purpose, a dose-effect study was conducted using an experimental protocol with 7 groups of rats who received a diet in which the oleic acid level varied from 0 to 6000 mg per 100 g diet, but the other ingredients were identical (in particular the essential fatty acids, linoleic and alpha-linolenic acid). Female rats were fed the diets from two weeks before mating, and their pups were killed aged either 21 or 60 days. When the level of oleic acid in the diet was increased, the main modifications observed in 21-day-old deficient pups were as follows: (i) for 18:1n-9, in the liver, muscle, heart, kidney, and testis, a plateau was reached at about 4 g oleic acid per 100 g diet. Below this level, the higher the dose the greater the response; (ii) for 16:1n-7, the concentration decreased in the liver, muscle, heart, kidney and testis; (iii) the concentration of 18:1n-7 decreased in the kidney, muscle, and testis; (iv) some minor modifications were noted for the other fatty acids. In mother's milk at 14 days of lactation, when dietary oleic acid increased, the levels of 18:1(n-9) also increased; the increase was regular and did not reach a plateau. In 60-day-old rats, the results were generally similar to those in 21-day-old rats, but with some differences, in particular a slight decrease in oleic acid concentration in the liver and kidney at the highest dietary oleic acid level.     

Protein dynamics and enzymatic catalysis: investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A

A growing body of evidence suggests a connection between protein dynamics and enzymatic catalysis. In this paper, we present a variety of computational studies designed to investigate the role of protein dynamics in the detailed mechanism of peptidyl-prolyl cis-trans isomerization catalyzed by human cyclophilin A. The results identify a network of protein vibrations, extending from surface regions of the enzyme to the active site and coupled to substrate turnover. Indications are that this network may have a role in promoting catalysis. Crucial parts of this network are found to be conserved in 10 cyclophilin structures from six different species. Experimental evidence for the existence of this network comes from previous NMR relaxation studies, where motions in several residues, forming parts of this network, were detected only during substrate turnover. The high temperature factors (from X-ray crystal structures) associated with the network residues provide further evidence of these vibrations. Along with the knowledge of enzyme structure, this type of network could provide new insights into enzymatic catalysis and the effect of distant ligand binding on protein function. The procedure outlined in this paper is general and can be applied to other enzymatic systems as well. This presents an interesting opportunity; collaborative experimental and theoretical investigations designed to characterize in detail the nature and function of this type of network could enhance the understanding of protein dynamics in enzymatic catalysis.     

Site-specific NMR monitoring of cis-trans isomerization in the folding of the proline-rich collagen triple helix

Understanding the folding of the proline-rich collagen triple helix requires consideration of the effects of proline cis-trans isomerization and may shed light on the misfolding of collagen in connective tissue diseases. Folding was monitored in real time by heteronuclear 2D NMR spectroscopy for the (15)N labeled positions in the triple-helical peptide T1-892 [GPAGPAGPVGPAGARGPAGPOGPOGPOGPOGV]. In the equilibrium unfolded monomer form, each labeled residue showed multiple peaks with interconversion rates consistent with cis-trans isomerization of Gly-Pro and Pro-Hyp bonds. Real-time NMR studies on the folding of T1-892 showed slow decay of monomer peaks and a concomitant increase in trimer peaks. Gly25 in the C-terminal rich (Gly-Pro-Hyp)(4) domain folds first, consistent with its being a nucleation domain. Analysis of the kinetics indicates that the folding of Gly25 is biphasic and the slower step represents cis-trans isomerization of imino acids. This illustrates that nucleation is limited by cis-trans isomerization. Monitoring Gly6, Gly10, Ala12, and Gly13 monomer and trimer peaks captures the C- to N-terminal propagation of the triple helix, which is also limited by Gly-Pro cis-trans isomerization events. The zipper-like nature of the propagation process is confirmed by the slower rate of folding of Ala6 compared to Gly13, reflecting the larger number of isomerization events encountered by the more N-terminal Ala6. The cis-trans isomerization events at multiple proline residues is a complex statistical process which can be visualized by these NMR studies.     

Photochemical cis-trans isomerization of furylacryloylpeptides and their different kinetic behavior as substrates for carboxypeptidase Y

Furylacryloyl substrates used in kinetic measurements of proteolytic enzymes are shown to cis-trans photoisomerize quickly in plain daylight. The enzymatic transformation of the two forms is sufficiently different to cause problems for such measurements without careful protection against light.     

Compact oleic acid in HAMLET

HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a complex between alpha-lactalbumin and oleic acid that induces apoptosis in tumor cells, but not in healthy cells. Heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the structure of 13C-oleic acid in HAMLET, and to study the 15N-labeled protein. Nuclear Overhauser enhancement spectroscopy shows that the two ends of the fatty acid are in close proximity and close to the double bond, indicating that the oleic acid is bound to HAMLET in a compact conformation. The data further show that HAMLET is a partly unfolded/molten globule-like complex under physiological conditions.     

Identification of activities that catalyze the cis-trans isomerization of the double bond of a mono-unsaturated fatty acid in Pseudomonas sp. strain E-3

A cell-free extract of Pseudomonas sp. strain E-3 catalyzed the conversion of 9-cis-hexadecenoic acid [16:1(9c)] to 9-trans-hexadecenoic acid [16:1(9t)] in the free acid form and when 16:1(9c) was esterified to phosphatidylethanolamine (PE). The cytosolic fraction catalyzed the isomerizations of free 16:1(9c) by itself and of 16:1(9c) esterified to PE in the presence of the membrane fraction. Tracer experiments using [2,2-²H₂]16:1(9c) demonstrated that the isomerization of free 16:1(9c) occurred independently of the isomerization of 16:1(9c) esterified to PE, indicating that this bacterium has two types of activities that catalyze the cis-trans isomerization of the double bond of a mono-unsaturated fatty acid. Received: 29 December 1995 / Accepted: 10 April 1996     

A crystallographic study of bright far-red fluorescent protein mKate reveals pH-induced cis-trans isomerization of the chromophore

The far-red fluorescent protein mKate (lambda(ex), 588 nm; lambda(em), 635 nm; chromophore-forming triad Met(63)-Tyr(64)-Gly(65)), originating from wild-type red fluorescent progenitor eqFP578 (sea anemone Entacmaea quadricolor), is monomeric and characterized by the pronounced pH dependence of fluorescence, relatively high brightness, and high photostability. The protein has been crystallized at a pH ranging from 2 to 9 in three space groups, and four structures have been determined by x-ray crystallography at the resolution of 1.75-2.6 A. The pH-dependent fluorescence of mKate has been shown to be due to reversible cis-trans isomerization of the chromophore phenolic ring. In the non-fluorescent state at pH 2.0, the chromophore of mKate is in the trans-isomeric form. The weakly fluorescent state of the protein at pH 4.2 is characterized by a mixture of trans and cis isomers. The chromophore in a highly fluorescent state at pH 7.0/9.0 adopts the cis form. Three key residues, Ser(143), Leu(174), and Arg(197) residing in the vicinity of the chromophore, have been identified as being primarily responsible for the far-red shift in the spectra. A group of residues consisting of Val(93), Arg(122), Glu(155), Arg(157), Asp(159), His(169), Ile(171), Asn(173), Val(192), Tyr(194), and Val(216), are most likely responsible for the observed monomeric state of the protein in solution.     

Microbial oxidation of oleic acid.

Resting cells of Saccharomyces cerevisiae (baker's yeast, type II; Sigma) were used to convert oleic acid into 10-hydroxyoctadecanoic acid with a 45% yield. Nocardia aurantia (ATCC 12674), Nocardia sp. (NRRL 5646), and Mycobacterium fortuitum (UI 53378) all converted oleic acid into 10-oxo-octadecanoic acid with 65, 55, and 80% yields, respectively. Structures of all metabolites were suggested by 1H and 13C nuclear magnetic resonance and by infrared and mass spectrometry. Structures of isomeric hydroxystearate and oxostearate derivatives and the stereochemical purity of hydroxystearates are difficult to prove unambiguously unless authentic standard compounds are available for spectral comparison. We describe the use of the chemical Baeyer-Villiger oxidation technique with 10-oxo-octadecanoic acid followed by mass spectral analysis of neutral extracts as a simple method to confirm the position of oxo-functional groups in the structures of fatty acid ketones. We further introduce a simple method based on 1H nuclear magnetic resonance analysis of diastereomeric S-(+)-O-acetylmandelate esters of hydroxystearates as a means of ascertaining stereochemical purities of hydroxy fatty acids.