151
|
Edwardraja S, Sriram S, Govindan R, Budisa N, Lee SG. Enhancing the thermal stability of a single-chain Fv fragment by in vivo global fluorination of the proline residues. ACTA ACUST UNITED AC 2011; 7:258-65. [DOI: 10.1039/c0mb00154f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
152
|
Stavrakoudis A. Cis-transisomerization of the Epstein-Barr virus determinant peptide EENLLDFVRF after the DM1 TCR recognition of the HLA-B*4405/peptide complex. FEBS Lett 2010; 585:485-91. [DOI: 10.1016/j.febslet.2010.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 11/23/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
|
153
|
Kuemin M, Nagel YA, Schweizer S, Monnard FW, Ochsenfeld C, Wennemers H. Tuning the cis/trans conformer ratio of Xaa-Pro amide bonds by intramolecular hydrogen bonds: the effect on PPII helix stability. Angew Chem Int Ed Engl 2010; 49:6324-7. [PMID: 20665611 DOI: 10.1002/anie.201001851] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Michael Kuemin
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | | | | | | | | | | |
Collapse
|
154
|
Weinzierl ROJ. The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain. BMC Biol 2010; 8:134. [PMID: 21034443 PMCID: PMC2988716 DOI: 10.1186/1741-7007-8-134] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 10/29/2010] [Indexed: 01/24/2023] Open
Abstract
Background Cellular RNA polymerases (RNAPs) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-HC) plays a critical role in controlling the catalytic rate. Results Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-HN) is presented. The nanomechanical properties of BH-HN emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC). BH-HN displays functional properties that are distinct from BH-HC, suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms. Conclusions The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains.
Collapse
|
155
|
Byun BJ, Song IK, Chung YJ, Ryu KH, Kang YK. Conformational Preferences of X-Pro Sequences: Ala-Pro and Aib-Pro Motifs. J Phys Chem B 2010; 114:14077-86. [DOI: 10.1021/jp107200f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Byung Jin Byun
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Il Keun Song
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Yong Je Chung
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Keun Ho Ryu
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Young Kee Kang
- Department of Chemistry, Department of Biochemistry, and Database/Bioinformatics Laboratory, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| |
Collapse
|
156
|
Kuemin M, Nagel Y, Schweizer S, Monnard F, Ochsenfeld C, Wennemers H. Tuning the cis/trans Conformer Ratio of Xaa-Pro Amide Bonds by Intramolecular Hydrogen Bonds: The Effect on PPII Helix Stability. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001851] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
157
|
Kim TY, Valentine SJ, Clemmer DE, Reilly JP. Gas-phase conformation-specific photofragmentation of proline-containing peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1455-65. [PMID: 20483641 DOI: 10.1016/j.jasms.2010.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 04/07/2010] [Accepted: 04/13/2010] [Indexed: 05/16/2023]
Abstract
Singly-protonated proline-containing peptides with N-terminal arginine are photodissociated with vacuum ultraviolet (VUV) light in an ESI linear ion trap/orthogonal-TOF (LIT/o-TOF). When proline is the nth residue from the N-terminus, unusual b(n) + 2 and a(n) + 2 ions are observed. Their formation is explained by homolytic cleavage of the C(alpha)-C bond in conjunction with a rearrangement of electrons and an amide hydrogen. The latter is facilitated by a proline-stabilized gas-phase peptide conformation.
Collapse
Affiliation(s)
- Tae-Young Kim
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | | | | | | |
Collapse
|
158
|
Nguyen K, Iskandar M, Rabenstein DL. Kinetics and equilibria of cis/trans isomerization of secondary amide peptide bonds in linear and cyclic peptides. J Phys Chem B 2010; 114:3387-92. [PMID: 20136113 DOI: 10.1021/jp1000286] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The secondary amide peptide bonds that comprise up to one-third of the bonds of peptide or protein backbones can exist as cis and trans isomers, with the trans isomer being highly favored. However, there is little quantitative data on the kinetics and equilibria of cis-trans isomerization of secondary amide peptide bonds due to the difficulty of detecting the very small population of cis isomers. Knowledge of factors that influence the kinetics and equilibria of cis-trans isomerization of secondary amide peptide bonds will contribute to a more complete understanding of the structural and dynamic behavior of the backbones of peptides and unfolded proteins and of complex protein folding kinetics. We have characterized the kinetics and equilibria of cis-trans isomerization of the Xaa-Yaa secondary amide peptide bonds of the linear dithiol and cyclic disulfide forms of the peptides Ac-Cys-Xaa-Yaa-Cys-His-NH(2), where Xaa-Yaa is Ala-Phe, Phe-Ala, Ala-Tyr, and Tyr-Ala, by (1)H NMR. Resolved resonances were observed for the Ala-methyl protons of the trans and the much less abundant cis isomers due to differential shielding of the Ala-methyl protons of the trans and cis isomers by ring current effects from the Phe and Tyr side chains. The population of the cis isomers was determined from the relative intensities of the Ala-methyl resonances for the trans and cis isomers, and rate constants for cis-to-trans and trans-to-cis isomerization were determined by the magnetization transfer NMR method. The population of the cis isomers ranges from 0.07 to 0.12%, and the rate constants indicate that, when there is a trans-to-cis interchange, it is rapidly followed by a cis-to-trans interchange back to the more stable trans conformation. Although cyclization by disulfide bond formation imposes conformational constraints on the peptide backbones, cyclization is found to have relatively small affects on the dynamics of cis-trans isomerization.
Collapse
Affiliation(s)
- Khanh Nguyen
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | | | | |
Collapse
|
159
|
Inhibition of FK506 binding proteins reduces alpha-synuclein aggregation and Parkinson's disease-like pathology. J Neurosci 2010; 30:2454-63. [PMID: 20164329 DOI: 10.1523/jneurosci.5983-09.2010] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
alpha-Synuclein (alpha-SYN) is a key player in the pathogenesis of Parkinson's disease (PD). In pathological conditions, the protein is present in a fibrillar, aggregated form inside cytoplasmic inclusions called Lewy bodies. Members of the FK506 binding protein (FKBP) family are peptidyl-prolyl isomerases that were shown recently to accelerate the aggregation of alpha-SYN in vitro. We now established a neuronal cell culture model for synucleinopathy based on oxidative stress-induced alpha-SYN aggregation and apoptosis. Using high-content analysis, we examined the role of FKBPs in aggregation and apoptotic cell death. FK506, a specific inhibitor of this family of proteins, inhibited alpha-SYN aggregation and neuronal cell death in this synucleinopathy model dose dependently. Knockdown of FKBP12 or FKBP52 reduced the number of alpha-SYN aggregates and protected against cell death, whereas overexpression of FKBP12 or FKBP52 accelerated both aggregation of alpha-SYN and cell death. Thus, FK506 likely targets FKBP members in the cell culture model. Furthermore, oral administration of FK506 after viral vector-mediated overexpression of alpha-SYN in adult mouse brain significantly reduced alpha-SYN aggregate formation and neuronal cell death. Our data explain previously described neuroregenerative and neuroprotective effects of immunophilin ligands and validate FKBPs as a novel drug target for the causative treatment of PD.
Collapse
|
160
|
Exarchos KP, Exarchos TP, Papaloukas C, Troganis AN, Fotiadis DI. PBOND: web server for the prediction of proline and non-proline cis/trans isomerization. GENOMICS PROTEOMICS & BIOINFORMATICS 2010; 7:138-42. [PMID: 19944386 PMCID: PMC5054403 DOI: 10.1016/s1672-0229(08)60042-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PBOND is a web server that predicts the conformation of the peptide bond between any two amino acids. PBOND classifies the peptide bonds into one out of four classes, namely cis imide (cis-Pro), cis amide (cis-nonPro), trans imide (trans-Pro) and trans amide (trans-nonPro). Moreover, for every prediction a reliability index is computed. The underlying structure of the server consists of three stages: (1) feature extraction, (2) feature selection and (3) peptide bond classification. PBOND can handle both single sequences as well as multiple sequences for batch processing. The predictions can either be directly downloaded from the web site or returned via e-mail. The PBOND web server is freely available at http://195.251.198.21/pbond.html.
Collapse
Affiliation(s)
- Konstantinos P Exarchos
- Unit of Medical Technology and Intelligent Information Systems, Department of Computer Science, University of loannina, loannina 45110, Greece
| | | | | | | | | |
Collapse
|
161
|
Chung MK, White PS, Lee SJ, Gagné MR. Synthesis of interlocked 56-membered rings by dynamic self-templating. Angew Chem Int Ed Engl 2010; 48:8683-6. [PMID: 19816896 DOI: 10.1002/anie.200903478] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mee-Kyung Chung
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | | | | | | |
Collapse
|
162
|
Implications for the active form of human insulin based on the structural convergence of highly active hormone analogues. Proc Natl Acad Sci U S A 2010; 107:1966-70. [PMID: 20133841 DOI: 10.1073/pnas.0911785107] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Insulin is a key protein hormone that regulates blood glucose levels and, thus, has widespread impact on lipid and protein metabolism. Insulin action is manifested through binding of its monomeric form to the Insulin Receptor (IR). At present, however, our knowledge about the structural behavior of insulin is based upon inactive, multimeric, and storage-like states. The active monomeric structure, when in complex with the receptor, must be different as the residues crucial for the interactions are buried within the multimeric forms. Although the exact nature of the insulin's induced-fit is unknown, there is strong evidence that the C-terminal part of the B-chain is a dynamic element in insulin activation and receptor binding. Here, we present the design and analysis of highly active (200-500%) insulin analogues that are truncated at residue 26 of the B-chain (B(26)). They show a structural convergence in the form of a new beta-turn at B(24)-B(26). We propose that the key element in insulin's transition, from an inactive to an active state, may be the formation of the beta-turn at B(24)-B(26) associated with a trans to cis isomerisation at the B(25)-B(26) peptide bond. Here, this turn is achieved with N-methylated L-amino acids adjacent to the trans to cis switch at the B(25)-B(26) peptide bond or by the insertion of certain D-amino acids at B(26). The resultant conformational changes unmask previously buried amino acids that are implicated in IR binding and provide structural details for new approaches in rational design of ligands effective in combating diabetes.
Collapse
|
163
|
Limapichat W, Lester HA, Dougherty DA. Chemical scale studies of the Phe-Pro conserved motif in the cys loop of Cys loop receptors. J Biol Chem 2010; 285:8976-84. [PMID: 20068044 DOI: 10.1074/jbc.m109.060939] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The functions of two conserved residues, Phe(135) and Pro(136), located at the apex of the Cys loop of the nicotinic acetylcholine receptor are investigated. Both residues were substituted with natural and unnatural amino acids, focusing on the role of aromaticity at Phe(135), backbone conformation at Pro(136), side chain polarity and volume, and the specific interaction between the aromatic side chain and the proline. NMR spectroscopy studies of model peptides containing proline and unnatural proline analogues following a Phe show a consistent increase in the population of the cis conformer relative to peptides lacking the Phe. In the receptor, a strong interaction between the Phe and Pro residues is evident, as is a strong preference for aromaticity and hydrophobicity at the Phe site. A similar influence of hydrophobicity is observed at the proline site. In addition, across a simple homologous series of proline analogues, the results reveal a correlation between receptor function and cis bias at the proline backbone. This could suggest a significant role for the cis proline conformer at this site in receptor function.
Collapse
Affiliation(s)
- Walrati Limapichat
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | | | | |
Collapse
|
164
|
SOUMA H, KUROSU H, SHOJI A. Precise Structural Analysis of Polypeptides by Quantum Chemical Calculation. KOBUNSHI RONBUNSHU 2010. [DOI: 10.1295/koron.67.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hiroyuki SOUMA
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University
| | - Hiromichi KUROSU
- Graduate School of Humanities and Sciences, Nara Women's University
| | - Akira SHOJI
- Department of Chemistry and Chemical Biology, Graduate School of Engineering, Gunma University
| |
Collapse
|
165
|
Lee BL, Li X, Liu Y, Sykes BD, Fliegel L. Structural and functional analysis of extracellular loop 2 of the Na+/H+ exchanger. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2481-8. [DOI: 10.1016/j.bbamem.2009.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 09/30/2009] [Accepted: 10/06/2009] [Indexed: 10/20/2022]
|
166
|
Kang YK, Park HS. Conformational preferences and cis-trans isomerization of L-3,4-dehydroproline residue. Biopolymers 2009; 92:387-98. [PMID: 19373924 DOI: 10.1002/bip.21203] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The conformational study of N-acetyl-N'-methylamide of L-3,4-dehydroproline (Ac-Dhp-NHMe, the Dhp dipeptide) is carried out using hybrid density functional methods with the self-consistent reaction field method in the gas phase and in solution (chloroform and water). The incorporation of a double bond between C(beta) and C(gamma) into the prolyl ring results in the puckering, backbone population, and barriers to prolyl cis-trans isomerization different from those of the Pro dipeptide. For local minima of the Dhp dipeptide in the gas phase and in water, the C(beta)-C(gamma) bonds become shorter by approximately 0.2 A and the bond angles C(alpha)-C(beta)-C(gamma) and C(beta)-C(gamma)-C(delta) are widened by approximately 8 degrees than those of the Pro dipeptide, and the puckering amplitude is computed to be 0.01-0.07 A, indicating that the 3,4-dehydroprolyl ring is quite less puckered. However, polyproline-like conformations become preferred and the relative stability of the conformation tC with a C(7) intramolecular hydrogen bond decreases as the solvent polarity increases, as found for the Pro dipeptide. The barriers to cis-trans isomerization of the Ac-Dhp peptide bond increase with the increase of solvent polarity and the isomerization is likely to proceed through the clockwise rotation in water, as found for the prolyl peptide bond. The hydrogen bond between the prolyl nitrogen and the following amide N-H group seems to contribute in stabilizing the transition state structures.
Collapse
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
| | | |
Collapse
|
167
|
Chung MK, White P, Lee S, Gagné M. Synthesis of Interlocked 56-Membered Rings by Dynamic Self-Templating. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903478] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
168
|
Hull JJ, Copley KS, Schegg KM, Quilici DR, Schooley DA, Welch WH. De novo molecular modeling and biophysical characterization of Manduca sexta eclosion hormone. Biochemistry 2009; 48:9047-60. [PMID: 19670911 PMCID: PMC2792118 DOI: 10.1021/bi901078y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Eclosion hormone (EH) is an integral component in the cascade regulating the behaviors culminating in emergence of an insect from its old exoskeleton. Little is known regarding the EH solution structure; consequently, we utilized a computational approach to generate a hypothetical structure for Manduca sexta EH. The de novo algorithm exploited the restricted conformational space of disulfide bonds (Cys14-Cys38, Cys18-Cys34, and Cys21-Cys49) and predicted secondary structure elements to generate a thermodynamically stable structure characterized by 55% helical content, an unstructured N-terminus, a helical C-terminus, and a solvent-exposed loop containing Trp28 and Phe29. Both the strain and pseudo energies of the predicted peptide compare favorably with those of known structures. The 62-amino acid peptide was synthesized, folded, assayed for activity, and structurally characterized to confirm the validity of the model. The helical content is supported by circular dichroism and hydrogen-deuterium exchange mass spectrometry. Fluorescence emission spectra and acrylamide quenching are consistent with the solvent exposure predicted for Trp28, which is shielded by Phe29. Furthermore, thermodynamically stable conformations that deviated only slightly from the predicted Manduca EH structure were generated in silico for the Bombyx mori and Drosophila melanogaster EHs, indicating that the conformation is not species-dependent. In addition, the biological activities of known mutants and deletion peptides were rationalized with the predicted Manduca EH structure, and we found that, on the basis of sequence conservation, functionally important residues map to two conserved hydrophobic clusters incorporating the C-terminus and the first loop.
Collapse
Affiliation(s)
| | | | | | | | - David A. Schooley
- Correspondence to: David A. Schooley, Dept. of Biochemistry, University of Nevada, Reno, Nevada 89557; ; Phone: (775)-784-4136; Fax: (775)-784-1419
| | | |
Collapse
|
169
|
De Poli M, Moretto A, Crisma M, Peggion C, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Is the backbone conformation of C(alpha)-methyl proline restricted to a single region? Chemistry 2009; 15:8015-8025. [PMID: 19579242 DOI: 10.1002/chem.200900688] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
C(alpha)-methyl-L-proline, or L-(alphaMe)Pro, is probably the most conformationally constrained alpha-amino acid. In particular, its omega and phi torsion angles are restricted to about 180 and -60 degrees, respectively, and only three ranges of values are theoretically available for psi in mono- or longer peptides, namely, about -30 degrees (cis', 3(10)/alpha-helical structure), 60 degrees (inverse gamma turn), or 140 degrees (trans', poly(L-Pro)(n) II structure). In this work, we examined the tendency of a number of N(alpha)-acyl dipeptide N'-alkylamides of the type RCO-(alphaMe)Pro-Xxx-NHR' or RCO-Xxx-(alphaMe)Pro-NHR', in which Xxx is L (or D)-Ala, Aib (alpha-aminoisoburyric acid), or L (or D)-(alphaMe)Pro, long enough to fold into intramolecularly hydrogen-bonded gamma or beta turns. The results are compared with those obtained for the corresponding dipeptides based on Pro, a well-known turn-forming residue. For the crystal-state 3D-structural analysis we used X-ray diffraction, whereas our solution conformational analysis was heavily based on the FTIR absorption and (1)H and (13)C NMR spectroscopy techniques. We conclude that (alphaMe)Pro is able to explore both trans' and cis' psi areas of the conformational space, but in (alphaMe)Pro the latter is overwhelmingly more populated, in marked contrast to the Pro preference. This finding is a clear indication that in (alphaMe)Pro the major 3D-structural determinant is the C(alpha)-methyl group. The circular dichroism (CD) signature of a peptide type III' beta-turn conformation is also proposed.
Collapse
Affiliation(s)
- Matteo De Poli
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova via Marzolo 1, 35131 Padova, Italy
| | | | | | | | | | | | | | | |
Collapse
|
170
|
Murase T, Zheng RB, Joe M, Bai Y, Marcus SL, Lowary TL, Ng KK. Structural Insights into Antibody Recognition of Mycobacterial Polysaccharides. J Mol Biol 2009; 392:381-92. [DOI: 10.1016/j.jmb.2009.06.074] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 06/26/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
|
171
|
Abstract
Adhesion pili (fimbriae) play a critical role in initiating the events that lead to intestinal colonization and diarrheal disease by enterotoxigenic Escherichia coli (ETEC), an E. coli pathotype that inflicts an enormous global disease burden. We elucidate atomic structures of an ETEC major pilin subunit, CfaB, from colonization factor antigen I (CFA/I) fimbriae. These data are used to construct models for 2 morphological forms of CFA/I fimbriae that are both observed in vivo: the helical filament into which it is typically assembled, and an extended, unwound conformation. Modeling and corroborative mutational data indicate that proline isomerization is involved in the conversion between these helical and extended forms. Our findings affirm the strong structural similarities seen between class 5 fimbriae (from bacteria primarily causing gastrointestinal disease) and class 1 pili (from bacteria that cause urinary, respiratory, and other infections) in the absence of significant primary sequence similarity. They also suggest that morphological and biochemical differences between fimbrial types, regardless of class, provide structural specialization that facilitates survival of each bacterial pathotype in its preferred host microenvironment. Last, we present structural evidence for bacterial use of antigenic variation to evade host immune responses, in that residues occupying the predicted surface-exposed face of CfaB and related class 5 pilins show much higher genetic sequence variability than the remainder of the pilin protein.
Collapse
|
172
|
Kang YK, Park HS, Byun BJ. Puckering transitions of pseudoproline residues. Biopolymers 2009; 91:444-55. [DOI: 10.1002/bip.21150] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
173
|
Paulsen IM, Martin IL, Dunn SMJ. Isomerization of the proline in the M2-M3 linker is not required for activation of the human 5-HT3A receptor. J Neurochem 2009; 110:870-8. [PMID: 19457066 DOI: 10.1111/j.1471-4159.2009.06180.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Each subunit of the cation-selective members of the Cys-loop family of ligand-gated ion channels contains a conserved proline residue in the extracellular loop between the second and third transmembrane domains. In the mouse homomeric 5-hydroxytryptamine type 3A (5-HT(3)A) receptor, the effects of substitution of this proline by unnatural amino acids led to the suggestion that trans-cis isomerization of the protein backbone at this position is integral to agonist-induced channel opening [Nature (2005) vol. 438, pp. 248-252]. We explored the generality of this conclusion using natural amino acid mutagenesis of the homologous human 5-HT(3)A receptor. The conserved proline (P303) was substituted by either a histidine or tryprophan and the mutant receptors were expressed in Xenopus oocytes. These mutations did not significantly affect the magnitude of agonist-mediated currents, compromise channel gating by 5-HT or inhibition of 5-HT-induced currents by either picrotoxin or d-tubocurarine. The mutations did, however, result in altered dependence on extracellular Ca(2+) concentration and a 10-fold increase in the rate of receptor desensitization. These results demonstrate an important role for P303 in 5-HT(3)A receptor function but indicate that trans-cis isomerization at this proline is unlikely to be a general mechanism underlying the gating process.
Collapse
Affiliation(s)
- Isabelle M Paulsen
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | | | | |
Collapse
|
174
|
Kang YK, Kang NS. Conformational preferences ofN-methoxycarbonyl proline dipeptide. J Comput Chem 2009; 30:1116-27. [DOI: 10.1002/jcc.21136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
175
|
Exarchos KP, Exarchos TP, Papaloukas C, Troganis AN, Fotiadis DI. Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation. BMC Bioinformatics 2009; 10:113. [PMID: 19379512 PMCID: PMC2678097 DOI: 10.1186/1471-2105-10-113] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Accepted: 04/20/2009] [Indexed: 11/29/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Konstantinos P Exarchos
- Unit of Medical Technology and Intelligent Information Systems, Department of Computer Science, University of Ioannina, Ioannina, Greece.
| | | | | | | | | |
Collapse
|
176
|
Laufer B, Chatterjee J, Frank AO, Kessler H. Can N-methylated amino acids serve as substitutes for prolines in conformational design of cyclic pentapeptides? J Pept Sci 2009; 15:141-6. [PMID: 18985637 DOI: 10.1002/psc.1076] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The incorporation of proline into cyclic peptides seems to be the most promising way to induce beta-turn structures. Recently, however, it was shown that N-methylated amino acids might be even better suited than proline for introducing turn structures. Another property of proline, the ability to effect cis-peptide bonds, has also been reported for N-methylated amino acids. These findings raise the question if it might be possible to replace a proline by an N-methylated amino acid without altering the desired conformational features. The most important benefit of replacing proline by an N-methylated residue is that one recovers the side-chain functionalities, which could be used for enhancing binding selectivity, or to tune a cyclic peptide concerning its pharmacological properties.Here, we compare cyclic peptides containing one or two prolines or N-methylated alanines and a combination of both with respect to preferred conformations and cis-peptide bonds. In addition, the positions have been investigated where an N-alkylated amino acid has to be incorporated to mimic structural aspects usually introduced by proline residues.
Collapse
Affiliation(s)
- Burkhardt Laufer
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747 Germany
| | | | | | | |
Collapse
|
177
|
Caputo R, Dellagreca M, de Paola I, Mastroianni D, Longobardo L. Novel sulfur and selenium containing bis-alpha-amino acids from 4-hydroxyproline. Amino Acids 2009; 38:305-10. [PMID: 19214702 DOI: 10.1007/s00726-009-0251-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 09/17/2008] [Indexed: 10/21/2022]
Abstract
The synthesis of new substituted prolines carrying at C-4 a second alpha-amino acid residue is reported. The amino acid, L-cysteine or L-selenocysteine, is linked to the proline ring through the sulfur or the selenium atom, respectively. The products were prepared with different stereochemistry at C-4, in few and clean high-yielding steps, with suitable protections for solid phase applications. The introduction of both sulfur and selenium atoms at C-4 of the proline ring seems to enhance significantly the cis geometry at the prolyl amide bond.
Collapse
Affiliation(s)
- Romualdo Caputo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, 80126, Naples, Italy
| | | | | | | | | |
Collapse
|
178
|
Kantharaju, Raghothama S, Raghavender US, Aravinda S, Shamala N, Balaram P. Conformations of heterochiral and homochiral proline-pseudoproline segments in peptides: Context dependentcis-transpeptide bond isomerization. Biopolymers 2009; 92:405-16. [DOI: 10.1002/bip.21207] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
179
|
Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
180
|
Clegg JK, Cochrane JR, Sayyadi N, Skropeta D, Turner P, Jolliffe KA. Solid-State and Solution-Phase Conformations of Pseudoproline-Containing Dipeptides. Aust J Chem 2009. [DOI: 10.1071/ch09151] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The conformations of 14 threonine-derived pseudoproline-containing dipeptides (including four d-allo-Thr derivatives) have been investigated by NMR. In solution, the major conformer observed for all dipeptides is that in which the amide bond between the pseudoproline and the preceding amino acid is cis. For dipeptides in which the N-terminus is protected, the ratio of cis- to trans-conformers does not depend significantly on the side chain of the N-terminal amino acid, or the stereochemistry of the Thr residue. However, for dipeptides bearing a free N-terminus, there are significant differences in the ratios of cis- to trans-conformers depending on the side chain present. Three dipeptides were crystallized and their X-ray structures determined. In two cases, (benzyloxycarbonyl (Cbz)-Val-Thr(ΨMe,Mepro)-OMe and Cbz-Val-Thr(ΨMe,Mepro)-OH), the dipeptides adopt a trans-conformation in the solid state, in contrast to the structures observed in solution. In the third case, (9-fluorenylmethoxycarbonyl (Fmoc)-Val-d-allo-Thr(ΨMe,Mepro)-OH), a cis-amide geometry is observed. These structural differences are attributed to crystal-packing interactions.
Collapse
|
181
|
Wang ML, Li WJ, Wang ML, Xu WB. Support vector machines for prediction of peptidyl prolyl cis/trans isomerization. ACTA ACUST UNITED AC 2008; 63:23-8. [PMID: 14984570 DOI: 10.1046/j.1399-3011.2004.00100.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
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.
Collapse
Affiliation(s)
- M-L Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Southern Yangtze University, Wuxi 214036, China.
| | | | | | | |
Collapse
|
182
|
Flores-Ortega A, Casanovas J, Nussinov R, Alemán C. Conformational preferences of beta- and gamma-aminated proline analogues. J Phys Chem B 2008; 112:14045-55. [PMID: 18842022 PMCID: PMC2836598 DOI: 10.1021/jp807638p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical calculations have been used to investigate how the incorporation of an amino group to the Cbeta- or Cgamma-positions of the pyrrolidine ring affects the intrinsic conformational properties of the proline. Specifically, a conformational study of the N-acetyl-N'-methylamide derivatives of four isomers of aminoproline, which differ not only in the beta- or gamma-position of the substituent but also in its cis or trans relative disposition, has been performed. To further understand the role of the intramolecular hydrogen bonds between the backbone carbonyl groups and the amino side group, a conformational study was also performed on the corresponding four analogues of (dimethylamino)proline. In addition, the effects of solvation on aminoproline and (dimethylamino)proline dipeptides have been evaluated using a self-consistent reaction field model, and considering four different solvents (carbon tetrachloride, chloroform, methanol and water). Results indicate that the incorporation of the amino substituent into the pyrrolidine ring affects the conformational properties, with backbone...side chain intramolecular hydrogen bonds detected when it is incorporated in a cis relative disposition. In general, the incorporation of the amino side group tends to stabilize those structures where the peptide bond involving the pyrrolidine nitrogen is arranged in cis. The aminoproline isomer with the substituent attached to the Cgamma-position with a cis relative disposition is the most stable in the gas phase and in chloroform, methanol and water solutions. Replacement of the amino side group by the dimethylamino substituent produces significant changes in the potential energy surfaces of the four investigated (dimethylamino)proline-containing dipeptides. Thus, these changes affect not only the number of minima, which increases considerably, but also the backbone and pseudorotational preferences. In spite of these effects, comparison of the conformational preferences, i.e., the more favored conformers, calculated for different isomers of aminoproline and (dimethylamino)proline dipeptides showed a high degree of consistency for the two families of compounds.
Collapse
Affiliation(s)
- Alejandra Flores-Ortega
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| |
Collapse
|
183
|
Glaves R, Baer M, Schreiner E, Stoll R, Marx D. Conformational Dynamics of Minimal Elastin-Like Polypeptides: The Role of Proline Revealed by Molecular Dynamics and Nuclear Magnetic Resonance. Chemphyschem 2008; 9:2759-65. [DOI: 10.1002/cphc.200800474] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
184
|
Nascimento AS, Krauchenco S, Golubev AM, Gustchina A, Wlodawer A, Polikarpov I. Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A. J Mol Biol 2008; 382:763-78. [PMID: 18675276 PMCID: PMC2711637 DOI: 10.1016/j.jmb.2008.07.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2008] [Revised: 07/12/2008] [Accepted: 07/17/2008] [Indexed: 10/21/2022]
Abstract
The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 A resolution and 15.8% (R(free)=19.2%) at 1.85 A resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity.
Collapse
Affiliation(s)
- Alessandro S. Nascimento
- Grupo de Cristalografia, Departamento de Física e Informática, Instituto de Física de São Carlos (IFSC), Universidade de São Paulo (USP), Av. Trabalhador Saocarlense, 400, CEP 13560-970, São Carlos, SP, Brazil
| | - Sandra Krauchenco
- Grupo de Cristalografia, Departamento de Física e Informática, Instituto de Física de São Carlos (IFSC), Universidade de São Paulo (USP), Av. Trabalhador Saocarlense, 400, CEP 13560-970, São Carlos, SP, Brazil
| | | | - Alla Gustchina
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Igor Polikarpov
- Grupo de Cristalografia, Departamento de Física e Informática, Instituto de Física de São Carlos (IFSC), Universidade de São Paulo (USP), Av. Trabalhador Saocarlense, 400, CEP 13560-970, São Carlos, SP, Brazil
| |
Collapse
|
185
|
Dasgupta B, Chakrabarti P. pi-Turns: types, systematics and the context of their occurrence in protein structures. BMC STRUCTURAL BIOLOGY 2008; 8:39. [PMID: 18808671 PMCID: PMC2559839 DOI: 10.1186/1472-6807-8-39] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 09/22/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue gamma-turn to six-residue pi-turn. The Schellman motif occurring at the C-terminal end of alpha-helices is a classical example of hydrogen bonded pi-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded beta- and alpha-turns have been identified previously; likewise, a systematic characterization of pi-turns would provide valuable insight into turn structures. RESULTS An analysis of protein structures indicates that at least 20% of pi-turns occur independent of the Schellman motif. The two categories of pi-turns, designated as pi-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length beta- and alpha-turns, pi-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal C alpha-atoms, and this resulted in a comparable number of non-hydrogen-bonded pi-turns (pi-NHB). The presence of shorter beta- and alpha-turns within all categories of pi-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. CONCLUSION pi-turns have been characterized, first using hydrogen bond and the distance between C alpha atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the pi-HB turns, being located on surface cavities, have functional role and there is also sequence conservation.
Collapse
|
186
|
Chatterjee B, Saha I, Raghothama S, Aravinda S, Rai R, Shamala N, Balaram P. Designed peptides with homochiral and heterochiral diproline templates as conformational constraints. Chemistry 2008; 14:6192-204. [PMID: 18491347 DOI: 10.1002/chem.200702029] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a) isolated D-Pro-L-Pro segments which form type II' beta-turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II'-I (betaII'-I, consecutive beta-turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive beta-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa beta-turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5-->1 hydrogen bonded alpha-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx=L-Ala (19).
Collapse
Affiliation(s)
- Bhaswati Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | | | | | | | | | | | | |
Collapse
|
187
|
Jamet H, Jourdan M, Dumy P. NMR and Theoretical Calculations: A Unified View of the Cis/Trans Isomerization of 2-Substituted Thiazolidines Containing Peptides. J Phys Chem B 2008; 112:9975-81. [DOI: 10.1021/jp7118982] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Helene Jamet
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607,CNRS, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| | - Muriel Jourdan
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607,CNRS, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| | - Pascal Dumy
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607,CNRS, 301 rue de la Chimie, 38041 Grenoble Cedex 9, France
| |
Collapse
|
188
|
Mathieu S, Poteau R, Trinquier G. Estimating the "steric clash" at cis peptide bonds. J Phys Chem B 2008; 112:7894-902. [PMID: 18543981 DOI: 10.1021/jp711082d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
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.
Collapse
Affiliation(s)
- Simon Mathieu
- Laboratoire de Chimie et Physique Quantique, IRSAMC, Université Paul-Sabatier, Toulouse Cedex 9, France
| | | | | |
Collapse
|
189
|
A functional proline switch in cytochrome P450cam. Structure 2008; 16:916-23. [PMID: 18513977 DOI: 10.1016/j.str.2008.03.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2008] [Revised: 03/18/2008] [Accepted: 03/22/2008] [Indexed: 11/21/2022]
Abstract
The two-protein complex between putidaredoxin (Pdx) and cytochrome P450(cam) (CYP101) is the catalytically competent species for camphor hydroxylation by CYP101. We detected a conformational change in CYP101 upon binding of Pdx that reorients bound camphor appropriately for hydroxylation. Experimental evidence shows that binding of Pdx converts a single X-proline amide bond in CYP101 from trans or distorted trans to cis. Mutation of proline 89 to isoleucine yields a mixture of both bound camphor orientations, that seen in Pdx-free and that seen in Pdx-bound CYP101. A mutation in CYP101 that destabilizes the cis conformer of the Ile 88-Pro 89 amide bond results in weaker binding of Pdx. This work provides direct experimental evidence for involvement of X-proline isomerization in enzyme function.
Collapse
|
190
|
Exarchos KP, Papaloukas C, Exarchos TP, Troganis AN, Fotiadis DI. Prediction of cis/trans isomerization using feature selection and support vector machines. J Biomed Inform 2008; 42:140-9. [PMID: 18586558 DOI: 10.1016/j.jbi.2008.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 04/26/2008] [Accepted: 05/12/2008] [Indexed: 10/22/2022]
Abstract
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.
Collapse
Affiliation(s)
- Konstantinos P Exarchos
- Unit of Medical Technology and Intelligent Information Systems, Department of Computer Science, University of Ioannina, P.O. Box 1186, GR 45110 Ioannina, Greece
| | | | | | | | | |
Collapse
|
191
|
Flores-Ortega A, Jiménez AI, Cativiela C, Nussinov R, Alemán C, Casanovas J. Conformational preferences of alpha-substituted proline analogues. J Org Chem 2008; 73:3418-27. [PMID: 18351745 PMCID: PMC2679371 DOI: 10.1021/jo702710x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DFT calculations at the B3LYP/6-31+G(d,p) level have been used to investigate how the replacement of the alpha hydrogen by a more sterically demanding group affects the conformational preferences of proline. Specifically, the N-acetyl-N'-methylamide derivatives of L-proline, L-alpha-methylproline, and L-alpha-phenylproline have been calculated, with both the cis/trans isomerism of the peptide bonds and the puckering of the pyrrolidine ring being considered. The effects of solvation have been evaluated by using a Self-Consistent Reaction Field model. As expected, tetrasubstitution at the alpha carbon destabilizes the conformers with one or more peptide bonds arranged in cis. The lowest energy minimum has been found to be identical for the three compounds investigated, but important differences are observed regarding other energetically accessible backbone conformations. The results obtained provide evidence that the distinct steric requirements of the substituent at C (alpha) may play a significant role in modulating the conformational preferences of proline.
Collapse
Affiliation(s)
- Alejandra Flores-Ortega
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
| |
Collapse
|
192
|
Exarchos KP, Exarchos TP, Papaloukas C, Troganis AN, Fotiadis DI. Predicting peptide bond conformation using feature selection and the Naïve Bayes approach. ACTA ACUST UNITED AC 2008; 2007:5009-12. [PMID: 18003131 DOI: 10.1109/iembs.2007.4353465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
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.
Collapse
Affiliation(s)
- Kostas P Exarchos
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Computer Science, University of Ioannina, GR 45110, Ioannina, Greece.
| | | | | | | | | |
Collapse
|
193
|
Steiner T, Hess P, Bae JH, Wiltschi B, Moroder L, Budisa N. Synthetic biology of proteins: tuning GFPs folding and stability with fluoroproline. PLoS One 2008; 3:e1680. [PMID: 18301757 PMCID: PMC2243022 DOI: 10.1371/journal.pone.0001680] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 01/27/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Proline residues affect protein folding and stability via cis/trans isomerization of peptide bonds and by the C(gamma)-exo or -endo puckering of their pyrrolidine rings. Peptide bond conformation as well as puckering propensity can be manipulated by proper choice of ring substituents, e.g. C(gamma)-fluorination. Synthetic chemistry has routinely exploited ring-substituted proline analogs in order to change, modulate or control folding and stability of peptides. METHODOLOGY/PRINCIPAL FINDINGS In order to transmit this synthetic strategy to complex proteins, the ten proline residues of enhanced green fluorescent protein (EGFP) were globally replaced by (4R)- and (4S)-fluoroprolines (FPro). By this approach, we expected to affect the cis/trans peptidyl-proline bond isomerization and pyrrolidine ring puckering, which are responsible for the slow folding of this protein. Expression of both protein variants occurred at levels comparable to the parent protein, but the (4R)-FPro-EGFP resulted in irreversibly unfolded inclusion bodies, whereas the (4S)-FPro-EGFP led to a soluble fluorescent protein. Upon thermal denaturation, refolding of this variant occurs at significantly higher rates than the parent EGFP. Comparative inspection of the X-ray structures of EGFP and (4S)-FPro-EGFP allowed to correlate the significantly improved refolding with the C(gamma)-endo puckering of the pyrrolidine rings, which is favored by 4S-fluorination, and to lesser extents with the cis/trans isomerization of the prolines. CONCLUSIONS/SIGNIFICANCE We discovered that the folding rates and stability of GFP are affected to a lesser extent by cis/trans isomerization of the proline bonds than by the puckering of pyrrolidine rings. In the C(gamma)-endo conformation the fluorine atoms are positioned in the structural context of the GFP such that a network of favorable local interactions is established. From these results the combined use of synthetic amino acids along with detailed structural knowledge and existing protein engineering methods can be envisioned as a promising strategy for the design of complex tailor-made proteins and even cellular structures of superior properties compared to the native forms.
Collapse
Affiliation(s)
- Thomas Steiner
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Hess
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jae Hyun Bae
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Luis Moroder
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | |
Collapse
|
194
|
|
195
|
Moretto A, Terrenzani F, Crisma M, Formaggio F, Kaptein B, Broxterman QB, Toniolo C. Cα-Methyl proline: A unique example of split personality. Biopolymers 2008; 89:465-70. [PMID: 17806106 DOI: 10.1002/bip.20839] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Methylation at the C(alpha)-position of a Pro residue was expected to lock the preceding tertiary amide (omega) torsion angle of the resulting (alphaMe)Pro to the trans disposition and to restrict the phi,psi surface to the single region where the 3(10)/alpha-helices are found (in this five-membered ring residue phi is severely constrained to about +/-65 degrees by its cyclic nature). The results of the present X-ray diffraction work on a selected set of four N(alpha)-blocked, (alphaMe)Pro-containing, dipeptide N'-alkylamides clearly show that, although the region of the conformational map largely preferred by (alphaMe)Pro would indeed be that typical of 3(10)/alpha-helices, the semi-extended [type-II poly(Pro)(n) helix] region can also be explored by this extremely sterically demanding C(alpha)-tetrasubstituted alpha-amino acid. In addition, the known high propensity for beta-turn formation of the Pro residue is further enhanced in peptides based on its C(alpha)-methylated derivative.
Collapse
Affiliation(s)
- Alessandro Moretto
- Department of Chemistry, University of Padova, Institute of Biomolecular Chemistry, 35131 Padova, Italy
| | | | | | | | | | | | | |
Collapse
|
196
|
Abstract
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.
Collapse
Affiliation(s)
- Kun Ping Lu
- Cancer Biology Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 1030, Boston, Massachusetts 02215, USA.
| | | | | | | |
Collapse
|
197
|
Aliev AE, Courtier-Murias D. Conformational analysis of L-prolines in water. J Phys Chem B 2007; 111:14034-42. [PMID: 18027925 DOI: 10.1021/jp076729c] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The results of the ring conformational analysis of L-proline, N-acetyl-L-proline, and trans-4-hydroxy-L-proline by NMR combined with calculations using density functional theory (DFT) and molecular dynamics (MD) are reported. Accurate values of 1H-1H J-couplings in water and other solvents have been determined. Using a two-site equilibrium model, the Cgamma-endo conformer of L-proline in water has been identified as intermediate between gammaTdelta [twist(Cgamma-endo, Cdelta-exo)] and gammaE [envelope(Cgamma-endo)] and the Cgamma-exo conformer as betaTgamma. Both conformers were equally populated at room temperature. The N-acetyl [cis-rotamer gammaTbeta(80%)/gammaE(20%) and trans-rotamer gammaTbeta(61%)/gammaE(39%)] and 4-hydroxy (gammaEpsilon) derivatives showed significant changes in both the population and the geometries of the preferred ring conformers. The combination of NMR predicted populations with the DFT B3LYP/6-311+G(2d,p)/IEFPCM calculations proved successful, resulting in fairly accurate predictions of J-couplings. Simulations using MD were mostly in favor of the two-site equilibrium model between Cgamma-endo and Cgamma-exo conformers, similar to that used for the analysis of NMR J-couplings. Various force fields examined for MD simulations failed to reproduce the ring conformational geometries and populations of L-proline in water accurately, while significantly better agreement with NMR was found for trans-N-acetyl-L-proline using GROMOS and AMBER force fields.
Collapse
Affiliation(s)
- Abil E Aliev
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom.
| | | |
Collapse
|
198
|
Crystal Structure of Glycoside Hydrolase Family 78 α-L-Rhamnosidase from Bacillus sp. GL1. J Mol Biol 2007; 374:384-98. [DOI: 10.1016/j.jmb.2007.09.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 08/31/2007] [Accepted: 09/04/2007] [Indexed: 11/21/2022]
|
199
|
Kang YK, Park HS. Conformational Preferences of Pseudoproline Residues. J Phys Chem B 2007; 111:12551-62. [DOI: 10.1021/jp074128f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
| | - Hae Sook Park
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea, and Department of Radiotechnology, Cheju-halla College, Cheju 690-708, Republic of Korea
| |
Collapse
|
200
|
|