Peptide bonds revisited

Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation

Background

Polypeptides are composed of amino acids covalently bonded via a peptide bond. The majority of peptide bonds in proteins is found to occur in the trans conformation. In spite of their infrequent occurrence, cis peptide bonds play a key role in the protein structure and function, as well as in many significant biological processes.

Results

We perform a systematic analysis of regions in protein sequences that contain a proline cis peptide bond in order to discover non-random associations between the primary sequence and the nature of proline cis/trans isomerization. For this purpose an efficient pattern discovery algorithm is employed which discovers regular expression-type patterns that are overrepresented (i.e. appear frequently repeated) in a set of sequences. Four types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, iii) pattern discovery using a structural equivalency set and iv) pattern discovery using certain amino acids' physicochemical properties. The extracted patterns are carefully validated using a specially implemented scoring function and a significance measure (i.e. log-probability estimate) indicative of their specificity. The score threshold for the first three types of pattern discovery is 0.90 while for the last type of pattern discovery 0.80. Regarding the significance measure, all patterns yielded values in the range [-9, -31] which ensure that the derived patterns are highly unlikely to have emerged by chance. Among the highest scoring patterns, most of them are consistent with previous investigations concerning the neighborhood of cis proline peptide bonds, and many new ones are identified. Finally, the extracted patterns are systematically compared against the PROSITE database, in order to gain insight into the functional implications of cis prolyl bonds.

Conclusion

Cis patterns with matches in the PROSITE database fell mostly into two main functional clusters: family signatures and protein signatures. However considerable propensity was also observed for targeting signals, active and phosphorylation sites as well as domain signatures.

Support vector machines for prediction of peptidyl prolyl cis/trans isomerization

A new method for peptidyl prolyl cis/trans isomerization prediction based on the theory of support vector machines (SVM) was introduced. The SVM represents a new approach to supervised pattern classification and has been successfully applied to a wide range of pattern recognition problems. In this study, six training datasets consisting of different length local sequence respectively were used. The polynomial kernel functions with different parameter d were chosen. The test for the independent testing dataset and the jackknife test were both carried out. When the local sequence length was 20-residue and the parameter d = 8, the SVM method archived the best performance with the correct rate for the cis and trans forms reaching 70.4 and 69.7% for the independent testing dataset, 76.7 and 76.6% for the jackknife test, respectively. Matthew's correlation coefficients for the jackknife test could reach about 0.5. The results obtained through this study indicated that the SVM method would become a powerful tool for predicting peptidyl prolyl cis/trans isomerization.

Estimating the "steric clash" at cis peptide bonds

To account for the scarcity of cis peptide bonds in proteins, especially in nonproline (or secondary amide) cases, a steric-clash argument is often put forward, in a scheme where the R lateral chains are facing parallel one another, and the backbone is kept in an "all- trans"-like arrangement. Although such a steric conflict can be partly relieved through proper adjustment of the backbone dihedral angles, one can try to estimate its associated energy cost. To this end, quantum-chemistry approaches using a differential-torsion protocol and bond-separation-energy analyses are applied to N-ethyl propionamide CH3-CH2-CO-NH-CH2-CH3, regarded as a model capable of exhibiting C beta...C beta interaction as in alanine succession. The calculations provide an increment of 9 kcal/mol, quite close to that obtained in the nearly isostere (gsg) rotamer of n-hexane (10 kcal/mol), suggesting the local effects induced by methyl-methyl contact are similar in both cases. Analogous treatments on larger radicals as encountered in leucine or phenylalanine dimers do not change this increment much, which therefore defines the basic reference per-plaque quota to be overcome along all- cis chains. Explicit modeling indicated it can be reduced by up to a factor of 4.

Prediction of cis/trans isomerization using feature selection and support vector machines

In protein structures the peptide bond is found to be in trans conformation in the majority of the cases. Only a small fraction of peptide bonds in proteins is reported to be in cis conformation. Most of these instances (>90%) occur when the peptide bond is an imide (X-Pro) rather than an amide bond (X-nonPro). Due to the implication of cis/trans isomerization in many biologically significant processes, the accurate prediction of the peptide bond conformation is of high interest. In this study, we evaluate the effect of a wide range of features, towards the reliable prediction of both proline and non-proline cis/trans isomerization. We use evolutionary profiles, secondary structure information, real-valued solvent accessibility predictions for each amino acid and the physicochemical properties of the surrounding residues. We also explore the predictive impact of a modified feature vector, which consists of condensed position-specific scoring matrices (PSSMX), secondary structure and solvent accessibility. The best discriminating ability is achieved using the first feature vector combined with a wrapper feature selection algorithm and a support vector machine (SVM). The proposed method results in 70% accuracy, 75% sensitivity and 71% positive predictive value (PPV) in the prediction of the peptide bond conformation between any two amino acids. The output of the feature selection stage is investigated in order to identify discriminatory features as well as the contribution of each neighboring residue in the formation of the peptide bond, thus, advancing our knowledge towards cis/trans isomerization.

Predicting peptide bond conformation using feature selection and the Naïve Bayes approach

Distinguishing cis peptide bonds from trans isomers in protein sequences facilitates the exploration of protein structures and functions. In this study, we evaluated the effect of a large and informative feature vector, towards the reliable prediction of peptide bond conformation between any two amino acids. We used multiple sequence alignment, secondary structure information, real valued solvent accessibility predictions for each amino acid and physicochemical properties of the surrounding residues. A three stage schema was developed, comprising of feature extraction, feature selection and peptide bond classification between any two amino acids. We also explored the performance achieved when using the full feature vector without performing feature selection. The best discriminating ability was achieved using a Naïve Bayes classifier, combined with wrapper feature selection. The proposed approach yielded prediction accuracy 86%, sensitivity 82% and specificity 90% in discriminating cis and trans peptide bond conformations.

Enhanced stability of cis Pro-Pro peptide bond in Pro-Pro-Phe sequence motif

Identification of sequence motifs that favor cis peptide bonds in proteins is important for understanding and designing proteins containing turns mediated by cis peptide conformations. From (1)H NMR solution studies on short peptides, we show that the Pro-Pro peptide bond in Pro-Pro-Phe almost equally populates the cis and trans isomers, with the cis isomer stabilized by a CHc...pi interaction involving the terminal Pro and Phe. We also show that Phe is over-represented at sequence positions immediately following cis Pro-Pro motifs in known protein structures. Our results demonstrate that the Pro-Pro cis conformer in Pro-Pro-Phe sequence motifs is as important as the trans conformer, both in short peptides as well as in natively folded proteins.

Cation-Modulated Electron-Transfer Channel: H-Atom Transfer vs Proton-Coupled Electron Transfer with a Variable Electron-Transfer Channel in Acylamide Units

The mechanism of proton transfer (PT)/electron transfer (ET) in acylamide units was explored theoretically using density functional theory in a representative model (a cyclic coupling mode between formamide and the N-dehydrogenated formamidic radical, FF). In FF, PT/ET normally occurs via a seven-center cyclic proton-coupled electron transfer (PCET) mechanism with a N-->N PT and an O-->O ET. However, when different hydrated metal ions are bound to the two oxygen sites of FF, the PT/ET mechanism may significantly change. In addition to their inhibition of PT/ET rate, the hydrated metal ions can effectively regulate the FF PT/ET cooperative mechanism to produce a single pathway hydrogen atom transfer (HAT) or a flexible proton coupled electron transfer (PCET) mechanism by changing the ET channel. The regulation essentially originates from the change in the O...O bond strength in the transition state, subject to the binding ability of the hydrated metal ions. In general, the high valent metal ions and those with large binding energies can promote HAT, and the low valent metal ions and those with small binding energies favor PCET. Hydration may reduce the Lewis acidity of cations, and thus favor PCET. Good correlations among the binding energies, barrier heights, spin density distributions, O...O contacts, and hydrated metal ion properties have been found, which can be used to interpret the transition in the PT/ET mechanism. These findings regarding the modulation of the PT/ET pathway via hydrated metal ions may provide useful information for a greater understanding of PT/ET cooperative mechanisms, and a possible method for switching conductance in nanoelectronic devices.

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.

Proline isomerization of histone H3 regulates lysine methylation and gene expression

The cis-trans isomerization of proline serves as a regulatory switch in signaling pathways. We identify the proline isomerase Fpr4, a member of the FK506 binding protein family in Saccharomyces cerevisiae, as an enzyme which binds the amino-terminal tail of histones H3 and H4 and catalyses the isomerization of H3 proline P30 and P38 in vitro. We show that P38 is necessary for methylation of K36 and that isomerization by Fpr4 inhibits the ability of Set2 to methylate H3 K36 in vitro. These results suggest that the conformational state of P38, controlled by Fpr4, is important for methylation of H3K36 by Set2. Consistent with such an antagonistic role, abrogation of Fpr4 catalytic activity in vivo results in increased levels of H3K36 methylation and delayed transcriptional induction kinetics of specific genes in yeast. These results identify proline isomerization as a novel noncovalent histone modification that regulates transcription and provides evidence for crosstalk between histone lysine methylation and proline isomerization.

A three-dimensional model of the human transglutaminase 1: insights into the understanding of lamellar ichthyosis

The stratum corneum, the outer layer of the epidermis, serves as a protective barrier to isolate the skin from the external environment. Keratinocyte transglutaminase 1 (TGase 1) catalyzes amide crosslinking between glutamine and lysine residues on precursor proteins forming the impermeable layers of the epidermal cell envelopes (CE), the highly insoluble membranous structures of the stratum corneum. Patients with the autosomal recessive skin disorder lamellar ichthyosis (LI) appear to have deficient cross-linking of the cell envelope due to mutations identified in TGase 1, linking this enzyme to LI. In the absence of a crystal structure, molecular modeling was used to generate the structure of TGase 1. We have mapped the known mutations of TGase 1 from our survey obtained from a search of PubMed and successfully predicted the impact of these mutations on LI. Furthermore, we have identified Ca(2+) binding sites and propose that Ca(2+) induces a cis to trans isomerization in residues near the active site as part of the enzyme transamidation activation. Docking experiments suggest that substrate binding subsequently induces the reverse cis to trans isomerization, which may be a significant part of the catalytic process. These results give an interpretation at the molecular level of previously reported mutations and lead to further insights into the structural model of TGase 1, providing a new basis for understanding LI.

Accurate prediction of protein torsion angles using chemical shifts and sequence homology

Torsion angle restraints are frequently used in the determination and refinement of protein structures by NMR. These restraints may be obtained by J coupling, cross-correlation measurements, nuclear Overhauser effects (NOEs) or secondary chemical shifts. Currently most backbone (phi/psi) torsion angles are determined using a combination of J(HNHalpha) couplings and chemical shift measurements while most side-chain (chi1) angles and cis/trans peptide bond angles (omega) are determined via NOEs. The dependency on multiple experimental (and computational) methods to obtain different torsion angle restraints is both time-consuming and error prone. The situation could be greatly improved if the determination of all torsion angles (phi, psi, chi and omega) could be made via a single type of measurement (i.e. chemical shifts). Here we describe a program, called SHIFTOR, that is able to accurately predict a large number of protein torsion angles (phi, psi, omega, chi1) using only 1H, 13C and 15N chemical shift assignments as input. Overall, the program is 100x faster and its predictions are approximately 20% better than existing methods. The program is also capable of predicting chi1 angles with 81% accuracy and omega angles with 100% accuracy. SHIFTOR exploits many of the recent developments and observations regarding chemical shift dependencies as well as using information in the Protein Databank to improve the quality of its shift-derived torsion angle predictions. SHIFTOR is available as a freely accessible web server at http://wishart.biology.ualberta.ca/shiftor.

Conservation of cis prolyl bonds in proteins during evolution

In proteins and peptides, the vast majority of peptide bonds occurs in trans conformation, but a considerable fraction (about 5%) of X-Pro bonds adopts the cis conformation. Here we study the conservation of cis prolyl residues in evolutionary related proteins. We find that overall, in contrast to local, protein sequence similarity is a clear indicator for the conformation of prolyl residues. We observe that cis prolyl residues are more often conserved than trans prolyl residues, and both are more conserved than the surrounding amino acids, which show the same extent of conservation as the whole protein. The pattern of amino acid exchanges differs between cis and trans prolyl residues. Also, the cis prolyl bond is maintained in proteins with sequence identity as low as 20%. This finding emphasizes the importance of cis peptide bonds in protein structure and function.

Ab initio conformational study of N-acetyl-L-proline-N',N'-dimethylamide: a model for polyproline

We report here the results on N-acetyl-l-proline-N',N'-dimethylamide (Ac-Pro-NMe2) as a model for polyproline at the HF/6-31+G(d) level with the conductor-like polarizable continuum model of self-consistent reaction field methods to figure out the conformational preference and cis-trans isomerization of polyproline in the gas phase, chloroform, methanol, and water. The second methyl substitution at the carboxyl amide end results in different backbone structures and their populations from those of N-acetyl-L-proline-N-methylamide (Ac-Pro-NHMe). In particular, all conformations with the C7 hydrogen bond between acetyl and amide ends, which is the most probable conformations of Ac-Pro-NHMe in the gas phase and in nonpolar solvents, disappeared for Ac-Pro-NMe2 even in the gas phase due to the lack of amide hydrogen. The dominant conformation for Ac-Pro-NMe2 is the polyproline II structure with the trans prolyl peptide bond in the gas phase and in solutions. In methanol, the population of the polyproline I structure with the cis prolyl peptide bond is calculated to be larger than that in water, which is consistent with experiments. It should be noted that Ac-Pro-NMe2 has higher rotational barriers for the cis-trans isomerization of the Ac-Pro peptide bond than Ac-Pro-NHMe in the gas phase and in solutions, which could be due to the lack of the intramolecular hydrogen bond between prolyl nitrogen and carboxyl N-H group for the transition state of Ac-Pro-NMe2. The rotational barriers for Ac-Pro-NMe2 are increased with the increase of solvent polarity, as seen for Ac-Pro-NHMe.

Allosteric regulation of Hsp70 chaperones by a proline switch

Crucial to the function of Hsp70 chaperones is the nucleotide-regulated transition between two conformational states, the ATP bound state with high association and dissociation rates for substrates and the ADP bound state with two and three orders of magnitude lower association and dissociation rates. The spontaneous transition between the two states is extremely slow, indicating a high energy barrier for the switch that regulates the transition. Here we provide evidence that a universally conserved proline in the ATPase domain constitutes the switch that assumes alternate conformations in response to ATP binding and hydrolysis. The conformation of the proline, acting through an invariant arginine as relay, determines and stabilizes the opened and closed conformation of the substrate binding domain and thereby regulates the chaperone activity of Hsp70.

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background

The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function.

Results

In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively.

Conclusion

A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

The crystal structure of the cis-proline to glycine variant (P114G) of ribonuclease A

Replacement of a cis-proline by glycine at position 114 in ribonuclease A leads to a large decrease in thermal stability and simplifies the refolding kinetics. A crystallographic approach was used to determine whether the decrease in thermal stability results from the presence of a cis glycine peptide bond, or from a localized structural rearrangement caused by the isomerization of the mutated cis 114 peptide bond. The structure was solved at 2.0 A resolution and refined to an R-factor of 19.5% and an R(free) of 21.9%. The overall conformation of the protein was similar to that of wild-type ribonuclease A; however, there was a large localized rearrangement of the mutated loop (residues 110-117-a 9.3 A shift of the Calpha atom of residue 114). The peptide bond before Gly114 is in the trans configuration. Interestingly, a large anomalous difference density was found near residue 114, and was attributed to a bound cesium ion present in the crystallization experiment. The trans isomeric configuration of the peptide bond in the folded state of this mutant is consistent with the refolding kinetics previously reported, and the associated protein conformational change provides an explanation for the decreased thermal stability.

All-cis Cyclic Peptides

Amide bonds -NH-CO- preferentially exist in trans conformations, the cis conformation being thermodynamically unfavored with respect to the trans by about 2 kcal/mol. Yet, the main reason most proteins or peptides cannot be made from cis-peptide plaques only lies in that connecting them into open chains appears to be sterically impracticable. It is possible, however, to build all-cis cyclic peptides in which all cis-plaques are efficiently locked. The present work examines, through quantum calculations, the structural and energetic issues associated with these peculiar arrangements. Systematic exploration at DFT-B3LYP level of the potential-energy surfaces for all-cis cyclopolyglycines cG(n)(c) (n = 2-10,15), and to a lesser extent, for all-cis cyclopolyalanines and all-cis cyclopolyphenylalanines confirms that all these structures are true minima. Optimal ring size occurs around eight peptide units, resulting in planar cG7(c), cG8(c), and cG9(c). In smaller systems, the ring strain is relieved through nonplanar cup-like distortions, particularly in cG6(c). From 10 peptide units and beyond, the ring framework distorts into a saddle-edge shape. These molecules disclose some molecular flexibility, as combinatorial tilting of the plaques may give sets of minima close in energy. Indexes based on isodesmic reactions are used to estimate the energy for joining all-cis or all-trans plaques into cyclic peptides. One of them, the mean plaque-junction energy (MPJE) suggests that within sensible sizes from six peptide units and beyond, all-cis plaque association is almost equally favorable as all-trans one. The frame of radiating cis-amide bonds can be considered as defining a new kind of peptidic material, endowed with specific self-assembling properties.

The crystal structure of free human hypoxanthine-guanine phosphoribosyltransferase reveals extensive conformational plasticity throughout the catalytic cycle

Human hypoxanthine-guanine phosphoribosyltransferase (HGPRT) catalyses the synthesis of the purine nucleoside monophosphates, IMP and GMP, by the addition of a 6-oxopurine base, either hypoxanthine or guanine, to the 1-beta-position of 5-phospho-alpha-d-ribosyl-1-pyrophosphate (PRib-PP). The mechanism is sequential, with PRib-PP binding to the free enzyme prior to the base. After the covalent reaction, pyrophosphate is released followed by the nucleoside monophosphate. A number of snapshots of the structure of this enzyme along the reaction pathway have been captured. These include the structure in the presence of the inactive purine base analogue, 7-hydroxy [4,3-d] pyrazolo pyrimidine (HPP) and PRib-PP.Mg2+, and in complex with IMP or GMP. The third structure is that of the immucillinHP.Mg(2+).PP(i) complex, a transition-state analogue. Here, the first crystal structure of free human HGPRT is reported to 1.9A resolution, showing that significant conformational changes have to occur for the substrate(s) to bind and for catalysis to proceed. Included in these changes are relative movement of subunits within the tetramer, rotation and extension of an active-site alpha-helix (D137-D153), reorientation of key active-site residues K68, D137 and K165, and the rearrangement of three active-site loops (100-128, 165-173 and 186-196). Toxoplasma gondii HGXPRT is the only other 6-oxopurine phosphoribosyltransferase structure solved in the absence of ligands. Comparison of this structure with human HGPRT reveals significant differences in the two active sites, including the structure of the flexible loop containing K68 (human) or K79 (T.gondii).

Pivotal molecular determinants of peptidic and collagen triple helicase activities reside in the S3' subsite of matrix metalloproteinase 8 (MMP-8): the role of hydrogen bonding potential of ASN188 and TYR189 and the connecting cis bond

The mechanism of triple helical collagen unwinding and cleavage by collagenases in the matrix metalloproteinase (MMP) family is complex and remains enigmatic. Recent reports show that triple helicase activity is initiated by the hemopexin C domain of membrane type 1-MMP, whereas catalytically inactive full-length interstitial collagenase (MMP-1) exhibits full triple helicase functionality pointing to active site determinants that are needed to complete the triple helicase mechanism. In MMP-8, the neutrophil collagenase, a conserved Gly at the S(3)' substrate specificity subsite is replaced by Asn(188) that forms a highly unusual cis bond with Tyr(189), a conserved active site residue in the collagenases. Only in MMP-1 is the S(3)' Gly also replaced, and there too a cis configured Glu-Tyr occurs. Thus, this high energy peptide bond coupled to the canonical Tyr may be important in the collagenolytic process. In a systematic mutagenesis investigation of the MMP-8 S(3)' subsite we found that introducing an S(3)' Gly(188) into MMP-8 reduced collagenolytic efficiency by approximately 30% with a corresponding reduction in cleavage of a synthetic peptide fluorescence resonance energy transfer substrate analogue of the alpha2(I) collagen chain cleavage site. The substitution of Asn(188) to Leu, a hydrophobic residue of similar size to the highly polar Asn and designed to retain the cis bond, revealed the importance of hydrogen bonding to bound substrate with both collagenolytic and peptidic activities reduced approximately 3-fold. In contrast, the specificity for type I collagen of the mutant Y189F dropped 3-fold without any significant alteration in general peptidase activity. Therefore, S(3)' and in particular the hydrogen bonding potential of Tyr(189) is a specific molecular determinant for MMP-8 triple helicase activity. The cis bond connection to Asn(188) juxtaposes these two side chains for closely spaced hydrogen bonding with substrate that improves collagenolytic and general catalytic efficiency that could be exploited for new collagenase-specific inhibitor drugs.

COPS--Cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information

COPS predicts for all 20 naturally occurring amino acids whether the peptide bond in a protein is in cis or trans conformation. The algorithm is based only on secondary structure information of amino acid triplets without considering the amino acid sequence information. Conformation parameters are derived from solved 3D structures deposited in the PDB and led to propensities based on modified Chou-Fasman parameters. COPS analyses amino acid triplets taking only their respective secondary structure into consideration and upon application of a set of rules utilizing the conformation parameters, the N-terminal peptide bond conformation of the middle residue is predicted. COPS was tested on a random selection of protein datasets.

AVAILABILITY

The COPS program and further information are freely available from the FMP website at http://www.fmp-berlin.de/nmr/cops

CONTACT

labudde@fmp-berlin.de.

Structural mechanism governing cis and trans isomeric states and an intramolecular switch for cis/trans isomerization of a non-proline peptide bond observed in crystal structures of scorpion toxins

Non-proline cis peptide bonds have been observed in numerous protein crystal structures even though the energetic barrier to this conformation is significant and no non-prolyl-cis/trans-isomerase has been identified to date. While some external factors, such as metal binding or co-factor interaction, have been identified that appear to induce cis/trans isomerization of non-proline peptide bonds, the intrinsic structural basis for their existence and the mechanism governing cis/trans isomerization in proteins remains poorly understood. Here, we report the crystal structure of a newly isolated neurotoxin, the scorpion alpha-like toxin Buthus martensii Karsch (BmK) M7, at 1.4A resolution. BmK M7 crystallizes as a dimer in which the identical non-proline peptide bond between residues 9 and 10 exists either in the cis conformation or as a mixture of cis and trans conformations in either monomer. We also determined the crystal structures of several mutants of BmK M1, a representative scorpion alpha-like toxin that contains an identical non-proline cis peptide bond as that observed in BmK M7, in which residues within or neighboring the cis peptide bond were altered. Substitution of an aspartic acid residue for lysine at residue 8 in the BmK M1 (K8D) mutant converted the cis form of the non-proline peptide bond 9-10 into the trans form, revealing an intramolecular switch for cis-to-trans isomerization. Cis/trans interconversion of the switch residue at position 8 appears to be sequence-dependent as the peptide bond between residues 9 and 10 retains its wild-type cis conformation in the BmK M1 (K8Q) mutant structure. The structural interconversion of the isomeric states of the BmK M1 non-proline cis peptide bond may relate to the conversion of the scorpion alpha-toxins subgroups.

Cis–trans isomerization and puckering of proline residue

We report here the results on N-acetyl-L-proline-N'-methylamide (Ac-Pro-NHMe) calculated at the HF/6-31+G(d) level with the conductor-like polarizable continuum model (CPCM) of self-consistent reaction field methods to investigate the changes of backbone and prolyl ring along the cis-trans isomerization of the prolyl peptide bond. From the potential energy surface, the barrier to ring flip from the down-puckered conformation to the up-puckered one is estimated to be 2.5 and 3.2 kcal/mol for trans and cis conformers of Ac-Pro-NHMe, respectively. In particular, the ring flip seems to be inaccessible in the intermediate regions between trans and cis conformations, because of higher barriers (approximately 13-19 kcal/mol) to rotation of the prolyl peptide bond. The torsion angles for backbone and prolyl ring vary largely around the transition states at omega' approximately 120 degrees and -70 degrees for the prolyl peptide bond. Three kinds of puckering amplitudes show the same trend of puckering along the cis-trans isomerization although their absolute values are different. In particular, trans and cis conformations have the almost same degree of puckering. The cis populations and barriers to rotation of the prolyl peptide bond for Ac-Pro-NHMe are increased with the increase of solvent polarity, which is mainly ascribed to the decreases of relative free energies for cis conformations and the increase of relative free energies for transition states.

Substituted 2-Azabicyclo[2.1.1]hexanes as Constrained Proline Analogues: Implications for Collagen Stability

Among the proteinogenic amino acids, only proline is a secondary amine and only proline has a saturated ring. Electronegative substituents on C-4 (that is, C(gamma)) have a substantial effect on the trans/cis ratio of the prolyl peptide bond and the pucker of the pyrrolidine ring. 2-Azabicyclo[2.1.1]hexane is, in essence, a proline analogue with two C(gamma) atoms, one in each of the two prevalent ring puckers of proline. Here, 2-azabicyclo[2.1.1]hexane analogues of 2S-proline, (2S,4S)-4-hydroxyproline, and (2S,4S)-4-fluoroproline residues were synthesized, and their trans/cis ratios were shown to be invariant in a particular solvent. Thus, the substitution of a proline residue on C-4 affects the trans/cis ratio by altering the pucker of its pyrrolidine ring. This finding has implications for the conformation of collagen, which has an abundance of 2S-proline and (2S,4R)-4-hydroxyproline residues, and can be stabilized by (2S,4R)-4-fluoroproline and (2S,4S)-4-fluoroproline residues.

Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations

A systematic comparison is made between experimental and computational data gained on vicinal disulfide bridges in proteins and peptides. Structural and stability data of ab initio and density functional theory (DFT) calculations on the model compound 4,5-ditiaheptano-7-lactam and the model peptide HCO-ox-[Cys-Cys]-NH2 at RHF/3-21G*, B3LYP/6-31+G(d), and B3LYP/6-311++G(d,p) levels of theory are presented. The data on Xxx-Cys-Cys-Yyy type amino acid sequence units retrieved from PDB SELECT, along with data on sequence units that have vicinal disulfide bridge, taken from the Brookhaven Protein Data Bank, are conformationally characterized. Amino acid backbone conformations, cis-trans isomerism of the amide bond between the two cysteine residues, and ring puckering are studied. Ring puckers are characterized by their relation to the conformers of the parent 4,5-ditiaheptano-7-lactam. Computational precision and accuracy are proved by frequency calculation and solvent model optimization on selected conformers. It is found that the ox-[Cys-Cys] unit is able to accept types I, II, VIa, VIb, and VIII beta-turn structures.

Protein prosthesis: a nonnatural residue accelerates folding and increases stability

Nonnatural residues can endow proteins with desirable properties. Here, replacing a proline residue that has a cis peptide bond in native ribonuclease A with 5,5-dimethyl-l-proline is shown to accelerate protein folding by 6-fold and enhance conformational stability by DeltaTm = 2.8 +/- 0.3 degrees C while having no effect on enzymatic activity. The rational use of this and other prosthetic segments could enable chemotherapeutic proteins to survive longer in vivo or retain activity after oral administration.

An electronic effect on protein structure

The well-known preference of the peptide bond for the trans conformation has been attributed to steric effects. Here, we show that a proline residue with an N-formyl group (H(i-1)-C'(i-1)=O(i-1)), in which H(i-1) presents less steric hindrance than does O(i-1), likewise prefers a trans conformation. Thus, the preference of the peptide bond for the trans conformation cannot be explained by steric effects alone. Rather, an n --> pi* interaction between the oxygen of the peptide bond (O(i-1)), and the subsequent carbonyl carbon in the polypeptide chain (C'(i)) also contributes to this preference. The O(i-1) and C'(i) distance and O(i-1).C'(i)=O(i) angle are especially favorable for such an n --> pi* interaction in a polyproline II helix. We propose that this electronic effect provides substantial stabilization to this and other elements of protein structure.

Parallel channels and rate-limiting steps in complex protein folding reactions: prolyl isomerization and the alpha subunit of Trp synthase, a TIM barrel protein

A kinetic folding mechanism for the alpha subunit of tryptophan synthase (alphaTS) from Escherichia coli, involving four parallel channels with multiple native, intermediate and unfolded forms, has recently been proposed. The hypothesis that cis/trans isomerization of several Xaa-Pro peptide bonds is the source of the multiple folding channels was tested by measuring the sensitivity of the three rate-limiting phases (tau(1), tau(2), tau(3)) to catalysis by cyclophilin, a peptidyl-prolyl isomerase. Although the absence of catalysis for the tau(1) (fast) phase leaves its assignment ambiguous, our previous mutational analysis demonstrated its connection to the unique cis peptide bond preceding proline 28. The acceleration of the tau(2) (medium) and tau(3) (slow) refolding phases by cyclophilin demonstrated that cis/trans prolyl isomerization is also the source of these phases. A collection of proline mutants, which covered all of the remaining 18 trans proline residues of alphaTS, was constructed to obtain specific assignments for these phases. Almost all of the mutant proteins retained the complex equilibrium and kinetic folding properties of wild-type alphaTS; only the P217A, P217G and P261A mutations caused significant changes in the equilibrium free energy surface. Both the P78A and P96A mutations selectively eliminated the tau(1) folding phase, while the P217M and P261A mutations eliminated the tau(2) and tau(3) folding phases, respectively. The redundant assignment of the tau(1) phase to Pro28, Pro78 and Pro96 may reflect their mutual interactions in non-random structure in the unfolded state. The non-native cis isomers for Pro217 and Pro261 may destabilize an autonomous C-terminal folding unit, thereby giving rise to kinetically distinct unfolded forms. The nature of the preceding amino acid, the solvent exposure, or the participation in specific elements of secondary structure in the native state, in general, are not determinative of the proline residues whose isomerization reactions can limit folding.

A cis-prolyl peptide bond isomerization dominates the folding of the alpha subunit of Trp synthase, a TIM barrel protein

The cis/trans isomerization of prolyl peptide bonds has been suggested to dominate the folding of the alpha subunit of tryptophan synthase from Escherichia coli (alphaTS). To test the role of the unique cis isomer between Asp27 and Pro28, the folding properties of P28A, P28G and G(3)P28G, a three-glycine insertion mutant between Asp27 and Gly28, were investigated using urea as a denaturant. Circular dichroism analysis demonstrated that none of the mutations perturb the secondary structure significantly, although the aromatic side-chain packing is altered for P28A and P28G. All three mutant proteins inherited the three-state thermodynamic behavior observed in wild-type alphaTS, ensuring that the fundamental features of the energy surface are intact. Kinetic studies showed that neither alanine nor glycine substitutions at Pro28 results in the elimination of any slow-refolding phases. By contrast, the G(3)P28G mutant eliminates the fastest of the slow-refolding phases and one of the two unfolding phases. Double-jump experiments on G(3)P28G confirm the assignment of the missing refolding phase to the isomerization of the Asp27-Pro28 peptide bond. These results imply that the local stability conveyed by the tight, overlapping turns containing the cis peptide bond is sufficient to favor the cis isomer for several non-prolyl residues. The free energy required to drive the isomerization reaction is provided by the formation of the stable intermediate, demonstrating that the acquisition of structure and stability is required to induce subsequent rate-limiting steps in the folding of alphaTS.

Preferred proline puckerings in cis and trans peptide groups: implications for collagen stability

The interplay between side-chain and main-chain conformations is a distinctive characteristic of proline residues. Here we report the results of a statistical analysis of proline conformations using a large protein database. In particular, we found that proline residues with the preceding peptide bond in the cis state preferentially adopt a down puckering. Indeed, out of 178 cis proline residues, as many as 145 (81%) are down. By analyzing the 1-4 and 1-5 nonbonding distances between backbone atoms, we provide a structural explanation for the observed trend. The observed correlation between proline puckering and peptide bond conformation suggests a new mechanism to explain the reported shift of the cis-trans equilibrium in proline derivatives. The implications of these results for the current models of collagen stability are also discussed.

Exploring the impact of different thioesterase domains for the design of hybrid peptide synthetases

BACKGROUND

A large number of pharmacologically important peptides are synthesized by multifunctional enzymes, the nonribosomal peptide synthetases (NRPSs). The thioesterase (Te) domain at the C-terminus of the last NRPS catalyzes product cleavage by hydrolysis or complex macrocyclization. Recent studies with excised Te domains and peptidyl-S-N-acetyl cysteamine substrate substitutes led to substantial insights in terms of cyclization activity and substrate tolerance of these enzymes. Their use in engineered hybrid NRPSs is an interesting but yet only little explored target for approaches to achieve new structural diversity and designed products.

RESULTS

To study the capability of various Te domains to function in hybrid NRPSs, six different Te domains that catalyze different modes of termination in their natural systems were fused to a bimodular model NRPS system, consisting of the first two modules of tyrocidine NRPS, TycA and ProCAT. All Te domains were active in hydrolyzing the enzymatically generated dipeptide substrate D-Phe-Abu from the NRPS template with, however, greatly varying turnover rates. Two Te domains were also capable of hydrolyzing the substrate D-Phe-Pro and partially cyclized the D-Phe-Abu dipeptide, indicating that in an artificial context Te domains may display hydrolytic and cyclization activities that are not easily predictable.

CONCLUSIONS

Te domains from heterologous NRPSs can be utilized for the construction of hybrid NRPSs. This is the first comparative study to explore their influence on the product pattern. The inherent specificity and regioselectivity of Te domains should allow control of the desired product cleavage, but can also lead to other modes of termination potentially useful for generating structural diversity. Our results provide the first data for choosing the proper Te domain for a particular termination reaction.

Structural analysis of free and enzyme-bound amaranth alpha-amylase inhibitor: classification within the knottin fold superfamily and analysis of its functional flexibility

The three-dimensional structure of the amaranth alpha-amylase inhibitor (AAI) adopts a knottin fold of abcabc topology. Upon binding to alpha-amylase, it adopts a more compact conformation characterized by an increased number of intramolecular hydrogen bonds, a decreased volume and in addition a trans to cis isomerization of Pro20. A systematic analysis of the 3-D structural databanks revealed that similar proteins and domains share with AAI the characteristic presence of proline residues, many of which are in a cis backbone conformation. As these proteins fulfil a variety of functional roles and are expressed in very different organisms, we conclude that the structure of the knottin fold, including the propensity of the cis bond, are the result of convergent evolution.

The interrelationships of side-chain and main-chain conformations in proteins

The accurate determination of a large number of protein structures by X-ray crystallography makes it possible to conduct a reliable statistical analysis of the distribution of the main-chain and side-chain conformational angles, how these are dependent on residue type, adjacent residue in the sequence, secondary structure, residue-residue interactions and location at the polypeptide chain termini. The interrelationship between the main-chain (phi, psi) and side-chain (chi 1) torsion angles leads to a classification of amino acid residues that simplify the folding alphabet considerably and can be a guide to the design of new proteins or mutational studies. Analyses of residues occurring with disallowed main-chain conformation or with multiple conformations shed some light on why some residues are less favoured in thermophiles.

C-H...pi-interactions in proteins

A non-redundant set of 1154 protein structures from the Protein Data Bank was examined with respect to close interactions between C-H-donor and pi-acceptor groups. A total of 31,087 interactions were found to satisfy our selection criteria. Their geometric parameters suggest that these interactions can be classified as weak hydrogen bonds.A set of 12 interaction classes were defined based on the division of the donors into three groups and the acceptors into four groups. These classes were examined separately, and the respective interactions described in detail in each class. Most prominent were interactions between aliphatic C-H donors and aromatic pi-acceptors and interactions between aromatic C-H donors and aromatic pi-acceptors. About three-quarters of the Trp-rings, half of all Phe and Tyr-rings and a quarter of all His-rings were found to be involved as acceptors in C-H...pi-interactions. On the donor side, a preference for aromatic C-H groups was observed, but also for the aliphatic side-chains of the long, extended amino acid residues Lys, Arg and Met, and the Pro ring. The average distance between the C-donor and the center-of-mass of the pi-acceptor was observed to be significantly longer in the 174 protein structures determined at >2.5 A resolution. Also, the distribution is significantly wider. This resolution dependence suggests that the force fields commonly used for the refinement of protein structures may not be adequate. C-H...pi-interactions involving aromatic groups either as donor or as acceptor groups are found mostly in the interior of the protein. The more hydrophilic the participating groups are, the closer to the surface are the interactions located. About 40 % of all C-H...pi-interactions occur between amino acid residue side-chains that are separated by nine or less residues in sequence. Dependent on the interaction class, different preferences for secondary structure, residue type and side-chain conformation were observed. It is likely that the C-H...pi-interactions contribute significantly to the overall stability of a protein.

Solvent-dependent stabilization of the E configuration of propargylic secondary amides

Secondary amides typically exist 98-99% in the Z rotamer to avoid steric repulsion between the substituent on the carbonyl carbon and the nitrogen. In contrast, secondary amide 3a displays 24% E rotamer at room temperature in aqueous solution. The analogous ester displays 6% E rotamer in chloroform, which suggests that the relatively high E conformer population observed for 3a in water results in part from the low steric bulk of the sp-hybridized carbons and in part from the hydrophobic effect.

The structural features of concanavalin A governing non-proline peptide isomerization

The reversible binding of manganese and calcium to concanavalin A determines the carbohydrate binding of the lectin by inducing large conformational changes. These changes are governed by the isomerization of a non-proline peptide bond, Ala-207-Asp-208, positioned in a beta-strand in between the calcium binding site S2 and the carbohydrate specificity-determining loop. The replacement of calcium by manganese allowed us to investigate the structures of the carbohydrate binding, locked state and the inactive, unlocked state of concanavalin A, both with and without metal ions bound. Crystals of unlocked metal-free concanavalin A convert to the locked form with the binding of two Mn(2+) ions. Removal of these ions from the crystals traps metal-free concanavalin A in its locked state, a minority species in solution. The ligation of a metal ion in S2 to unlocked concanavalin A causes bending of the beta-strand foregoing the S2 ligand residues Asp-10 and Tyr-12. This bending disrupts conventional beta-sheet hydrogen bonding and forces the Thr-11 side chain against the Ala-207-Asp-208 peptide bond. The steric strain exerted by Thr-11 is presumed to drive the trans-to-cis isomerization. Upon isomerization, Asp-208 flips into its carbohydrate binding position, and the conformation of the carbohydrate specificity determining loop changes dramatically.

Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations

An analysis of a non-redundant set of protein structures from the Brookhaven Protein Data Bank has been carried out to find out the residue preference, local conformation, hydrogen bonding and other stabilizing interactions involving cis peptide bonds. This has led to a reclassification of turns mediated by cis peptides, and their average geometrical parameters have been evaluated. The interdependence of the side and main-chain torsion angles of proline rings provided an explanation why such rings in cis peptides are found to have the DOWN puckering. A comparison of cis peptides containing proline and non-proline residues show differences in conformation, location in the secondary structure and in relation to the centre of the molecule, and relative accessibilities of residues. Relevance of the results in mutation studies and the cis-trans isomerization during protein folding is discussed.