Catalytic Mechanism of Peptide Bond CisTrans Isomerases
Despite the amount of data and the simplicity of the chemical reaction catalyzed, the molecular basis of the catalytic mechanism of PPIases and APIases is still only poorly understood 155 . The considerable degree of amino acid sequence dissimilarity between the subgroups of peptide bond cis-trans isomerases also raises the challenging question of the mechanistic relatedness among the enzymes. At present there is a lack of detailed mechanistic investigations on APIases and multidomain PPIases....
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Theoretical calculations by statistical mechanical simulation, in agreement with experimental data, have shown that polar solvents affect the energy of E isomers of esters more than that of the Z rotamer. The energy difference was reduced from 5.2 kcal mol-1 in the gas phase e 1 to 1.6 kcal mol-1 in the acetonitrile e 35.9 and from 8.5 to 5.2 kcal mol-1 for methyl formate and methyl acetate, respectively. This may be explained by the increased polar character of the carbon-yl group in the more...
Homolytic CisTrans Isomerization
Since the elucidation of the photoisomerization of alkenes in 1928, numerous CTI pathways have been proposed. In fact, many unsaturated compounds may isomerize via different pathways depending on the conditions. For example, polyenes may photoisomerize via either the p,p singlet or triplet excited states and also via photosensitization by singlet-singlet and triplet-triplet intersystem crossing 1 via a perpendicular radical transition state that accounts for the formation of the least stable Z...
Cyclophilins and FKBPs Similar Molecular Basis for Distinct Catalytic Mechanisms
The PPIase domains of cyclophilin and FKBPs do not display any similarities whereas members within each subfamily show a high degree of homology in sequence and in three-dimensional structure, suggesting that conservation of the overall shape of the active site and of certain residues is essential for PPIase activity. Moreover, both enzymes feature structural differences from parvulins, in particular Pinl Fig. 12.2 1,9,12 . Fig. 12.2 Ribbon three-dimensional structures of hCyp18 and hFKBP12 and...
Green Fluorescent Protein and Other GFPlike Proteins
Green fluorescent protein GFP , its mutants and homologs are widely used as biological markers 14-17 . They are particularly useful due to their stability, and the fact that the chromophore is formed in an autocatalytic cyclization that does not require a cofactor. This means that unlike most other bioluminescent reporters GFP fluoresces in the absence of any other proteins, substrates, or cofactors. Furthermore, it appears that fusion of GFP to a protein does not alter the function or location...
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The carbamate anti rotamer is usually favored by 1.0-1.5 kcal mol-1 for steric and electrostatic reasons 33 . Energy difference may be even close to zero in the case of certain carbamates which may be roughly found as a 50 50 mixture of syn and anti isomers. This is the case with many amino acid Boc derivatives, which appear as two well-defined upfield singlets at 1.23 and 1.28 ppm in JH NMR spectroscopy at room temperature instead of the lone singlet at 1.40-1.45 ppm. Rotational barriers are...
Primary Process in Bacterial Photosynthesis and Light Sensor Studied by
Unlike visual rhodopsins that bleach upon illumination, archaeal rhodopsins exhibit photocycle. This is highly advantageous in ultrafast spectroscopic studies and these techniques have been extensively applied in addition to low-temperature spectroscopy 2,12,13 . In particular, bacteriorhodopsin has been regarded historically as the model system to test new spectroscopic methods. As in visual rhodop-sins, the light absorption of archaeal rhodopsins causes formation of red-shifted primary...
Hydroxyprolines
The occurrence of 3S -Hyp is much less frequent than that of 4R -Hyp in the total amino acid content of collagens and in contrast to 4R -Hyp, which exclusively occupies the Yaa position of the Xaa-Yaa-Gly repetitive collagen triplets, 3S -Hyp is found only in the Xaa sequence position, with 4R -Hyp in the Yaa position 6-9 . Since structural analysis of native collagens is difficult to perform, most information about the stabilizing effects of the collagen triple helix has been derived from...
Info Keh
Resolution of the structures of several PPIase effector complexes by X-ray crystallography and NMR as well as SAR studies have opened the way to the development of pseudopeptide and peptidomimetic inhibitors which bind PPIases in the 1-50 imol L-1 range. The ketoamide motif redundant to all natural FK506-like macrolides was proposed to be a mimic of the twisted transition state since both carbonyl groups lie in orthogonal planes. Therefore, two independent research groups synthesized Alaw...
PPIases and Infectious Diseases
PPIases are also found in many unicellular organisms such as bacteria, fungi and parasites and, in most cases, are essential for maintaining membrane integrity, multiplication, virulence, and infectivity of these organisms 2,93,94 . In particular, deletion of PPIase genes attenuates the virulence of pathogenic strains such as Salmonella typhimurium FKBPs , Salmonella enterica SurA , Legionella pneumophila FKBP25 , and Cyanobacterium synechococcus Cyp15 2 . For example, the macrophage...
Pseudoprolines for Enhancing Peptide Cyclization and Turn Induction
Due to its capacity for modulating the cis trans ratio in linear peptides, the WPro concept has been applied for enhancing the well-known tendency of Pro for peptide cyclization 184,185 and the induction of turn conformations 186-188 . As a most challenging target, the linear tripeptide H-Pro-WPro-Pro-OH containing a preformed cis-Pro Thr WMe gt Mepro tertiary amide bond cyclizes instantaneously and free of formation of oligomeric structures to cyclo- Pro-Thr WMe-Mepro -Pro with all peptide...
Conclusions and Perspectives
Since its introduction in the early 1990s, the concept of pseudoprolines is presently becoming recognized as versatile strategy for the synthesis of difficult peptides. The commercial availability of Fmoc-protected building blocks of the type Fmoc-Xaa-WPro facilitates the introduction of this solubilizing, structure-disrupting dipeptide as a temporary protection technique for Ser, Thr, and Cys. Comparative studies have documented the superiority of the WPro strategy in comparison to other...
Structure and Function of Archaeal Rhodopsin
Halobacteria contain four rhodopsins bacteriorhodopsin, halorhodopsin, sensor-yrhodopsin, and phoborhodopsin Fig. 4.2A 11-17 . Bacteriorhodopsin and halorhodopsin are light-driven ion pumps, which act as an outward proton pump and an inward Cl- pump, respectively. Sensoryrhodopsin and phoborhodopsin are photoreceptors that act to produce attractant and repellent responses in phototaxis, respectively. These four archaeal rhodopsins have similar structures seven helices constitute the...
Pseudoprolines for Modulating Polyproline Helices
The use of pseudoprolines to induce and lock in oligopeptides in an all-cis conformation was demonstrated on the example of a polyproline I helix 167 . Depending on the experimental conditions, the formation and oligomerization of C2 monoarylated pseudoproline dipeptide building units can be controlled with respect to their configuration and conformation by aromatic stacking interactions 165 . Electrophilically induced cyclic acetyl formation of O-benzyl dipeptide esters e.g. Fmoc-Pro-Thr-OBn...
Isomerization of Phosphatidylcholine in Large Unilamellar Vesicles
Liposomes such as large unilamellar vesicles obtained by extrusion technique LUVET are generally accepted as close models of cell membranes. Figure 6.3 represents a sketch of a vesicle, where it can be seen that the system consists of two distinct compartments - the aqueous and lipid phases. The phospholipid polar heads face the aqueous internal and external phases, whereas the fatty acid chains form the hydrophobic bilayer of the model membrane. Fig. 6.3 Schematic representation of Large...
Natural PPIase Inhibitors and Their Analogs
CsA, the most potent peptide inhibitor of many members of the cyclophilin family Ki hCypl8 6 nmol L-1 , is a cyclic ll-mer that contains exclusively hydrophobic amino acids, most of them N-methylated. Moreover, it displays an atypical MeBmt residue which is essential for CsA activity though it does not interact with cyclo-philins. The interaction network that stabilizes Cyp CsA complexes was resolved by NMR and X-ray crystallography more than 10 years ago and, as anticipated, involves five...
Pseudoprolines for Modulating Structure and Function of Cyclosporins
Numerous chemical methods for the modulation or optimization of the physico-chemical, pharmacological, and biological properties of natural peptides or lead compounds have been successfully applied in drug development. Pseudoprolines are a versatile alternative to existing strategies for chemical modification of bioac-tive peptides. So far, the incorporation of Pro systems into peptide backbones has been achieved by performing the corresponding WPro building blocks and subsequent coupling to...
Secondary Amide Peptide Bond CisTrans Isomerases
The dynamics of CTI demonstrate the fundamental similarity between prolyl bonds and secondary amide peptide bonds, making it probable that enzymes exist for the rate acceleration of both types of reactions. The relatively low spontaneous rates indicate the potential importance of CTI of secondary amide peptide bonds as rate-limiting step in protein backbone rearrangements preceding the formation of biologically active proteins. Whereas peptidyl prolyl cis-trans isomerases constitute a...
Parvulins
In 1994, the PPIase family of parvulins was discovered by characterizing the prototypical enzyme Par10 from E. coli 129,130 . This PPIase does not exhibit sequence similarity to either cyclophilins or FKBPs. The mature enzyme, which is 92 amino acids long, is enzymatically active in its monomeric state. A similarly small enzyme has, to the best of our knowledge, not been reported so far. Also, no other organism was reported to possess such a small parvulin. Using a PPIase activity approach, E....
Mercaptoproline
The 4R - and 4S -mercaptoproline diastereoisomers, as chalcogen analogs ofthe related hydroxyprolines, were synthesized 42-44 and used sporadically for side-chain cyclizations of peptides via thioether or disulfide bridges to restrict the con-formational space of peptidic macrocycles 45-47 . However, a possible effect of the thiol group on the conformational preferences of the pyrrolidine ring has not been investigated to date. Compared with the hydroxyl group, the effect of a thiol group is...
Pseudoprolines in Bioactive Peptides
More recently, the WPro concept was extended to targeting cis-amide bonds in biologically relevant recognition processes Fig. 11.16 . Fig. 11.16 The WProline concept in molecular recognition and drug design. A Direct insertion of WPro units into biologically active, all-trans peptide sequences containing Ser, Thr, or Cys allows modulation of the physicochemical, biological, and pharmacokinetic properties e.g. as applied in prodrug design . B In Pro-containing peptides the dynamic process of CTI...
Specific Color Regulation of the Retinal Chromophore in Protein
The human eye Fig. 4.1A is an excellent light sensor, possessing high photosensitivity, low noise, wide dynamic range, high spatial and time resolution, etc. Visual excitation is initiated by light absorption through visual pigments present in our eyes 1-10 . Therefore, the excellent light-sensing ability of our vision is due to the properties of the light-sensor proteins in the retina. Protonated 11-cis-retinal Schiff base is a chromophore molecule in visual rhodopsins Fig. 4.1B . Protonated...
Synthesis of Pseudoprolines
The facile synthetic accessibility of WPro building blocks exhibiting differential chemical stabilities and cis trans ratios allows us to mimic and even to enhance the unique properties of Pro in natural peptides and proteins, opening a broad palette of applications in bioorganic chemistry. Pseudoprolines WPro are obtained by reacting the free amino acids Ser, Thr, or Cys with aldehydes or ketones 153-161 Fig. 11.13 . The coupling of amino acid derivatives to a growing peptide chain containing...
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Geometric Isomerization of Unsaturated Fatty Acids in Solution Reactive species such as RS , RSO2 , NO2 , or R3Sn radicals and Br or I atoms have been known for a long-time to induce CTI of double bonds by addition-elimination steps 30 . Scheme 6.4 shows a reaction mechanism that consists of a reversible addition of reactive species X to the double bond to form the radical adduct 1. The reconstitution of the double bond is obtained by b-elimination of X and the result is in favor of trans...
Structural Changes of the Chromophore and Protein upon Retinal
It is well known that rhodopsin is an excellent molecular switch for converting a light signal to an electric response in the photoreceptor cell. As mentioned in the preceding chapter, the highly efficient photoisomerization of rhodopsin quantum yield 0.67 is assured by the extremely fast CTI of the chromophore that is facilitated by the protein environment 10 . How is such a reaction achieved in protein What is the role of protein environment To understand the role of protein, we need to...
EnzymeCatalyzed CisTrans Isomerization of Unsaturated Fatty Acid Residues in
In living cells, membrane properties such as permeability and fluidity have to be flexible to the various conditions therefore there are different mechanisms to effect the necessary modification. Focusing on phospholipids, these mechanisms include changing the saturated unsaturated ratio, changing the chain length or branching of the fatty acid residues, and the phospholipid polar headgroup. There is a strict correlation between the physical properties of biological membranes, going from a...
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26 C. Roach, S. E. Feller, J. A. Ward, S. Raza Shaikh, M. Zerouga, W. Stillwell, Biochemistry 2004, 43, 6344-6351. 27 C. Ferreri, S. Pierotti, A. Barbieri, L. Zambonin, L. Landi, S. Rasi, P. L. Luisi, F. Barigelletti, C. Chatgilialoglu, Photochem. Photobiol. 2006, 82, 274-280. 28 A. von Wallbrun, H. H. Richnow, H. J. Heipieper, J. Bacteriol. 2003, 185, 1730-1733. 29 R. Holtwick, H. Keweloh, F. Meinhardt, Appl. Environ. Microbiol. 1999, 65, 2644-2649. 30 P. Renaud, M. P. Sibi, Eds. Radicals in...
Mechanisms of CisTrans Isomerization around the CarbonCarbon Double Bonds via
Yasushi Koyama, Yoshinori Kakitani, and Hiroyoshi Nagae 3.1 A Concept of a Triplet-Excited Region 15 3.2 Triplet-State Isomerization in Retinal 17 3.2.1 Cis-Trans Isomerization Examined by Electronic Absorption and Raman Spectroscopies and by High-Performance Liquid Chromatography Analysis 17 3.2.2 Triplet-Excited Region in All-trans-Retinal Shown in Terms of Stretching Force Constants Determined by Raman Spectroscopy and Normal Coordinate Analysis 22 3.2.3 Dynamic Triplet-Excited Region in...
Modulation of Ion Channels by PPIases
The ryanodine receptor Ryr , the major calcium release channel in the ER of skeletal and cardiac muscle, is required for excitation-contraction coupling. The Ryr protein forms a tetrameric channel in specific regions of the ER and includes four associated hFKBP proteins. hFKBP12 is associated with Ryrl channels found in skeletal muscle whereas hFKBP12.6 binds specifically to cardiac muscle Ryr2 channels. Ryr molecules are organized in regular arrays in which channels are in close contact with...
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Imidic and secondary amide peptide bonds, echoing motifs of the backbone of oligopeptides and proteins, are among the most widespread functional groups of bioactive molecules. Nineteen out of the 20 gene-coded amino acids form secondary amide peptide bonds, whereas the peptide bond preceding proline is imidic in its chemical nature. Planarity and strong conformational preferences are general features of peptide bonds. Nevertheless, slight deviation from planarity is common in folded polypeptide...
Imidic Peptide Bonds
As the only example of an imidic peptide bond-forming proteinaceous amino acid, proline has long been recognized to play a unique role in the conformational dynamics and reactivity of native and unfolded polypeptide chains, as well as being a structural determinant 33,34 . There is a stabilizing effect in the cis imide bond preceding proline that can also be found for proline surrogates, which can be introduced by posttranslational modifications of the proline ring and by nonribosomal synthesis...
Trigger Factor
Trigger factors merit special attention in that they constitute a subfamily of FKBPs. They are present in all species of eubacteria but lack affinity for FK506. Trigger factors are the only ribosome-bound PPIases identified to date 112,113 . Apparently, bacterial cells contain only a single member of this FKBP subfamily. A cellular concentration of 20 imol L-1 promotes the characterization of this CsA and FK506 insensitive PPIase activity in the E. coli cytosol 112 . In principle, the trigger...
Unique Photochemistry of the Retinal Chromophore in Protein
The photochemistry of the rhodopsin chromophore is also unique in proteins. For instance, the quantum yield of the photoreaction of rhodopsin is known to be high, which forms the molecular basis of the high sensitivity of human vision 2 . The quantum yield is essentially independent of temperature and excitation wavelength. Its fluorescence quantum yield was found to be very low f 10-5 , and an ultrafast reaction was inferred through barrierless excited-state potential surfaces 2,10,12 ....
FK506 Binding Proteins FKBPs
Among the PPIases, FKBPs constitute a large family discovered in 1989 7,8 . At this time, the prototypic human enzyme FKBP12 was identified as a FK506 binding molecule the term FKBP includes all proteins that share amino acid sequence homology with FKBP12, although high-affinity FK506 binding is not a common property of FKBP. Our current thinking is that cellular conditions play a decisive role in the affinity of FKBP for FK506, and FK506-mediated enzyme inhibition may occur in a large part of...
Nomenclature
Molecules in which free rotation around one or more bonds is restricted may exist as distinct stable rotamers in proportions that depend on the free enthalpy difference AG of each rotamer. They can interconvert provided the intrinsic rotational barrier AGi is not too high Fig. 1.1 . In the simplest case, there are two marked energy minima separated by energy barriers to rotation, which often implies either the effective breaking of a chemical bond i.e. C C photoisomerization in ethylene...
Biological Consequences
The relevance of catalyzed and spontaneous peptide bond CTI to the biological function of peptides and proteins has inspired considerable effort in research. Thus, distinct pathways have been identified that allow peptide bond isomers to affect physiological signaling differently. To fully understand isomer specificity of bioreactions at the molecular level, it is essential to characterize the structural and electronic differences between cis and trans peptide bond isomers. Most importantly,...
Bridged Bicyclic Proline Analogs
Among the naturally occurring and synthetic bridged bicyclic proline analogs 2228 82-95 , compounds 24 87,96 and 25 86,97,98 have been analyzed for their effects on the amide bond conformation Fig. 11.6 . For example, in model Ac-2,4-MePro-NHMe or Ac-Tyr-2,4-MePro-NHMe the trans conformation of the peptide bond preceding the bridged proline analog is strongly stabilized gt 95 over the cis conformation, making this proline mimetic well suited for a selective stabilization of trans peptide bonds....
Solvent and pH Effects
Unimolecular CTI proceeds via a single nonplanar transition state that can realize four different configurations 5 . Because the peptide bonds strongly interact with water molecules, solvation was thought to be an important factor determining CTI. However, using 17O shielding constants, no isomer-specific differences in hydration was found in simple amides and proline-containing peptides selectively enriched in 17O at the amide carbonyl group 50 . For acetylproline the hydration state of the...
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In summary, ab initio and hybrid QM MM molecular dynamics studies provide a valuable tool for the investigation of photoinduced CTI. Excited-state MD simulations of two small organic molecules, PSB5 and formaldimine, were carried out in order to assess the performance of different excited-state methods for the description of cis-trans isomerization reactions. In contrast to the majority of previous studies of the same model systems, our approach has the advantage to allow a completely...
Acknowledgments
The author thanks many collaborators in the references. 1 G.Wald, Science 1968, 162, 230-239. 2 R. R. Birge, Biochim. Biophys. Acta 1990, 1016, 293-327. 3 T. Yoshizawa, H. Kandori, in Progress in-Retinal Research, N. Osborne, G. Chader, Ed. Pergamon Press, Oxford, 1992, 3355,. 4 H. G. Khorana, J. Biol. Chem. 1992, 267, 1-4. 5 H. Kandori, Chem. Industr. Lond. 1995, 18, 735-739. 6 Y. Shichida, H. Imai, Cell. Mol. Life Sci. 1998, 54, 1299-1315. 7 T. P. Sakmar, Prog. Nucleic Acid Res. Mol. Biol....
List of Contributors
Universidade Federal de Sao Carlos Departamento de Qu mica Campus Sao Carlos, Rodovia Washington Lu s Sao Carlos - SP 13565-905 Brazil Chryssostomos Chatgilialoglu I.S.O.F. Consiglio Nazionale delle Ricerche Via P. Gobetti 101 40129 Bologna Italy Consiglio Nazionale delle Ricerche Via P. Gobetti 101 40129 Bologna Italy Max Planck Research Unit for Enzymology of Protein Folding Weinbergweg 22 06120 Halle Saale Germany Kwansei Gakuin University Faculty of Science and Technology 2-1 Gakuen Sanda...
Other CisTrans Isomerizations in Organic Molecules and Biomolecules 295
13.2 Cis-Trans Isomerization around Single Bonds 295 13.2.1 Cis-Trans Isomerism of Aryl Compounds 295 13.2.3 Amide Surrogates with Restricted Rotation of a r-Bond 298 13.3 C N-containing Compounds 300 13.3.1 Oximes and Nitroso Compounds 300 13.3.2 Imines and Schiff Bases 300 13.4 Dehydroamino Acids and Dehydropeptides 303 13.4.1 Acryloyl Peptides, Acrylates and Related Molecules 303 13.4.2 Naturally Occurring Dehydroamino Acids and Dehydropeptides 305 13.4.3 Synthetic Dehydroamino Acids and...
Chemical Aspects of the Restricted Rotation of Esters Amides and Related
8.1 Thermodynamic and Kinetic Aspects of Cis-Trans Isomerization 143 8.1.1 Esters and Thioesters 144 8.1.2 Amides and Thioxoamides 145 8.1.3 Oxalamides and Hydrazides 147 8.2 Influence of the Environment on CTI 150 8.2.1 Solvent and Concentration 150 8.3 The Study of CTI of Amides and other Conjugated p-Systems 154 8.3.1 Spectroscopic Techniques 154 8.3.1.2 Spectrometric and Fluorimetric Assays 155 8.3.1.3 Other Spectroscopic Techniques 157 8.3.2 Separation of Z and E Isomers 158 8.3.3 Models...