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An empirical model, based on classic kinetics, was developed for quantitative prediction of electron-transfer dissociation (ETD) and electron-capture dissociation (ECD) spectra of peptides. The model includes most fragmentation pathways described in the literature plus some additional pathways based on the author's assumptions and observations. The ETD model was trained with more than 7000 ETD spectra, with and without supplemental activation. The ECD model was trained with more than 6000 ECD spectra. The trained ETD and ECD models are able to predict ETD and ECD spectra with reasonable accuracy in ion intensities for peptide precursors up to 4000 u in mass. 10.1021/ac902733z

Natural and non-natural cyclic peptides are a crucial component in drug discovery programs because of their considerable pharmaceutical properties. Cyclosporin, microcystins, and nodularins are all notable pharmacologically important cyclic peptides. Because these biologically active peptides are often biosynthesized nonribosomally, they often contain nonstandard amino acids, thus increasing the complexity of the resulting tandem mass spectrometry data. In addition, because of the cyclic nature, the fragmentation patterns of many of these peptides showed much higher complexity when compared to related counterparts. Therefore, at the present time it is still difficult to annotate cyclic peptides MS/MS spectra. In this current work, an annotation program was developed for the annotation and characterization of tandem mass spectra obtained from cyclic peptides. This program, which we call MS-CPA is available as a web tool (http://lol.ucsd.edu/ms-cpa_v1/Input.py). Using this program, we have successfully annotated the sequence of representative cyclic peptides, such as seglitide, tyrothricin, desmethoxymajusculamide C, dudawalamide A, and cyclomarins, in a rapid manner and also were able to provide the first-pass structure evidence of a newly discovered natural product based on predicted sequence. This compound is not available in sufficient quantities for structural elucidation by other means such as NMR. (1) In addition to the development of this cyclic annotation program, it was observed that some cyclic peptides fragmented in unexpected ways resulting in the scrambling of sequences. In summary, MS-CPA not only provides a platform for rapid confirmation and annotation of tandem mass spectrometry data obtained with cyclic peptides but also enables quantitative analysis of the ion intensifies. This program facilitates cyclic peptide analysis, sequencing, and also acts as a useful tool to investigate the uncommon fragmentation phenomena of cyclic peptides and aids the characterization of newly discovered cyclic peptides encountered in drug discovery programs.

We present an algorithm for the deconvolution of isotope-resolved mass spectra of complex peptide mixtures where peaks and isotope series often overlap. The algorithm formulates the problem of mass spectrum deconvolution as a classical statistical problem of variable selection, which aims to interpret the spectrum with the least number of peptides. The LASSO method is used to perform automatic variable selection. The algorithm also makes use of the quantized distribution of peptide masses in the NCBInr database after in silico trypsin digestion as filters to aid the deconvolution process. Errors in the expected isotope pattern are accounted for to avoid spurious isotope series. The effectiveness of the algorithm is demonstrated with annotated ESI spectrum of known peptides for which the peaks and isotope series are highly overlapping. The algorithm successfully finds all correct masses in the experimental spectrum, except for one spectrum where an additional refinement procedure is required to obtain the correct results. Our results compare favorably to those from a widely used commercial program.

Cysteine-scanning and spin-labeling methods are used to prepare singly spin labeled recombinant peptides for electron paramagnetic resonance studies of the partial domain regions at the tetramerization site of erythroid spectrin. The result provides strong evidence that the region identified via sequence homology as the partial domain in the C-terminus of betaI spectrin consists of helical regions.

Time-resolved ultraviolet (UV) spectroscopic and conductivity studies were conducted for defining the potential reactions of Met radical cations in (beta)AP (amyloid peptide) and for determining whether the Met radical cations can be stabilized through bond formation with either oxygen or nitrogen atoms of the adjacent peptide bonds. Results indicate that the carbon-centered radicals are the precursors for peroxyl radicals.

The backbone conformation of a peptide or protein defines its circular dischroism spectrum in the range 190-240 nm, providing a uniquely convenient tool for assigning secondary structure. A two-state helix-coil model underlies all calculation all calculation of fractional helicities FH from CD spectra of helical polypeptides.

The function of hydrogen bonding in the evolution of the nine typical amide bonds are discussed on the basis of force field calculations on the monomer and multimers (n=6) and solution spectra of N-methylacetamide (NMA). The effects of temperature on the structure and the changes in the strength of the hydrogen bonding within a structure of NMA are presented to explain the shortcomings in the results obtained from vibrational spectroscopy.

Nonplanarity of peptide bonds is studied by the conformationally dependent variations of the N-C tortional angle and by using a database of ab initio gradient optimized structures. Ab initio calculations of ALA-ALA provided a good estimate of the flexibility as a function of interactions between its neighboring residues.

A cold ion trap in combination with table-top lasers is used to measure a vibrationally resolved UV spectrum of doubly protonated gramicidin S (GS) in the gas phase and a highly resolved, conformer-specific IR spectrum in the 6 [mu]m fingerprint region. The derived qualitative constraints, along with the measured vibrational frequencies for the GS offer a benchmark for computations of peptide structure.

The influence of laser wavelength on electron detachment from peptide dianions is studied. It is observed that at 260 nm the detachment yield depends on the absorption coefficients of the aromatic amino acids present in the peptide and at 220 nm the sequence and structure of the peptide influences the detachment process.

The studies of [C.sub.18]IIGLM-N[H.sub.2] which is utilized as a biomimic model compound to form aggregates, and interactions of its Langmuir monolayer with congo red aqueous solution are presented.

Several first-principles studies are conducted to measure the ultraviolet absorption and circular dichroism (CD) of a cyclic dipeptide. The results show that the CD spectrum of the peptides exhibit amide, as well as aromatic units transitions.

An analysis explains the solution structure of a peptide with high population of a stable [alpha]-helical structure in its center. The bending of the peptide [alpha]-helix is found to be a result of the interaction between N-terminal tryptophan and leucine at the middle of the peptide sequence.

Hairpin peptide beacons (HPB) are designed to maximize fluorescence quenching in the absence of a protein target by forming stable hairpins. The advantage of the hairpin peptide beacons includes the increased fluorescence responsiveness and the generic design.

The formation of the cleavage of the amino acid backbone and the modification of its side chains by its oxidation by an iron-based oxidant is discussed. The oxidation technique can also be applied easily to various peptides and proteins.

The replica exchange molecular dynamic (REMD) simulations of GB1 peptide is carried out in which 20 peptide ensembles are generated as a function of temperature. It is observed that the peptide ensembles in the middle range of temperature around 400 K are suitable to the low temperature experimental NMR data and provide groups of models for observing the heterogeneity present in the empirical ensembles.

An ab initio integrated computational approach is applied to evaluate the interpretation of the continuous wave electron spin resonance (CW-ESR) spectra of the double-spin labeled, [3.sub.10]-helical, peptide Fmoc-[(Aib-Aib-TOAC).sub.2]-Aib-OMe dissolved in acetonitrile. It is suggested that combination of sensitive ESR spectroscopy and sophisticated modeling can provide three-dimensional (3D) structural and dynamic information on molecular systems.

Four new cyclodepsipeptides, pteratides I-IV (1-4), are isolated from the extract of a Pterula species collected from a Malaysian tropical forest. The Pterula sp. is found to be a source of the pterulamides, six highly N-methylated linear peptides with unusual N- and C-end groups.

Protein circular dichroism (CD) calculations to compute CD spectrum of a protein from its atomic coordinates, which use the addition charge-transfer chromophores to the matrix method, are presented. The calculations significantly improve the accuracy of calculated protein CD spectra between 170 and 190 nm and also give the first assignment of an interpeptide charge-transfer band in a CD spectrum.

A structural biology technique is developed by which spin-labeled EPR spectroscopy is used to determine the membrane topology of an integral membrane protein inserted into magnetically aligned phospholipid layers (bicelles). The helical tilt of the peptide can be easily and directly calculated by the corresponding EPR spectra in this method without conducting spectral simulations, due to the high sensitivity of EPR spectroscopy.

Infrared (IR)/ultraviolet (UV) hole-burning spectroscopy is performed on individual conformers of the protected dipeptide Z-Alb-Pro-NHMe to elucidate both the H-bonding motif as well as the backbone structure. The results are compared with density functional theory (DFT) calculations, showing that the backbone is locally constrained to an alpha-conformation by Alb and to a gamma-turn by Pro.

The quartz crystal microbalance-dissipation (QCM-D), atomic force microscopy (AFM) and sum frequency generation (SFG) techniques are employed to understand and compare the in situ adsorption of a model amphiphilic peptide, Ac(LKKLLKLLKKLLKL)NH2 (LK(sub 14)), at the hydrophobic surface/water and hydrophilic surface/water interface. This combined approach is advantageous for analyzing the peptide behavior at the aqueous/solid interface as it independently examines the morphological and mechanical behavior in response to the surface hydrophobicity.

An investigation is conducted on peptide molecules consisting of a peptide linkage with one or two substituents in the gas phase by Fourier transform microwave spectroscopy, paying special attention to the internal rotation of the substituents relative to the central linkage framework. It is found that, in sharp contrast with the stiff structure around the central C-N bond of the linkage, the internal rotations of the substituents are of low frequency and thus of large amplitude and are extremely susceptible to their local environment.

For simulating the response of peptides to sequences of IR pulses, two algorithms are developed and applied to N-methyl acetamide (NMA) and a 17 residue alpha-helical peptide (YKKKH17) in D(sub 2)O. a fluctuating vibrational-exciton for the amide 1 mode is constructed form molecular dynamics trajectories, coupling with the environment is described using a density functional theory electrostatic map, Gaussian fluctuation is adequate for NA and for isotopically labeled bands in large peptides.

Large molecule mass spectroscopy is shown to be a new, unbiased assay for screening a pool of potential substrates that load carrier domains found in nonribosomal peptide synthetase. Combining the high resolving power of Fourier transform mass spectroscopy with the ability of adenylation domains to select their own substrate, the mass change that takes place upon the formation of a covalent intermediate thus identifies the substrate.

The use of high performance mass spectrometry (MS) continues to evolve as a powerful complement to more widespread assays for the analysis of nonribosomal peptide/polyketide syntheses. The MS-based approach provides valuable information with minimal bias concerning intermediate localization, structural heterogeneity and occupancy on carrier sites without the use of radioactive substrates.

The aggregation and packing of a membrane-disruptive beta-hairpin antimicrobial peptide, protegrin-1 (PG-1), in the solid state are investigated to understand its oligomerization and hydrogen-bonding propensity. The intermolecular packing of PG-1 found in the solid state is consistent with its oligomerization in lipid bilayers.

The structure of the complex of the cyclic peptide bound to BIV TAR RNA determining using heteronuclear NMR methods is reported. The structure reveals a beta-hairpin conformation in the bound peptide, which adopts an unexpected orientation in the major groove of the RNA opposite those observed for peptides derived from the Tat protein.

A site-directed fluorescence labeling and quenching strategy is used to investigate the orientation of different peptides bound to DnaK from Escherichia coli. Results indicate that differential hydrogen-bonding patterns and steric constraints of the central peptide residues are likely causes for differences in their-binding orientations.

The first solid-state NMR, crystallographic, and quantum chemical investigation of the origins of the (super 13)C NMR chemical shifts of the imidazole group in histidine-containing dipeptides is reported. Incorporation of hydrogen bond partner molecules is found to be essential in order to reproduce the chemical shifts observed experimentally.

Octadecapeptides carrying a ferrocene moiety at the molecular terminal are self-assembled on gold, and long-range electron transfer from the ferrocene moiety to gold is investigated by electrochemical methods. Effects on electron transfer of dipole moment of helical peptides, linkers connecting the peptide to gold, and chromophores introduced into the side are discussed.

Single-crystal NMR is used to determine (super 15)N shielding tensors for the central peptide groups in GGV, AGG, and APG. The findings show that the angle between the downfield component [delta(sub 11)] and the N-H or the N-C(super delta)(pro) bonds is in the range of 20-23 degree.

Single-crystal NMR is used to determine (super 15)N shielding tensors for the central peptide groups in GGV, AGG, and APG. The findings show that the angle between the downfield component [delta(sub 11)] and the N-H or the N-C(super delta)(pro) bonds is in the range of 20-23 degree.

The application of infrared photofragment spectroscopy to the amino acids tyrosine and phenylalanine, and two pentapeptides, bradykinin fragment 1-5 and [Leu]-enkephalin, all bound to a potassium cation is presented. The striking feature in the [Leu]-enkephalin spectrum is the high infrared activity of the tyrosine side-chain modes, which can be clearly identified from comparison to the experimental spectrum, but which is not reproduced by the DFT calculations.

The positive character of the peptide and the specific affinity for negatively charged micelles indicate the driving force of the interaction is primarily electrostatic, thus suggesting that, as observed for peptides with potency at micromolar concentration, indeed the target of Hb33-61a is the lipid membrane and not a specific receptor (66). It concluded that Hb33-61a constitute an interesting model to progress in the understanding of the molecular basis of antimicrobial peptides (AMP's) biological activity.

The linear-infrared and two-dimensional infrared (2D IR) spectra in the amide-I' region of the alanine dipeptide and its (super 13)C isotopomers in aqueous solution (D2O) are reported. The experimental results and simulations are consistent with a PP(sub II)-like conformation for the alanine dipeptide in aqueous solution, in which two amide-I' modes are highly localized and whose frequency distributions are uncorrelated.

Sequence-selective recognition of peptides is expected to be an essential process for the site-specific recognition of protein surfaces, which leads to the control of protein functions and to the understanding of biological events at protein surfaces such as protein-protein or protein-oligopeptide interactions. The study aiming at the pinpoint recognition of protein surfaces by the self-assembled hollow receptors is presented.

The 204-nm UV resonance Raman spectra of the polyproline II and alpha-helical states of a 21-residue mainly alanine peptide is examined in different H2O/D2O mixtures is examined. The findings indicate that the UVR spectra of the AmIII and AmII' bands of both the PPII conformation and the alpha-helical conformation can be exactly modeled as the linear sum of the fully N-H protonated and N-D deuterated peptides.

Four analytical generalized Born models are implemented and their performance is investigated in conjunction with the GROMOS96 force field. A general strategy, which involves using different combinations of force fields and solvent models in different applications, is suggested.

Compounds consisting of the unsubstituted gamma-aminoxy acid cannot form intramolecular hydrogen bonds because the carbon backbone tends to adopt consecutive anti conformations. With the addition of a phenyl group at gamma-position, the resulting gamma-aminoxy peptide favors the anto orientation of bulky phenyl group relative to the consecutive homochiral 10-membered-ring hydrogen bonds form a novel helial structure.

A misconception among the protein design community is that a highly stable peptide scaffold is required to enforce a nonpreferred metal ion coordination environment. The presented research demonstrates that uncommon coordination geometries could be achieved even with relatively low peptide self-affinities.

The assignments and conformational dependencies of the UV resonance Raman bands of the amide peptide and its isotopically substituted derivatives in both their alpha-helical and PPII states is examined. The analysis confirms the complex nature of the amide III region, which contains many vibrational modes.

An attempt is made to combine the replica-exchange Monte Carlo method and the reference interaction site model (RISM) theory for simulating a peptide molecule in aqueous solution. It is argued that employing the combined approach reduces the number of replicas required for peptide molecule immersed in water.

Techniques such as X-ray crystallography and nuclear magnetic resonance (NMR) provided useful atomic resolution information but NMR only provided direct real time information on a millisecond time scale. Time-resolved X-ray diffraction was carried out with a picosecond resolution.

The recently developed method of analysis is applied to measure the binding of penetratin and its analogues PenArg (lysines of arginines) and PenLys (arginines for lysines) to negatively charged vesicles, in search of clues to the observed vast differences between the peptides in cell association. The significant changes of the contributions to circular dischroism (CD) spectra from aromatic residues due to their insertion into the membrane were observed.

Differential scanning calorimetry is used to study the thermal denaturation of murine major histocompatibility complex class II (MHC II), I-E(super k). All of the I-E(super k)-Hb(mut) molecules exhibited greater thermal stability at pH 5.5 than at pH 7.4 as for the I-E(super k)-Hb(wt) molecule, which can explain the peptide exchange function of MHC II.

A high-resolution solid-state NMR experiments of salt content like peptides and proteins, performed with less rf-field amplitudes, are reported. For the purpose of this experiment, to obtain high spectral resolution, the Magic-angle sample Spinning (MAS), and radio frequency (RF) pulse sequence are used.

The carbon-13 nuclear magnetic resonance spectra of a series of tryptophan-containing peptides and model systems, together with their X-ray crystallographic structures are presented. Quantum chemical methods are used to predict the C nuclear magnetic resonance (NMR) shifts or shieldings, for all nonprotonated aromatic carbons.

The complexation of vanadium (V) by five dipeptides differing by the nature of the side chains is studied using spectroscopic methods. The result shows that peptides or proteins cannot interact with vanadium by random binding at any peptide linkages as terminal amino and terminal carboxylate may be both required for a vanadium complexation.

A general and efficient synthetic approach toward unsymmetrical two-stranded peptide structures is developed starting from readily accessible endo-cis-(2S,3R)-norbornene dicarboxylic acid benzyl monoester. It is found that, in these structures the peptide strands are oriented in a parallel geometry.