Structural Analysis Of Peptides Research Articles

Hydrogen exchange-mass spectrometry analysis of beta-amyloid peptide structure.

beta-Amyloid peptide (A beta) is the primary protein component of senile plaques in Alzheimer's disease and is believed to be responsible for the neurodegeneration associated with the disease. A beta has proven to be toxic only when aggregated; however, the structure of the aggregated species associated with toxicity is unknown. In the present study, we use hydrogen-deuterium isotope exchange (HX)-electrospray ionization mass spectrometry (MS) along with enzymatic digestion as a tool to examine at near residue level, the changes in A beta structure associated with aggregation to a fibril form. Our results show that the structure of A beta intermediate species formed early in the course of fibrillogenesis is dependent upon solvent conditions. Additionally, the HX-MS data of peptic A beta fragments suggest that the C-terminal segment of the peptide is approximately 35% protected from exchange in fibril-containing samples, relative to monomeric A beta species prepared in DMSO/H(2)O. The N-terminus (residues 1-4) is completely unprotected from exchange, and the fragment containing residues 5-19 is over 50% protected from exchange in the fibril-containing samples. This work contributes to our understanding of A beta structure associated with aggregation and toxicity and further application of this approach may aid in the design of agents that intervene in the A beta aggregation processes associated with neurotoxicity.

Performance of hybrid methods for large-scale unconstrained optimization as applied to models of proteins.

Energy minimization plays an important role in structure determination and analysis of proteins, peptides, and other organic molecules; therefore, development of efficient minimization algorithms is important. Recently, Morales and Nocedal developed hybrid methods for large-scale unconstrained optimization that interlace iterations of the limited-memory BFGS method (L-BFGS) and the Hessian-free Newton method (Computat Opt Appl 2002, 21, 143-154). We test the performance of this approach as compared to those of the L-BFGS algorithm of Liu and Nocedal and the truncated Newton (TN) with automatic preconditioner of Nash, as applied to the protein bovine pancreatic trypsin inhibitor (BPTI) and a loop of the protein ribonuclease A. These systems are described by the all-atom AMBER force field with a dielectric constant epsilon = 1 and a distance-dependent dielectric function epsilon = 2r, where r is the distance between two atoms. It is shown that for the optimal parameters the hybrid approach is typically two times more efficient in terms of CPU time and function/gradient calculations than the two other methods. The advantage of the hybrid approach increases as the electrostatic interactions become stronger, that is, in going from epsilon = 2r to epsilon = 1, which leads to a more rugged and probably more nonlinear potential energy surface. However, no general rule that defines the optimal parameters has been found and their determination requires a relatively large number of trial-and-error calculations for each problem.

Design and synthesis of peptides that bind α-bungarotoxin with high affinity and mimic the three-dimensional structure of the binding-site of acetylcholine receptor

α-Bungarotoxin (α-BTX) is a highly toxic snake neurotoxin that binds to acetylcholine receptor (AChR) at the neuromuscular junction, and is a potent inhibitor of this receptor. In the following we review multi-phase research of the design, synthesis and structure analysis of peptides that bind α-BTX and inhibit its binding to AChR. Structure-based design concomitant with biological information of the α-BTX/AChR system yielded 13-mer peptides that bind to α-BTX with high affinity and are potent inhibitors of α-BTX binding to AChR (IC50 of 2 nM). X-Ray and NMR spectroscopy reveal that the high-affinity peptides fold into an anti-parallel β-hairpin structure when bound to α-BTX. The structures of the bound peptides and the homologous loop of acetylcholine binding protein, a soluble analog of AChR, are remarkably similar. Their superposition indicates that the toxin wraps around the binding-site loop, and in addition, binds tightly at the interface of two of the receptor subunits and blocks access of acetylcholine to its binding site. The procedure described in this article may serve as a paradigm for obtaining high-affinity peptides in biochemical systems that contain a ligand and a receptor molecule.

Dihedral Angles of Tripeptides in Solution Directly Determined by Polarized Raman and FTIR Spectroscopy

The amide I mode of the peptide linkage is highly delocalized in peptides and protein segments due to through-bond and through-space vibrationally coupling between adjacent peptide groups. Woutersen and Hamm (2000. J. Phys. Chem. B. 104:11316–11320) used coherent femtosecond infrared (IR) spectroscopy to determine the excitonic coupling energy and the orientational angle between the transition dipole moments of the interacting amide I modes of cationic tri-alanine in D2O. Recently, the same parameters were determined for all protonation states of tri-alanine by analyzing the amide I bands in the respective IR and isotropic Raman spectra (Schweitzer-Stenner et al., 2001. J. Am. Chem. Soc. 119:1720–1726.). In both studies, the dihedral angles ϕ and ψ were then obtained by utilizing the orientational dependence of the coupling energy obtained from ab initio calculations on tri-glycine in vacuo (Torri and Tasumi, 1998. J. Raman Spectrosc. 29:81–86) to obtain an extended 31 helix-like structure for the tripeptide. In the present paper, a novel algorithm for the analysis of excitonic coupling between amide I modes is presented, which is based on the approach by Schweitzer-Stenner et al. but avoids the problematic use of results from ab initio calculations. Instead, the dihedral angles are directly determined from infrared and visible polarized Raman spectra. First, the interaction energy and the corresponding degree of wave-function mixing were obtained from the amide I profile in the isotropic Raman spectrum. Second, the depolarization ratios and the amide I profiles in the anisotropic Raman and IR-absorption spectra were used to determine the orientational angle between the peptide planes and the transition dipole moments, respectively. Finally, these two geometric parameters were utilized to determine the dihedral angles ϕ and ψ between the interacting peptide groups. Stable extended conformations with dihedral angles in the β-sheet region were obtained for all protonation states of tri-alanine, namely ϕ+=−126°, ψ+=178°; ϕ±=−110°, ψ±=155°; and ϕ−=−127°, ψ−=165° for the cationic, zwitterionic, and anionic state, respectively. These values reflect an extended β-helix structure. Tri-glycine was found to be much more heterogeneous in that different extended conformers coexist in the cationic and zwitterionic state, which yield a noncoincidence between isotropic and anisotropic Raman scattering. Our study introduces vibrational spectroscopy as a suitable tool for the structure analysis of peptides in solution and tripeptides as suitable model systems for investigating the role of local interactions in determining the propensity of peptide segments for distinct secondary structure motifs.

Fast Peptide Sequencing without MS/MS? Peptide Primary Structure Elucidation by Mass Spectrometry using Partial Hydrolysis

A straightforward procedure for the primary structure elucidation of peptides is presented. It is found that hydrolysis attacks only the N- and C-ends of peptides leading to partial cleavage of adjacent amino acids. Depending on the peptide, either a single or two overlapping peptide ladders are created which can be analysed using a simple mass spectrometer such as a linear time-of-flight mass spectrometer (TOF-MS) with no MS/MS capabilities.The procedure is demonstrated on the peptide Melittin, a 26 amino acid single chain peptide. Melittin was partially hydrolysed. After only 1 min of hydrolysis time two peptide ladders were already fully developed and could be analysed. It was found that Melittin is cleaved from both the C- and the N-terminus. About 80% of the primary structure can be determined from the mass spectrum obtained by MALDI-linear TOF-MS. Advantages of the methodology described are its simplicity and quickness and the fact that there is no need for high-performance mass spectrometers.Besides its analytical value, the partial hydrolysis procedure can be used for educational purposes such as lab courses for students at Universities of Applied Sciences to introduce concepts of modern peptide structure analysis in combination with mass spectrometry.

Atmospheric pressure MALDI/ion trap mass spectrometry.

A new sample ionization technique, atmospheric pressure matrix-assisted laser desorption/ionization (AP MALDI), was coupled with a commercial ion trap mass spectrometer. This configuration enables the application-specific selection of external atmospheric ionization sources: the electrospray/APCI (commercially available) and AP MALDI (built in-house), which can be readily interchanged within minutes. The detection limit of the novel AP MALDI/ion trap is 10-50 fmol of analyte deposited on the target surface for a four-component mixture of peptides with 800-1700 molecular weight. The possibility of peptide structural analysis by MS/MS and MS3 experiments for AP MALDI-generated ions was demonstrated for the first time.

Capillary electrophoresis/tandem mass spectrometry for analysis of proteins from two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis.

Capillary electrophoresis/time-of-flight mass spectrometry(CE/TOFMS) has been used for analysis of in-gel digests of protein spots excised from two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (2-D SDS-PAGE). An off-line purification and preconcentration procedure with a Zip Tip is used before CE/TOFMS analysis which allows for detection of protein spots with <1 picomole of material from 2-D gels. The off-line procedure provides sufficient purification for analysis while maintaining the quality of the CE separation. Using this procedure, several proteins from Coomassie Blue and zinc negatively stained gels are identified by the peptide maps generated and database searching. CE/TOF tandem mass spectrometry is used for the confirmation of database searching results and structural analysis of peptides that do not match the expected peptide maps obtained from the database in order to identify structural modifications. Several modifications were pinpointed and identified by this method.

Localization of O-glycosylation sites in peptides by electron capture dissociation in a Fourier transform mass spectrometer.

The novel technique electron capture dissociation (ECD) of electrospray generated [M + nH]n+ polypeptide cations produces rapid cleavage of the backbone NH-Ca bond to form c and z ions (in the modified notation of Roepstorff and Fohlman). The potential of the Fourier transform mass spectrometry equipped with ECD in structure analysis of O-glycosylated peptides in the 3 kDa range has been investigated. Totally, 85% of the available interresidue bonds were cleaved in five glycopeptides; more stable c ions accounted for 62% of the observed fragmentation. The c series provided direct evidence on the glycosylation sites in every case studied, with no glycan (GalNAc and dimannose) losses observed from these species. Less stable z ions supported the glycan site assignment, with minor glycan detachments. These losses, as well as the observed formation of even-electron z ions, are attributed to radical-site-initiated reactions. In favorable cases, complete sequence and glycan position information is obtained from a single-scan spectrum. The "mild" character of ECD supports the previously proposed non-ergodic (cleavage prior to energy randomization) mechanism, and the low internal energy increment of fragments.

Peptide structural analysis by solid-state NMR spectroscopy.

Solid-state nmr spectroscopy provides a robust method for investigating polypeptides that have been prepared by chemical synthesis and that are immobilized by strong interactions with solid surfaces or large macroscopic complexes. Solid-state nmr spectroscopy has been widely used to investigate membrane polypeptides or peptide aggregates such as amyloid fibrils. Whereas magic angle spinning solid-state nmr spectroscopy allows one to measure distances and dihedral angles with high accuracy, static membrane samples that are aligned with respect to the magnetic field direction allow one to determine the secondary structure of bound polypeptides and their orientation with respect to the bilayer normal. Peptide dynamics and the effect of polypeptides on the macroscopic phase preference of phospholipid membranes have been investigated in nonoriented samples. Investigations of the structure and topology of membrane channels, peptide antibiotics, signal sequences as well as model systems that allow one to dissect the interaction contributions in phospholipid membranes will be presented in greater detail.

分子設計へのコンピュータ化学の貢献

Computational methods for drug design and its application for structure-based drug design using crystallographic data and NMR solution structural data were briefly described in view of interaction of ligands with or without structures of the target receptors. Analysis of the hydrolytic mechanism of β-lactamases whose 3D stuctures has been known led to understanding a specific recognition of β-lactam antibiotics and to design of a new candidate for anti-MRSA antibiotics. Conformational analysis of peptide derivatives whose receptor structures have not known is the other example for design of new skeletons of nonpeptide compounds. Receptor-bound structure analysis of antagonist or agonist peptides suggested different conformations of the peptides. This may be due to a different receptor structure as a consequence of a large structural change of receptors upon binding of agonists.

Gene cloning and amino acid sequence analysis of triose-phosphate isomerase of Schistosoma japonicum Chinese strain

A pair of primers was synthesized according to the DNA sequence of Schistosoma japonicum Philippine strain, and the mRNA of adult worms of S. japonicum Chinese strain was prepared. The gene of triose-phosphate isomerase of S. japonicum Chinese strain (SjC TPI) was successfully cloned from the mRNA through reverse transcription polymerase chain reaction (RT-PCR) technic with the primers. The DNA sequence of the gene showed that the open reading frame of encoding SjC TPI DNA includes 759bp, which has 84% homology to Sm TPI, 99.7% homology to SjP TPI. The analysis of deduced amino acid sequence of SjC TPI indicates that SjC TPI is 84.9% (214/252) identical with Sm TPI and 99.2% (250/252) with SjP TPI. The peptide-structure analysis presents 7 extra-surface, hydrophilic regions in the molecule of SjC TPI, the molecular weight of SjC TPI is 27,619. The isoelectric point is 7.38.

Determination of lumenal orientation of microsomal 50-kDa esterase/N-deacetylase.

The amino acid arrangements responsible for the insertion and specific lumenal orientation of proteins having an uncleaved signal-peptide-like anchor are poorly understood. A 50-kDa protein having a hydrophobic N-terminus similar to the lumenal glycoprotein 11beta-hydroxysteroid dehydrogenase [Ozols, J. (1995) J. Biol. Chem. 270, 2305-2312] was identified in detergent-solubilized microsomes. The posttranslational modifications and the membrane orientation of the 50-kDa protein were investigated using the approaches of protein structure analysis. Sequence analysis of the entire 50-kDa protein showed a lack of structural relatedness to the steroid dehydrogenase beyond the membrane binding segment. Structure analysis of peptides revealed that carbohydrate is attached at Asn-77 and Asn-281, implying that these sites of the 50-kDa protein are oriented toward the lumenal side of the endoplasmic membrane (ER). Specific enzymatic deglycosylation on the intact protein identified the two glycans as high mannose carbohydrate rather than of the complex type, suggesting that the protein had not undergone further trafficking steps beyond the lumen of ER. Chemical modification of cysteinyl residues showed a lack of free thiols in the intact protein. Peptide mapping identified one disulfide bond between Cys-115 and -340 further restricting the bulk of the protein to the lumenal compartment. Proteolysis of intact and solubilized microsomes showed that the 50-kDa protein is resistant to fragmentation at the conditions which led to the removal of the membranous segments from cytochrome b5 and the NADH-cytochrome b5 reductase. The proposed model of the 50-kDa protein predicts one transmembrane segment at the N-terminus, flanked by positively charged residues on the cytosolic surface and negatively charged residues on the lumenal side of the hydrophobic domain, with most of the polypeptide projecting into the lumen of the ER. The stated similarities in the topology between 11beta-steroid dehydrogenase and 50-kDa protein envision their transmembrane segment consisting of a basic residue(s) followed by an array of some 17 hydrophobic residues containing the Ala-Tyr-Tyr-X-Tyr cluster, where X represents a hydrophobic amino acid, which terminates with acidic residues. It is proposed here that such a motif may constitute a lumenal targeting signal for a set of single-membrane-spanning proteins that are otherwise structurally and functionally unrelated.

Structure analysis of collagen-model peptides with (Pro-Pro-Gly) and (Pro-Hyp-Gly) sequence repeats

Structure analysis of collagen-model peptides with (Pro-Pro-Gly) and (Pro-Hyp-Gly) sequence repeats

Peptide models XX. Aromatic side-chain–backbone interaction in phenylalanine-containing diamide model system. A systematic search for the identification of all the ab initio conformers of N-formyl-L-phenylalanine-amide

Phenylalanine is the simplest among the four natural amino acid residues that have aromatic side chains. The ab initio conformational analysis performed at the RHF/3-21G level on a phenylalanine-containing diamide model system (N-Formyl-L-Phe-NH2) revealed 19 different structures. Single-point energy calculations were performed using RHF/6-31+G* and DFT(B3LYP)/6-311++G** levels for all conformers. The inverse (γL) and the normal (γD) gamma turn, the extended (βL), the left-handed helical [Formula: see text], and the inverse polyproline II [Formula: see text] backbone conformers each have three (g+, a, and g−) side-chain (χ1,) rotamers. The [Formula: see text] and the [Formula: see text] type main-chain conformers have only two side-chain orientations, respectively. No minima have been found for the conformational building unit of the right-handed helical [Formula: see text] and for the polyproline II [Formula: see text] structures. The present ab initio conformational analysis for For-L-Phe-NH2 is a unique example in which a systematic and complete conformational set was established for a diamide system with an aromatic side chain. Analytic vibrational frequency calculations were established for all stationary points found as minima on the potential energy surface. These data may be used in the future as reference conformers in more detailed vibrational and (or) chemical shielding calculations or during the structural analysis of peptides and proteins by X-ray or NMR techniques. Keywords: ab initio peptide conformers, all RHF/3-21G structures of For-L-Phe-NH2, backbone – side-chain interaction in phenylalanine-containing peptide models.

Posttranslational modification of tubulin by palmitoylation: II. Identification of sites of palmitoylation.

As shown in the companion article, tubulin is posttranslationally modified in vivo by palmitoylation. Our goal in this study was to identify the palmitoylation sites by protein structure analysis. To obtain quantities of palmitoylated tubulin required for this analysis, a cell-free system for enzymatic [3H]palmitoylation was developed and characterized in our companion article. We then developed a methodology to examine directly the palmitoylation of all 451 amino acids of alpha-tubulin. 3H-labeled palmitoylated alpha-tubulin was cleaved with cyanogen bromide (CNBr). The CNBr digest was resolved according to peptide size by gel filtration on Sephadex LH60 in formic acid:ethanol. The position of 3H-labeled palmitoylated amino acids in peptides could not be identified by analysis of the Edman degradation sequencer product because the palmitoylated sequencer products were lost during the final derivatization step to phenylthiohydantoin derivatives. Modification of the gas/liquid-phase sequencer to deliver the intermediate anilinothiozolinone derivative, rather than the phenylthiohydantoin derivative, identified the cycle containing the 3H-labeled palmitoylated residue. Therefore, structure analysis of peptides obtained from gel filtration necessitated dual sequencer runs of radioactive peptides, one for sequence analysis and one to identify 3H-labeled palmitoylated amino acids. Further cleavage of the CNBr peptides by trypsin and Lys-C protease, followed by gel filtration on Sephadex LH60 and dual sequencer runs, positioned the 3H-labeled palmitoylated amino acid residues in peptides. Integration of all the available structural information led to the assignment of the palmitoyl moiety to specific residues in alpha-tubulin. The palmitoylated residues in alpha-tubulin were confined to cysteine residues only. The major site for palmitoylation was cysteine residue 376.

15N labeling method of peptides using a thioredoxin gene fusion expression system: an application to ACTH-(1–24)

For structure analysis of peptides by multinuclear NMR, stable isotope-labeled samples are required. A direct over-expression system by E. coli cells does not work for that purpose because of rapid degradation of the peptides and/or the mRNA in host cells. We here developed an over-expression system by means of thioredoxin gene fusion system. The fused protein composed of thioredoxin and the objective peptide was expressed in E. coli and then the peptide part was released by enterokinase. This system was successfully applied for the production of 15N-labeled human adrenocorticotropic hormone fragment (ACTH-(1-24)) as needed for multinuclear NMR analysis.

Chemical techniques employed for the primary structural analysis of proteins and peptides.

This chapter summarises modern microchemical approaches to the purification, identification and primary structure analysis of peptides and proteins. Discussion of high-sensitivity purification methods is restricted to two-dimensional polyacrylamide gel electrophoresis (2-DE) and microbore/capillary column reversed-phase high-performance liquid chromatography (RP-HPLC). Associated techniques are discussed, particularly with respect to analysis of the products with current automated amino acid sequencers and mass spectrometers.

A novel computer modeling approach to the structures of small bioactive peptides: the structure of gonadotropin releasing hormone.

A novel computer modeling approach suitable for the structure analysis of small bioactive peptides has been developed. This approach involves identification of conformational patterns in protein structure data bank based on the sequence homology with the bioactive peptide. The models built on the basis of this homology and having common conformational patterns are analyzed under the structural constraints derived from the activity data of various synthetic analogs of the peptide. Application of this procedure to the gonadotropin-releasing hormone (GnRH) resulted in a library of possible structures for GnRH, 9 among which shared a common beta-turn. Further analysis of the structures containing the beta-turn motif, in the context of the structure-activity data, led to a model for the active conformation of GnRH. The topology of the putative receptor binding site of the hormone is defined by a contiguous surface formed through an appropriate juxtaposition of the N-terminal pGlu1, the guanidyl group of Arg8, aromatic side chain of Trp3, and the Gly10-NH2 at the C-terminal end.

Isozyme developments in mammalian class-I alcohol dehydrogenase. cDNA cloning, functional correlations, and lack of evidence for genetic isozymes in rabbit.

Isozyme patterns differ widely among the classical type (class I) of mammalian alcohol dehydrogenases. For the rabbit enzyme, the possibility of isozymes has been reported but structural evidence is lacking. This system was now studied at both the mRNA/cDNA and protein levels. Ten cDNA clones, coding for class-I alcohol dehydrogenase, were isolated from a rabbit liver cDNA library using a human DNA fragment as probe. The cDNA spanned 1296 bp, including the entire coding region. All clones coded for the same polypeptide and Northern blots identified a single mRNA corresponding to about 1.5 kb. Comparison of two protein forms (CC and BC) by HPLC peptide fingerprinting and structural analysis revealed peptide segments identical in amino acid sequence. Consequently, direct protein analyses and Northern blots show the presence of only one primary translation product. The data suggest that lagomorphic alcohol dehydrogenase, like the rodent enzyme, is not as isozyme rich as it may appear superficially, and that secondary modifications contribute substantially to mammalian alcohol dehydrogenase multiplicity. The active center of the rabbit enzyme suggests similarities to the horse S, human gamma, and rat enzyme structures, compatible with a steroid dehydrogenase activity shown experimentally. Typical class-I properties were established by direct analysis and confirmed by structural properties (Km for cyclohexanol 0.8-1.1 mM, for ethanol 1.6-1.9 mM). The isozyme versus species differences mark the variability of class-I alcohol dehydrogenase versus class III and suggest a parallelism between rapid mutational differences and frequent duplicatory events.

Peptide/protein structure analysis using the chemical shift index method: Upfield α-CH values reveal dynamic helices and α L sites

The α-CH shifts observed by 1H NMR for medium-sized peptides and for an unusual small protein, hevein, which has a high density of α L conformations within its 43 residue length, reveal that the recently introduced chemical shift index (CSI) analysis places short dynamic helices (α R) and α L residues in the same category as stable helices. The method appears to be a promising addition to the arsenal of methods for peptide structure analysis and is clearly not limited to rigid protein systems.