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PubMed2004

A novel method of analyzing proline synonymous codons in E. coli.

Proline is a special imino acid in protein and the isomerization of the prolyl peptide bond has notable biological significance and influences the final structure of protein greatly, so the correlation between proline synonymous codon usage and local amino acid, the correlation between proline synonymous codon usage and the isomerization of the prolyl peptide bond were both investigated in the Escherichia coli genome by using a novel method based on information theory. The results show that in peptide chain, the residue at the first position C-terminal influences the usage of proline synonymous codon greatly and proline synonymous codons contain some factors influencing the isomerization of the prolyl peptide bond.

Codon↗
PubMed2026

Simultaneously PYCR-1 and ALH-6 inhibition exacerbates 6-PPD quinone toxicity via disrupting proline and glutamate metabolisms and activating insulin signals in Caenorhabditis elegans.

Glutamate synthesized from the proline can serve as a precursor for key intermediate metabolites of citric acid cycle. Recently, we observed reduced glutamate content and expression of alh-6 controlling glutamate synthesis by 6-PPD quinone (6-PPDQ) in Caenorhabditis elegans. However, possible effect of 6-PPDQ on proline synthesis and the association with 6-PPDQ toxicity induction remain unclear. After 0.1-10 μg/L 6-PPDQ exposure, proline content was further reduced, and expression of pycr-1 governing proline biosynthesis was decreased. In 6-PPDQ exposed nematodes, RNA interference (RNAi) of pycr-1 decreased α-ketoglutarate content, enhanced mitochondrial dysfunction, reduced nicotinamide adenine dinucleotide (NADH) and reduced flavine adenine dinucleotide (FADH₂) contents, inhibited mitochondrial complex I/II activities, and decreased expressions of gas-1 and mev-1. Moreover, compared to single RNAi, double RNAi of pycr-1 and alh-6 exacerbated the 6-PPDQ toxicity in reducing α-ketoglutarate, NADH, and FADH₂ contents, and suppressing mitochondrial complex I/II activities and gas-1 and mev-1 expressions. Additionally, double RNAi of pycr-1 and alh-6 intensified toxicity of 6-PPDQ on longevity and caused upregulation of insulin ligand and receptor genes and downregulation of daf-16 and its targeted genes in 6-PPDQ exposed nematodes. Furthermore, after 6-PPDQ exposure, daf-16 RNAi suppressed pycr-1 and alh-6 expressions, suggesting formation of a regulatory feedback loop between pycr-1/alh-6 and daf-16. Our findings highlight involvement of disrupted proline and glutamate metabolisms in 6-PPDQ-induced mitochondrial dysfunction and reduced longevity.

Animals↗
PubMed2004

Structural basis for the role in protein folding of conserved proline-rich regions in cytochromes P450.

The sequence PPGPXPXPXXGN is highly conserved in some cytochromes P450 across species from humans to plants. Within species, however, this specific sequence is not conserved although a proline-rich sequence is present. In CYP2C proteins, mutagenesis of the prolines and glycine in the PPGPXPXP part of the sequence results in less efficient assembly of native P450 molecules, but those molecules that are formed properly have specific activities similar to wild type suggesting that this region plays a role in folding of the protein. Further, the pattern of requirements for prolines was consistent with a left-handed polyproline II (PPII) helix structure in the PPGP segment. The recent determinations of the structures of CYP2C proteins permit a reinterpretation of these earlier experimental studies. In CYP2C5, the PPGPXPXP part of the sequence is in a left-handed polyproline II-like sequence with a 90 degrees bend at the glycine residue. The PXPXXGN part forms a hairpin structure with the remaining sequence protruding at a right angle. The structure forms tertiary interactions with protein segments centered on Tyr-61, Phe-219, and Tyr-376. van der Waals contacts of the rings of prolines with those of the equally highly conserved tyrosine residues may be particularly important. The proper positioning of the N-terminal segment containing Tyr-61 and the C-terminal segment containing Tyr-376 by interactions with the proline-rich region may be important for proper folding because these residues are in loops extending from four strands of a beta-sheet structure. A schematic model of the sequential folding interactions is presented, and although speculative, it is proposed that constraints required for the folding of a hydrophobic knob that will be inserted into the membrane contribute to the high conservation of the PPGPXPXPXXGN sequence in a subset of cytochromes P450.

Amino Acid Sequence↗
PubMed2004

Polyproline II helix conformation in a proline-rich environment: a theoretical study.

Interest centers here on whether a polyproline II helix can propagate through adjacent non-proline residues, and on shedding light on recent experimental observations suggesting the presence of significant PP(II) structure in a short alanine-based peptide with no proline in the sequence. For this purpose, we explored the formation of polyproline II helices in proline-rich peptides with the sequences Ac-(Pro)(3)-X-(Pro)(3)-Gly-Tyr-NH(2), with X = Pro (PPP), Ala (PAP), Gln (PQP), Gly (PGP), and Val (PVP), and Ac-(Pro)(3)-Ala-Ala-(Pro)(3)-Gly-Tyr-NH(2) (PAAP), by using a theoretical approach that includes a solvent effect as well as cis <--> trans isomerization of the peptide groups and puckering conformations of the pyrrolidine ring of the proline residues. Since (13)C chemical shifts have proven to be useful for identifying secondary-structure preferences in proteins and peptides, and because values of the dihedral angles (phi,psi) are the main determinants of their magnitudes, we have, therefore, computed the Boltzmann-averaged (13)C chemical shifts for the guest residues in the PXP peptide (X = Pro, Ala, Gln, Gly, and Val) with a combination of approaches, involving molecular mechanics, statistical mechanics, and quantum mechanics. In addition, an improved procedure was used to carry out the conformational searches and to compute the solvent polarization effects faster and more accurately than in previous work. The current theoretical work and additional experimental evidence show that, in short proline-rich peptides, alanine decreases the polyproline II helix content. In particular, the theoretical evidence accumulated in this work calls into question the proposal that alanine has a strong preference to adopt conformations in the polyproline II region of the Ramachandran map.

Amino Acid Sequence↗
PubMed1995

13C multiplet nuclear magnetic resonance relaxation-derived ring puckering and backbone dynamics in proline-containing glycine-based peptides.

13CH2-multiplet nuclear magnetic resonance relaxation studies on proline (P)-containing glycine (G)-based peptides, GP, PG, GPG, PGG, and GPGG, provided numerous dipolar auto- and cross-correlation times for various motional model analyses of backbone and proline-ring bond rotations. Molecular dynamics simulations and bond rotation energy profiles were calculated to assess which motions could contribute most to observed relaxation phenomena. Results indicate that proline restricts backbone psi 1, psi 2, and phi 2 motions by 50% relative to those found for a polyglycine control peptide. psi 1 rotations are more restricted in the trans-proline isomer state than in the cis form. A two-state jump model best approximates proline ring puckering which in water could occur either by the C gamma endo-exo or by the C2 interconversion mechanism. The temperature dependence (5 degrees to 75 degrees C) of C beta, and C gamma, and C delta angular changes is rather flat, suggesting a near zero enthalpic contribution to the ring puckering process. In lower dielectric solvents, dimethylsulfoxide and methanol, which may mimic the hydrophobic environment within a protein, the endo-exo mechanism is preferred.

Amino Acid Sequence↗
PubMed1983

Folding of homologous proteins. The refolding of different ribonucleases is independent of sequence variations, proline content and glycosylation.

The refolding kinetics of four different pancreatic ribonucleases have been compared. Bovine and ovine RNAase contain 4 proline residues, red deer RNAase has 5 prolines, the enzyme from roe deer 6 prolines. Despite the variation in the amount of prolines, all four proteins show a constant value of 20% fast refolding species UF. The extra proline residues of the deer enzymes do not increase the amount of slow refolding species US. Consequently these residues may be non-essential for folding. Despite many differences in the amino acid sequence, the rates if the fast and slow refolding reactions are very similar for all investigated ribonucleases. This indicates that the pathway of refolding has been conserved during evolution, i.e. the positions where amino acid substitutions occur are not critically important for the rate-determining steps of the folding process. A carbohydrate chain attached to ribonuclease does not alter the folding properties of the protein: RNAase A and RNAase B from roe deer show identical refolding kinetics.

Amino Acid Sequence↗
PubMed1997

Sodium-dependent proline and glutamate uptake by hippocampal synaptosomes during postnatal development.

NA(+)-dependent uptake of proline and glutamate by hippocampal synaptosomes was studied during postnatal development. At all ages from 9 days to adulthood, hippocampal synaptosomes transported proline by both a high-affinity and a low-affinity process, whereas glutamate was always transported predominantly by a high-affinity process. During the period of rapid synaptogenesis, the KT for high-affinity proline transport overshot the adult value, whereas the KT for glutamate transport increased steadily toward the adult value. The ratio of KT values for proline and glutamate was 2-3 times the adult value between 12 and 24 days of age. Although high-affinity transporters for proline and glutamate are expressed by nearly the same hippocampal pathways, they are differentially regulated during postnatal development.

Animals↗
PubMed1984

Radiochemical purity of [14C]-proline:implications for measurement of intracellular collagen degradation.

Measurement of intracellular degradation of newly synthesized collagen requires use of radiochemically pure [14C]-proline. It is particularly important that levels of contaminating hydroxy-[14C]-proline or other radioactive species that migrate with hydroxyproline on cation-exchange resins be very low. The objective of this study was to determine how far the levels of these impurities could be reduced. Commercially available [14C]-proline was subjected to preparative ion-exchange chromatography. The procedure was capable of adequately separating authentic hydroxyproline from proline, however, upon rechromatography of the "purified" isotope on an analytic resin it was found that background radioactivity in the hydroxyproline region could not be reduced below approximately 500 parts per 10(6) parts of [14C]-proline. The contaminants appear to be generated during the procedure itself, suggesting that further efforts to purify the material would be unproductive. The background level can be a limiting factor in attempting to measure degradation in systems that synthesize very small amounts of collagen.

Animals↗
PubMed2001

Proline residue 280 in the second extracellular loop (EC2) of the VPAC2 receptor is essential for the receptor structure.

Inspection of the amino acid sequence of the human VPAC1 and the VPAC2 receptors after alignment of the conserved residues indicates that the second extracellular loop (EC2) is one amino acid shorter in the VPAC1 receptor due to the lack of a proline residue in position 294. We hypothesized that this could be of importance for receptor structure and/or for ligand recognition. Insertion by directed mutagenesis of a proline in that position ( 294 VPAC1) had little consequence on the binding of several agonists but reduced the affinity for the VPAC1 antagonist. Coupling of the 294 VPAC1 receptor to adenylate cyclase was improved, as demonstrated by an increased affinity for VIP and other agonists, and by a shift of the VPAC1 antagonist to partial agonist behavior. Deletion of the proline 280 (DeltaPro280 VPAC2) in the VPAC2 receptor markedly reduced the apparent affinity for all the agonists tested. Replacement of the proline by a glycine residue had a smaller effect on the ligands affinities. The proline residue in the VPAC2 receptor EC2 is thus essential for the receptor structure, and the EC2 domain is involved in ligand recognition and receptor functionality.

Adenylyl Cyclases↗
PubMed1997

Proline-glutamate interactions in the CNS.

1. Crude synaptosomes (P2) and synaptosomal membranes were prepared from normal C57/B110 mouse brains and Wistar rats respectively. 2. [3H]Pro binding to mouse brain synaptic membranes was examined in the presence of competitive NMDA antagonist, MK-801, or HA-966. Conversely, the effects of l-proline on [3H]MK-801 binding were also probed. The effects of l-proline on glutamate-medicated [Ca+2]i levels were tested. 3. The authors could not detect any effect of proline on glutamate-mediated [CA+2]i levels using FURA-2 in synaptosomes or neuroblastoma cells. 4. NMDA competitive antagonists, AP-7, CPP, and CGS 19755 inhibit [3H]Pro binding to mouse brain synaptic membranes. 5. MK-801, a NMDA channel blocker, also inhibits [3H]Pro binding, but 200 mM proline is incapable of inhibiting [3H]MK-801 binding. 6. HA-966, a glycine site partial agonist inhibits [3H]Pro binding. Proline has modest effects on [3H]glycine binding.

Animals↗
PubMed1999

Catabolism of proline by procyclic culture forms of Trypanosoma congolense.

The effect of various metabolic inhibitors on the rate of oxygen consumption by procyclic culture forms of Trypanosoma congolense utilizing proline as substrate was investigated. Cyanide inhibited the rate of oxygen consumption by 81.0 +/- 6.7%, malonate inhibited the rate by 51.6 +/- 1.6% and Antimycin A by 73.1 +/- 5.9%. A combination of cyanide and malonate inhibited the rate of oxygen consumption by 84.9 +/- 6.7% while a combination of antimycin A and malonate inhibited the rate by 81.6 +/- 7.6%. Rotenone had no effect on the rate of respiration except when the intact cells were first permeabilized by digitonin after which rotenone decreased the rate of respiration by 20-30%. Salicylhydroxamate (SHAM) did not have any effect on the rate of oxygen consumption. Enzymes involved in the catabolism of proline with high activities were: proline dehydrogenase, alpha-ketoglutarate dehydrogenase, succinate dehydrogenase, fumarase, NADP-linked malic enzyme, alanine aminotransferase and malate dehydrogenase. Activities of 1-pyrroline-5 carboxylate dehydrogenase, glutamate dehydrogenase, aspartate aminotransferase and NAD-linked malic enzyme were detectable but lower. The end products of proline catabolism were alanine and glutamate. Unlike the case in Trypanosoma brucei brucei aspartate was not detected. Possible pathways of proline catabolism in procyclic culture forms of T. congolense and of electron transfer are proposed.

Animals↗
PubMed1983

Azetidine-2-carboxylic acid contaminated dietary proline as a cause of urinary excretion of 4-amino-2-(S-cysteinyl)butyric acid in patients on oral treatment with a synthetic diet.

Three children with branched-chain ketoaciduria (maple syrup urine disease) were found to excrete an abnormal amino acid when they were on an artificial diet. This substance was identified as 4-amino-2-(S-cysteinyl)butyric acid with the use of column liquid chromatography, gas chromatography--mass spectrometry of various derivatives, and 360 MHz 1H-NMR spectroscopy. The same compound was detected in urine samples from subjects undergoing an oral loading test with L-proline. The chromatographic analysis of commercial proline from two sources indicated that one of the batches was contaminated (less than 1%) with L-azetidine-2-carboxylic acid (the homologue of proline with a four-membered ring). The latter compound is probably metabolized by the human via ring-opening and addition of a cysteine moiety. It is highly probable that the artificial diet given to the patients contained the impure proline and that the L-azetidine-2-carboxylic acid in the proline gave rise to the excretion of the 4-amino-2-(S-cysteinyl)butyric acid.

Azetidinecarboxylic Acid↗
PubMed2000

[Proline accumulation by tomato leaf tissue in response to salinity].

The capacity of tomato leaf tissues to accumulate proline in response to a salt shock (150 mM NaCl) applied to excised shoots, leaves, leaflets or leaf discs was determined and compared to that of whole plants grown at the same salinity. The associated changes in free amino acids, Na+, K+ and Cl- contents were also investigated. In excised organs treated for 80 h, up to 200 mumol g-1 DW of proline were accumulated, whereas the amount of proline in leaf discs did not exceed a value ten-fold lower. In the whole plants subjected to salinity the Na+, Cl- and K+ contents remained low in comparison to that observed in excised organs. Proline and other amino acids increased more slowly in whole plants than in excised shoots. The contribution of roots and vascular tissues to the control of Na+ and Cl- accumulation and to the regulation of proline metabolism are discussed.

Amino Acids↗
PubMed2002

Proline biosynthesis genes and their regulation under salinity stress in the euryhaline copepod Tigriopus californicus.

Diverse organisms regulate concentrations of intracellular organic osmolytes in response to changes in environmental salinity or desiccation. In marine crustaceans, accumulation of high concentrations of proline is a dominant component of response to hyperosmotic stress. In the euryhaline copepod Tigriopus californicus, synthesis of proline from its metabolic precursor glutamate is tightly regulated by changes in environmental salinity. Here, for the first time in a marine invertebrate, the genes responsible for this pathway have been cloned and characterized. The two proteins display the sequence features of homologous enzymes identified from other eukaryotes. One of the cloned genes, delta1-pyrroline-5-carboxylase reductase (P5CR), is demonstrated to have the reductase enzyme activity when expressed in proline-auxotroph bacteria, while the second, delta1-pyrroline-5-carboxylase synthase (P5CS), does not rescue proline-auxotroph bacteria. In contrast to results from higher plants, neither levels of P5CS nor P5CR mRNAs increase in response to salinity stress in T. californicus. Hence, regulation of proline synthesis during osmotic stress in T. californicus is likely mediated by some form of post-transcriptional regulation of either P5CS or P5CR. Understanding the regulation this pathway may elucidate the mechanisms limiting the salinity ranges of marine taxa.

Amino Acid Sequence↗
PubMed1991

Folding of chymotrypsin inhibitor 2. 2. Influence of proline isomerization on the folding kinetics and thermodynamic characterization of the transition state of folding.

The refolding of chymotrypsin inhibitor 2 (CI2) is, at least, a triphasic process. The rate constants are 53 s-1 for the major phase (77% of the total amplitude) and 0.43 and 0.024 s-1 for the slower phases (23% of the total amplitude) at 25 degrees C and pH 6.3. The multiphase nature of the refolding reaction results from heterogeneity in the denatured state because of proline isomerization. The fast phase corresponds to the refolding of the fraction of protein that has all its prolines in a native trans conformation in the denatured state. It is not catalyzed by peptidyl-prolyl isomerase. The rate-limiting step of folding for the slower phases, however, is proline isomerization, and they are both catalyzed by peptidyl-prolyl isomerase. The slowest phase has properties consistent with a process involving proline isomerization in a denatured state. In particular, the activation enthalpy is large, 16 kcal mol-1 K-1, and the rate is independent of guanidinium chloride concentration ([GdnHCl]). In comparison, the intermediate phase shows properties consistent with a process involving proline isomerization in a partially structured state. The activation enthalpy is small, 8 kcal mol-1 K-1, and the rate has a strong dependence on [GdnHCl]. Temperature dependences of the rate constants for unfolding and for the fast refolding phase, both in the absence and in the presence of GdnHCl, were used to characterize the thermodynamic nature of the transition state and its relative exposure to solvent. The Eyring plot for unfolding is linear, indicating that there is relatively little change in heat capacity between native state and transition state.(ABSTRACT TRUNCATED AT 250 WORDS)

Catalysis↗
PubMed1991

Proline for alanine substitutions in the C-peptide helix of ribonuclease A.

The effect on overall alpha-helix content of substituting proline for alanine has been determined at 5 positions (1, 2, 4, 5, and 13) of a 13-residue peptide related in sequence to residues 1-13 of ribonuclease A. The helix content falls off rapidly as proline is moved inward, and the proline residue effectively truncates the helix. No helix-stabilizing effect of proline is found at positions 2 or 4 within the first turn of the helix. Proline substitution at either end position (1, 13) has little effect on overall helix content, in agreement with an earlier study of glycine for alanine substitutions. The two end residues of the helix appear to be strongly frayed.

Alanine↗
PubMed1983

Isomerization of proline-93 during the unfolding and refolding of ribonuclease A.

Using the method of isomer-specific proteolysis, the isomerization of proline-93 has been monitored directly during the time course of the unfolding and refolding reactions of RNase A. It has been found that proline-93 is 100% cis in the native protein and 70% cis in the reversibly unfolded protein. During the unfolding reaction, the change from 100% to 70% cis occurs as a first-order process with a relaxation time of 140 s in 8.5 M urea, 10 degrees C. For refolding, the change from 70% to 100% cis also occurs as a first-order process, with a relaxation time (10 degrees C) of 90 s in 0.3 M urea, 130 s in 1.0 M urea, and 310 s in 2.0 M urea. Parallel experiments which measured the recovery of enzyme activity during refolding were also conducted. These show that 30% of the activity recovers in a slow phase with a first-order relaxation time (10 degrees C) of 100 s in 0.3 M urea. Because of the excellent agreement of both the amplitude and relaxation time for trans-to-cis isomerization and for activity recovery, it is concluded that the slowest phase in the recovery of enzyme activity is rate limited by the isomerization of proline-93. These results demonstrate that proline-93 must be cis before refolding to the active form can take place, in contrast to previous suggestions, and argue against the existence of a nativelike intermediate form on the refolding pathway which contains proline-93 in the incorrect trans configuration.

Animals↗
PubMed1986

Basic proline-rich proteins from human parotid saliva: complete covalent structures of proteins IB-1 and IB-6.

The complete amino acid sequences of two basic proline-rich proteins, IB-1 and IB-6, from human parotid saliva have been determined. Fragments for sequence analysis were obtained by enzymatic digestions. The proteins have molecular weights of 9571 (IB-1) and 11,530 (IB-6) and contain 34 and 39 mol % proline, respectively. IB-1 and IB-6 contain an identical sequence of 54 residues except for an alanine in position 52 of IB-6, where IB-1 has proline. An unusually high number of repeated sequences occurs in both molecules. IB-1 has a blocked amino-terminal residue, pyroglutamic acid, and also contains one phosphoserine residue in position 8. The relationship of these proteins to the basic proline-rich protein IB-9 [Kauffman, D., Wong, R., Bennick, A., & Keller, P. (1982) Biochemistry 21, 6558-6562] and to other salivary proline-rich proteins is discussed.

Amino Acid Sequence↗