Conformational insights on the molecular recognition processes of carbohydrate molecules by proteins and enzymes: A 3D view by using NMR

This review focuses, in a non-exhaustive manner, on the essential structural and conformational features of protein-carbohydrate interactions and on some applications of NMR spectroscopy to deal with this topic from different levels of complexity.     

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions

Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin’s exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate–aromatic interactions including CH–π and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to β-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.     

Crystal structure of N-(benzyloxycarbonyl)aminoethyl-2,3,4,6-tetra-O-benzoyl-alpha-D-mannopyranoside: stabilization of the crystal lattice by a tandem network of N-H. . .O, C-H. . .O, and C-H. . .pi interactions

Single crystal X-ray analysis of an aminoethyl mannopyranoside, namely, N-(benzyloxycarbonyl)aminoethyl-2,3,4,6-tetra-O-benzoyl-alpha-D-mannopyranoside (1), shows that the compound crystallizes in the monoclinic space group P2(1), with two molecules in the unit cell. The mannopyranoside unit adopts a distorted 4C(1) conformation. An analysis of the intermolecular interactions reveals a tandem network of N-H. . .O, C-H. . .O, and C-H. . .pi interactions responsible for stabilizing the crystal lattice.     

Interactions and space requirement of the phosphate head group of membrane lipids: The single crystal structures of a triclinic and a monoclinic form of hexadecyl-2-deoxyglycerophosphoric acid monohydrate

The crystal structures of a triclinic form (HPA1) and a monoclinic form (HPA2) of hexadecyl-2-deoxyglycerophosphoric acid monohydrate were determined by single crystal analysis. The unit cell dimensions for HPA1 are $\text{a = 4.75, b = 5.72, c = 44.36}\text{A}\text{?}$ and α = 91.0, β = 101.5, γ = 100.5° (P$\text{1}$) and for HPA2, $\text{a = 4.75, b = 5.72, c = 88.72}\text{A}\text{?}$ and γ = 100.8° (P2₁). In both structures the molecules are fully extended and pack tail-to-tail in bilayers with tilting (47°) hydrocarbon chains. In HPA2, however, the chain tilt alternatingly changes direction in adjacent bilayers, giving rise to a doubled unit cell which spans two bilayers. The dihydrogen phosphate groups interact by hydrogen bonds and are arranged in rows. Laterally between these phosphate rows the water molecules are accommodated producing a compact two-dimensional network of hydrogen bonds. The packing cross-section in the layer plane of the dihydrogen phosphate monohydrate group is 26.7 Ų in both structures. The hydrocarbon chains pack according to the triclinic (T|) chain packing mode. In HPA2, however, the chain packing is somewhat less compact with accounts for a 2% increase in the molecular volume. In both structures the ether oxygen is accommodated into the hydrocarbon matrix without distortion of the chain packing.     

Hydrothermal synthesis, crystal structures and properties of new Fe, Co, Ni, and Zn complexes with 6-quinolinecarboxylate: Interplay of coordinative and noncovalent interactions

Reactions of Fe^II, Co^II, Ni^II, and Zn^II salts with 6-quinolinecarboxylic acid (HL) under the hydrothermal conditions afford three monomeric complexes [M(L)₂(H₂O)₄] (M = Fe^II for 1, Co^II for 2, and Ni^II for 3) and a 1-D polymeric species {[Zn(L)₂(H₂O)] · H₂O}_n (4). The crystal structures of the ligand HL and these four complexes have been determined by using the X-ray single-crystal diffraction technique. The results suggest that complexes 1-3 are isostructural, displaying novel 3-D pillar-layered networks through multiple intermolecular hydrogen bonds, whereas in coordination polymer 4, the 1-D comb-like coordination chains are extended to generate a hydrogen-bonded layer, which is further reinforced via aromatic stacking interactions. Solid-state properties such as thermal stability and fluorescence emission of the polymeric Zn^II complex 4 have also been investigated.     

New insights into the molecular basis of lectin-carbohydrate interactions: A calorimetric and structural study of the association of hevein to oligomers of N-acetylglucosamine

Isothermal titration calorimetry was used to characterize thermodynamically the association of hevein, a lectin from the rubber tree latex, with the dimer and trimer of N-acetylglucosamine (GlcNAc). Considering the changes in polar and apolar accessible surface areas due to complex formation, we found that the experimental binding heat capacities can be reproduced adequately by means of parameters used in protein-unfolding studies. The same conclusion applies to the association of the lectin concanavalin A with methyl-α-mannopyranoside. When reduced by the polar area change, binding enthalpy values show a minimal dispersion around 100°C. These findings resemble the convergence observed in protein-folding events; however, the average of reduced enthalpies for lectin-carbohydrate associations is largely higher than that for the folding of proteins. Analysis of hydrogen bonds present at lectin-carbohydrate interfaces revealed geometries closer to ideal values than those observed in protein structures. Thus, the formation of more energetic hydrogen bonds might well explain the high association enthalpies of lectin-carbohydrate systems. We also have calculated the energy associated with the desolvation of the contact zones in the binding molecules and from it the binding enthalpy in vacuum. This latter resulted 20% larger than the interaction energy derived from the use of potential energy functions. Proteins 29:467–477, 1997. © 1997 Wiley-Liss, Inc.     

Community organization in streams: the importance of species interactions,physical factors,and chance

Summary Experimental studies were used to examine the mechanisms governing the distribution and abundance of two major patch types in unshaded reaches of Augusta Creek, Michigan (USA). One patch type is dominated by Cladophora glomerata, a macroalga potentially able to monopolize space, whereas the other type is comprised of a low-growing, epilithic microalgal lawn inhabited by several species of sessile grazers (especially the caddisflies Leucotrichia pictipes and Psychomyia flavida). Cladophora patches are absent from mid-channel sites characterized by current velocities ca. 50 cm s^–1; caging experiments indicate that their absence is due to grazing by crayfish (Orconectes propinquus). Cladophora's presence in sites with velocities >50 cm s^–1 apparently results in part because crayfish foraging activity is impaired in high flow regimes. The presence of Cladophora strongly affects various other invertebrates due to its alteration of abiotic and biotic characteristics of the microhabitat. For example, the abundance of sessile grazers (e.g. Leucotrichia and Psychomyia) that inhabit microalgal patches is negatively correlated to the abundance of Cladophora, whereas the abundance of several other invertebrates (e.g. Stenonema mayflies and Taeniopteryx stoneflies) is positively correlated to Cladophora's abundance. Therefore, in some portions of this system, crayfish act as keystone predators because of their ability to regulate the abundance of Cladophora, which in turn has strong positive and negative effects on other components of the community. Cladophora does not always monopolize space at high velocities in the absence of crayfish, however. If sessile grazers arrive at such sites before Cladophora, they can prevent its establishment. Thus, where crayfish are absent, the likelihood that a site will be dominated by either Cladophora patches or sessile grazer — microalgal lawn patches depends on two sets of stochastic processes: (1) those that create bare space (e.g. disturbance and grazer emergence); and (2) those controlling the timing of recruitment by Cladophora or grazers at these bare sites. These priority effects (i.e. the ability of grazers and Cladophora to inhibit each other's establishment) contribute to the marked spatial heterogeneity of these two patch types. Collectively, these results demonstrate how interactions between competition, predation, and physical factors can generate a complex mixture of community patterns.     

A Low-Km 5'-Nucleotidase from Rat Brain Cytosolic Fraction: Purification, Kinetic Properties, and Description of Regulation by a Novel Factor that Increases Sensitivity to Inhibition by ATP and ADP

Abstract: A readily soluble 5'-nucleotidase was purified 1,800-fold from rat brain 105,000- g supernatant. The enzyme showed similarity to the 5'-nucleotidase ectoenzyme of plasma membranes. It exhibited a low K _m for AMP, which was preferred over IMP as substrate. It was inhibited by free ATP and ADP and by α,β-methylene ADP. The enzyme appeared to be a glycoprotein on the basis of its interaction with concanavalin A. It contained a phosphatidylinositol moiety because treatment with phosphatidylinositol-specific phospholipase C increased its hydrophilicity. A single subunit of M_r = 54,300 ± 800 was observed, which is appreciably smaller than published values for the 5'-nucleotidase ectoenzyme or for other low- K _m"soluble" 5'-nucleotidases. The soluble 5'-nucleotidase showed an elution profile on AMP-Sepharose affinity chromatography or on Mono Q ion-exchange chromatography different from that of the brain ectoenzyme. Forty-two percent of the soluble 5'-nucleotidase in brain 105,000- g supernatant did not bind to a Mono Q ion-exchange column because of its interaction with a soluble factor. This factor could be removed by chromatography on concanavalin A-Sepharose. The factor had the novel property of increasing the sensitivity of the purified soluble 5'-nucleotidase toward the inhibitor ATP by 20-fold. This factor was also able to increase the inhibition of brain 5'-nucleotidase ectoenzyme by ATP.     

Density functional theory molecular modelling,DNA interactions,antioxidant, antimicrobial,anticancer and biothermodynamic studies of bioactive water soluble mixed ligand complexes

A novel series of bioactive water soluble mixed ligand complexes (1–5) [M^II(L)(phen)AcO]. nH₂O {where M?=?Cu (1) n?=?2; Co (2), Mn (3), Ni (4), n?=?4 and Zn (5) n?=?2} were synthesized from 2-(2-Morpholinoethylimino) methyl)phenol Schiff base ligand (LH), 1, 10-phenanthroline and metal(II) acetate salt in a 1:1:1 stoichiometric ratio and characterized by several spectral techniques. The obtained analytical and spectral data suggest the octahedral geometry around the central metal ion. Density functional theory calculations have been further supportive to explore the optimized structure and chemical reactivity of these complexes from their frontier molecular orbitals. Gel electrophoresis result indicates that complex (1) manifested an excellent DNA cleavage property than others. The observed binding constants with free energy changes by electronic absorption technique and DNA binding affinity values by viscosity measurements for all compounds were found in the following order (1)?>?(2)?>?(4)?>?(5)?>?(3) > (LH). The binding results and thermodynamic parameters are described the intercalation mode. In vitro antioxidant properties disclose that complex (1) divulges high scavenging activity against DPPH^?, ^?OH, O₂^?? NO^?, and Fe³⁺. The antimicrobial reports illustrate that the complexes (1–5) were exhibited well defined inhibitory effect than ligand (LH) against the selected different pathogenic species. The observed percentage growth inhibition against A549, HepG2, MCF-7, and NHDF cell lines suggest that complex (1) has exhibited superior anticancer potency than others. Thus, the complex (1) may contribute as potential anticancer agent due to its unique interaction mode with DNA.GRAPHICAL ABSTRACT

Communicated by Ramaswamy H. Sarma     

Hydraulic lift and water use by plants: implications for water balance,performance and plant-plant interactions

During drought periods, sugar maple (Acer saccharum) demonstrates hydraulic lift; nocturnal uptake of water by roots from deep soil layers that is released from shallow roots into upper soil layers. Using standard water relations methods and stable hydrogen isotope analysis of both source-water and plant-water, I investigated (1) the magnitude and radial extent of hydraulic lift by mature, relatively open-grown trees, of A. saccharum, (2) the proportion of hydraulically-lifted water (HLW) used by shallow-rooted neighbors growing at different distances from target trees, and (3) the influence that this water source had on stomatal conductance to water vapor (g), water balance and growth of these neighbors. Soil water potentials (_s) at –20 and –35 cm showed a distinct diel fluctuation. Soil pits dug beneath three mature trees revealed a distinct hard-pan (e.g. fragipan) layer at a depth of approximately 50 cm. Examination of root distributions obtained from soil cores and soil pits revealed that some larger diameter roots (1.9–3.7 cm) did penetrate the fragipan and were established in the ground water table. The presence of the fragipan indicated that the rewetting of the upper soil layer during the night could not be explained by capillary rise from the shallow water table; it was the trees that were taking up ground water and then redepositing it at night into the upper 35 cm of soil, above the fragipan. The greatest fluctuations in _s occurred within 2.5 m of trees and only extended out to approximately 5 m. Application of a two-end-member linear mixing model which used stable hydrogen isotopic data obtained from environmental water sources and xylem-sap demonstrated that all neighbors used some fraction (3–60%) of HLW supplied by sugar maple trees. Plants that used a high proportion of HLW (e.g. rhizomatous or stoloniferous perennials) maintained significantly higher leaf water potentials and g, and showed greater aboveground growth when compared with (i) neighbors that used little or no HLW or (ii) conspecifics found growing at distances greater than about 3 m away from maple trees. Three important conclusions can be drawn from the results of this investigation that have not been demonstrated before: (1) hydraulic lift need not only occur in arid or semi-arid environments where chronic water deficits prevail, but can be important in relatively mesic environments when subjected to periodic soil water deficits, (2) that plants neighboring trees which conduct hydraulic lift can use a significant proportion of this water source, and (3) that the HLW source can effectively ameliorate the influence of drought on the performance and growth of neighboring vegetation. The results are also discussed in terms of their influence on plant nutrient relations (including plant-mycorrhizal associations), the nature of plant-plant interactions and the water balance of individuals, communities and floristic regions.     

Salt bridge interactions: Stability of the ionic and neutral complexes in the gas phase,in solution,and in proteins

A theoretical study on the stability of the salt bridges in the gas phase, in solution, and in the interior of proteins is presented. The study is mainly focused on the interaction between acetate and methylguanidinium ions, which were used as model compounds for the salt bridge between Asp (Glu) and Arg. Two different solvents (water and chloroform) were used to analyze the effect of varying the dielectric constant of the surrounding media on the salt bridge interaction. Calculations in protein environments were performed by using a set of selected protein crystal structures. In all cases attention was paid to the difference in stability between the ion pair and neutral hydrogen-bonded forms. Comparison of the results determined in the gas phase and in solution allows us to stress the large influence of the environment on the binding process, as well as on the relative stability between the ionic and neutral complexes. The high anisotropy of proteins and the local microenvironment in the interior of proteins make a decisive contribution in modulating the energetics of the salt bridge. In general, the formation of salt bridges in proteins is not particularly favored, with the ion pair structure being preferred over the interaction between neutral species. Proteins 32:67–79, 1998. © 1998 Wiley-Liss, Inc.     

Conserved water-mediated recognition and dynamics of NAD+ (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor

Inosine monophosphate dehydrogenase (IMPDH) enzyme involves in GMP biosynthesis pathway. Type I hIMPDH is expressed at lower levels in all cells, whereas type II is especially observed in acute myelogenous leukemia, chronic myelogenous leukemia cancer cells, and 10?ns simulation of the IMP–NAD⁺ complex structures (PDB ID. 1B3O and 1JCN) have revealed the presence of a few conserved hydrophilic centers near carboxamide group of NAD⁺. Three conserved water molecules (W1, W, and W1′) in di-nucleotide binding pocket of enzyme have played a significant role in the recognition of carboxamide group (of NAD⁺) to D274 and H93 residues. Based on H-bonding interaction of conserved hydrophilic (water molecular) centers within IMP–NAD⁺-enzyme complexes and their recognition to NAD⁺, some covalent modification at carboxamide group of di-nucleotide (NAD⁺) has been made by substituting the –CONH₂group by –CONHNH₂ (carboxyl hydrazide group) using water mimic inhibitor design protocol. The modeled structure of modified ligand may, though, be useful for the development of antileukemic agent or it could be act as better inhibitor for hIMPDH-II.     

Free energy simulations: Applications to the study of liquid water,hydrophobic interactions and solvent effects on conformational stability

Free energy simulations using the Metropolis Monte Carlo method and the coupling parameter approach with umbrella sampling are described for several problems of interest in structural biochemistry; the liquid water, the hydrophobic interaction of alkyl and phenyl groups in water and solvent effects on the conformational stability of the alanine dipeptide and the dimethyl phosphate anion in water. Proximity analysis of results is employed to identify stabilizing factors. Implications of result with respect to the structural chemistry of proteins and nucleic acids is considered.     

Effects of protein-protein interactions on electron transfer: docking and electron transfer calculations for complexes between flavodoxin and c-type cytochromes

 Theoretical studies of protein-protein association and electron transfer were performed on the binary systems formed by Desulfovibrio vulgaris Hildenborough (D. v. H.) flavodoxin and D. v. H. cytochrome c ₅₅₃ and by flavodoxin and horse heart cytochrome c. Initial structures for the complexes were obtained by rigid-body docking and were refined by MD to allow for molecular flexibility. The structures thus obtained were analysed in terms of their relative stability through the calculation of excess energies. Electrostatic, van der Waals and solvation energy terms showed all to have significant contributions to the stability of complexes. In the best association solutions found for both cytochromes, these bind to different zones of flavodoxin. The binding site of flavodoxin observed for cytochrome c is in accordance with earlier works [27]. The various association modes found were characterised in terms of electron transfer using the Pathways model. For complexes between flavodoxin and horse heart cytochrome c, some correlation was observed between electron tunnelling coupling factors and conformation energy; the best conformation found for electron transfer corresponded also to the best one in terms of energy. For complexes between flavodoxin and cytochrome c ₅₅₃ this was not the case and a lower correlation was observed between electron tunnelling coupling factors and excess energies. These results are in accordance with the differences in the experimental dependence of electron transfer rates with ionic strength observed between these two cases. Received: 29 December 1998 / Accepted: 22 March 1999     

Assessment of a protein fold recognition method that takes into account four physicochemical properties: Side-chain packing,solvation, hydrogen-bonding,and local conformation

A protein fold recognition method was tested by the blind prediction of the structures of a set of proteins. The method evaluates the compatibility of an amino acid sequence with a three-dimensional structure using the four evaluation functions: side-chain packing, solvation, hydrogen-bonding, and local conformation functions. The structures of 14 proteins containing 19 sequences were predicted. The predictions were compared with the experimental structures. The experimental results showed that 9 of the 19 target sequences have known folds or portions of known folds. Among them, the folds of Klebsiella aerogenes urease β subunit (KAUB) and pyruvate phosphate dikinase domain 4 (PPDK4) were successfully recognized; our method predicted that KAUB and PPDK4 would adopt the folds of macromomycin (Ig-fold) and phosphoribosylanthra-nilate isomerase:indoleglycerol-phosphate synthase (TIM barrel), respectively, and the experimental structure revealed that they actually adopt the predicted folds. The predictions for the other targets were not successful, but they often gave secondary structural patterns similar to those of the experimental structures. © 1995 Wiley-Liss, Inc.     

Supramolecular assemblies of new 2-D complexes: Syntheses, crystal structures, spectroscopic and magnetic properties of {[MnAu2(CN)4(NITpPy)2(H2O)2]}n and {[Co(N(CN)2)2(NITpPy)2(H2O)2]}n

Two new complexes, {[MnAu₂(CN)₄(NITpPy)₂(H₂O)₂]}_n (1) and {[Co(N(CN)₂)₂(NITpPy)₂(H₂O)₂]}_n (2), have been synthesized and characterized. The single-crystal X-ray analysis for the complexes 1 and 2 demonstrates that each M(II) (M = Mn or Co) ion assumes a distorted octahedral MN₄O₂ coordination polyhedron. Four nitrogen atoms come from the cyanide groups and the pyridyl rings in a common plane, and two oxygen atoms come from the H₂O molecules in trans-positions. The structures of complexes 1 and 2 illustrate that aurophilicity and/or hydrogen bonding interactions play important roles in increasing dimensionality. Magnetic investigations on complexes 1 and 2 show the presence of weak antiferromagnetic interactions.     

Structure,stability and water permeation of ([D-Leu-L-Lys-(D-Gln-L-Ala)3]) cyclic peptide nanotube: a molecular dynamics study

The structural stability of 8 × ([D-Leu-L-Lys-(D-Gln-L-Ala)₃]) cyclic peptide nanotube (CPN) in water and different phospholipid bilayers were explored by 100 ns independent molecular dynamics (MD) simulations. The role of non-bonded interaction energy between the side and main chains of cyclic peptide rings in different membrane environments assessed, wherein the repulsive electrostatic interaction energy between neighbouring cyclic peptide rings was found adequate to break hydrogen bond energy thereby to crumple CPN. Further, the water permeation across the CPN channel was studied in four types of phospholipid bilayers- DMPG (1,2-Dimyristoyl-sn-glycero-3-phosphorylglycerol), DMPS (1,2-Dimyristoyl-sn-glycero-3-phosphoserine), POPC (1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and POPE (1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) from MD simulations. DMPS membrane shows higher non-bonded interaction energies (?1913.06 kJ/mol of electrostatic interaction energy and ?994.13 kJ/mol of van der Waals interaction energy) with CPN due to the presence of polar molecules in lipid structure. Thusly, the non-bonded interaction energies were essential towards the stability of CPN than hydrogen bonds between the nearby cyclic peptides. The result also reveals the role of side chains, hydrogen bonds and non-bonded interaction energies in an aqueous environment. The diffusion coefficient of water obtained from means square deviation calculation shows similar coefficients irrespective of the lipid surroundings. However, the permeation coefficients demonstrate water flow in the channel relies upon the environment.     

Protonation and deprotonation enthalpies of alloxan and implications for the structure and energy of its complexes with water: a computational study

The optimized geometries, harmonic vibrational frequencies, and energies of the structures of monohydrated alloxan were computed at the DFT/ωB97X-D and B3LYP/6–311++G** level of theory. Results confirm that the monohydrate exists as a dipolar alloxan–water complex which represents a global minimum on the potential energy surface (PES). Trajectory dynamics simulations show that attempt to reorient this monohydrate, to a more favorable orientation for H-bonding, is opposed by an energy barrier of 25.07?kJ/mol. Alloxan seems to prefer acting as proton donor than proton acceptor. A marked stabilization due to the formation of N–H–OH₂ bond is observed. The concerted proton donor–acceptor interaction of alloxan with one H₂O molecule does not increase the stability of the alloxan–water complex. The proton affinity of the O and N atoms and the deprotonation enthalpy of the NH bond of alloxan are computed at the same level of theory. Results are compared with recent data on uracil, thymine, and cytosine. The intrinsic acidities and basicities of the four pyrimidines were discussed. Results of the present study reveal that alloxan is capable of forming stronger H-bonds and more stable cyclic complex with water; yet it is of much lower basicity than other pyrimidines.     

Utility of mass spectrometry for proteome analysis: part II. Ion-activation methods,statistics, bioinformatics and annotation

This is the second article in a series, intended as a tutorial to provide the interested reader with an overview of the concepts not covered in part I, such as: the principles of ion-activation methods, the ability of mass-spectrometric methods to interface with various proteomic strategies, analysis techniques, bioinformatics and data interpretation and annotation. Although these are different topics, it is important that a reader has a basic and collective understanding of all of them for an overall appreciation of how to carry out and analyze a proteomic experiment. Different ion-activation methods for MS/MS, such as collision-induced dissociation (including postsource decay) and surface-induced dissociation, electron capture and electron-transfer dissociation, infrared multiphoton and blackbody infrared radiative dissociation have been discussed since they are used in proteomic research. The high dimensionality of data generated from proteomic studies requires an understanding of the underlying analytical procedures used to obtain these data, as well as the development of improved bioinformatics tools and data-mining approaches for efficient and accurate statistical analyses of biological samples from healthy and diseased individuals, in addition to determining the utility of the interpreted data. Currently available strategies for the analysis of the proteome by mass spectrometry, such as those employed for the analysis of substantially purified proteins and complex peptide mixtures, as well as hypothesis-driven strategies, have been elaborated upon. Processing steps prior to the analysis of mass spectrometry data, statistics and the several informatics steps currently used for the analysis of shotgun proteomic experiments, as well as proteomics ontology, are also discussed.