Context-based identification of protein-protein interfaces and "hot-spot" residues

Reliable determination of protein-protein interaction sites is of critical importance for structure-based design of small molecules modulating protein function through macromolecular interfaces. We present an alignment-free computational method for prediction of protein-protein interface residues. The method ("iPred") is based on a knowledge-based scoring function adapted from the field of protein folding and small molecule docking. Based on a training set of 394 hetero-dimeric proteins iPred achieves sustained accuracy on an external unbound test set. Prediction robustness was assessed from more than 1500 diverse complexes containing homo- and hetero-dimers. The technique does not rely on sequence conservation, so that rapid interface identification is possible even for proteins for which homologs are unknown or lack conserved residue patterns in interface region. Functional "hot-spot" residues are enriched among the predicted interface residues, rendering the method predestined for macromolecular binding site identification and drug design studies aiming at modulating protein-protein interaction that might influence protein function. For a comparative structural model of peptidase HtrA from Helicobacter pylori, we performed mutation studies for predicted hot-spot residues, which were confirmed as functionally relevant for HtrA activity or oligomerization.     

Probing the photoinduced metal-nitrosyl linkage isomerism of sodium nitroprusside in solution using transient infrared spectroscopy

We study photoinduced metal-nitrosyl linkage isomerism in sodium nitroprusside (Na(2)[Fe(II)(CN)(5)NO]·2H(2)O, SNP) dissolved in methanol using picosecond transient infrared (IR) spectroscopy. The high sensitivity of this technique allows the simultaneous observation of two known metastable (MS) iron-nitrosyl linkage isomers of SNP, [Fe(II)(CN)(5)(η(1)-ON)](2-) (MS1) and [Fe(II)(CN)(5)(η(2)-NO)](2-) (MS2), at room temperature. The transient population of free nitrosyl radicals (NO·) is also measured in the sample solution. These three transient species are detected using their distinct nitrosyl stretching frequencies at 1794 cm(-1) (MS1), 1652 cm(-1) (MS2), and 1851 cm(-1) (NO·). The metastable isomers and NO· are formed on a subpicosecond time scale and have lifetimes greater than 100 ns. A UV (400 nm)-pump power dependence study reveals that MS1 can be formed with one photon, while MS2 requires two photons to be populated at room temperature in solution. Other photodissociation products including cyanide ion, Prussian blue, and [Fe(III)(CN)(5)(CH(3)OH)](2-) are observed. We develop a photochemical kinetic scheme to model our data, and the analysis reveals that photoisomerization and photodissociation of the metal-NO moiety are competing photochemical pathways in SNP dissolved in methanol at room temperature. Based on the analysis, the solvent-associated Fe(III) species and Prussian blue form on a 130 and 320 ps time scale, respectively. The simultaneous detection and characterization of photoinduced linkage isomerism (MS1 and MS2) and photodissociation of the metal-NO bond in SNP highlights the importance of understanding the role played by metastable metal-nitrosyl linkage isomers in the photochemistry of metal-nitrosyl compounds in chemistry and biology.     

Simulating the formation of sodium:electron tight-contact pairs: watching the solvation of atoms in liquids one molecule at a time

The motions of solvent molecules during a chemical transformation often dictate both the dynamics and the outcome of solution-phase reactions. However, a microscopic picture of solvation dynamics is often obscured by the concerted motions of numerous solvent molecules that make up a condensed-phase environment. In this study, we use mixed quantum/classical molecular dynamics simulations to furnish the molecular details of the solvation dynamics that leads to the formation of a sodium cation-solvated electron contact pair, (Na(+), e(-)), in liquid tetrahydrofuran following electron photodetachment from sodide (Na(-)). Our simulations reveal that the dominant solvent response is comprised of a series of discrete solvent molecular events that work sequentially to build up a shell of coordinating THF oxygen sites around the sodium cation end of the contact pair. With the solvent response described in terms of the sequential motion of single molecules, we are then able to compare the calculated transient absorption spectroscopy of the sodium species to experiment, providing a clear microscopic interpretation of ultrafast pump-probe experiments on this system. Our findings suggest that for solute-solvent interactions similar to the ones present in our study, the solvation dynamics is best understood as a series of kinetic events consisting of reactions between chemically distinct local structures in which key solvent molecules must be considered to be part of the identity of the reacting species.     

Protonation effects on the resonance Raman properties of a novel (terpyridine)Ru(4H-imidazole) complex: an experimental and theoretical case study

The optically active states in a novel (terpyridine)Ru(4H-imidazole) complex displaying an unusually broad and red-shifted absorption in the visible range are investigated experimentally and theoretically. Since this property renders the complex promising for an application as sensitizer in dye-sensitized solar cells, a detailed knowledge on the correlation between features in the absorption spectrum and structural elements is indispensable in order to develop strategies for spectroscopy/theory-guided design of such molecular components. To this aim, time-dependent density functional theory calculations, including solvent effects, are employed to analyze the experimental UV-vis absorption and resonance Raman (RR) spectra of the unprotonated and protonated forms of the complex. This provides a detailed photophysical picture for a complex belonging to a novel class of Ru-polypyridine black absorbers, which can be tuned by external pH stimuli. The complex presents two absorption maxima in the visible region, which are assigned by the calculations to metal-to-ligand charge transfer (MLCT) and intra-ligand states, respectively. RR simulations are performed in resonance with both bands and are found to correctly reproduce the observed effects of protonation. Finally, the examination of the molecular orbitals and of the RR spectra for the MLCT state shows that protonation favors a charge transfer excitation to the 4H-imidazole ligand.     

Diagnosing the Protonation Site of <Emphasis Type="BoldItalic">b</Emphasis><Subscript><Emphasis Type="BoldItalic">2</Emphasis></Subscript> Peptide Fragment Ions using IRMPD in the X–H (X = O,N, and C) Stretching Region

Charge-directed fragmentation has been shown to be the prevalent dissociation step for protonated peptides under the low-energy activation (eV) regime. Thus, the determination of the ion structure and, in particular, the characterization of the protonation site(s) of peptides and their fragments is a key approach to substantiate and refine peptide fragmentation mechanisms. Here we report on the characterization of the protonation site of oxazolone b ₂ ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR. In support of earlier work, here we provide complementary IR spectra in the 2800–3800 cm^–1 range acquired on a table-top laser system. Combining this tunable laser with a high power CO₂ laser to improve spectroscopic sensitivity, well resolved bands are observed, with an excellent correspondence to the IR absorption bands of the ring-protonated oxazolone isomer as predicted by quantum chemical calculations. In particular, it is shown that a band at 3445 cm^–1, corresponding to the asymmetric N–H stretch of the (nonprotonated) N-terminal NH₂ group, is a distinct vibrational signature of the ring-protonated oxazolone structure.     

A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors

Peptidases play vital roles in physiology through the biosynthesis, degradation, and regulation of peptides. Prolyl endopeptidase-like (PREPL) is a newly described member of the prolyl peptidase family, with significant homology to mammalian prolyl endopeptidase and the bacterial peptidase oligopeptidase B. The biochemistry and biology of PREPL are of fundamental interest due to this enzyme's homology to the biomedically important prolyl peptidases and its localization in the central nervous system. Furthermore, genetic studies of patients suffering from hypotonia-cystinuria syndrome (HCS) have revealed a deletion of a portion of the genome that includes the PREPL gene. HCS symptoms thought to be caused by lack of PREPL include neuromuscular and mild cognitive deficits. A number of complementary approaches, ranging from biochemistry to genetics, will be required to understand the biochemical, cellular, physiological, and pathological mechanisms regulated by PREPL. We are particularly interested in investigating physiological substrates and pathways controlled by PREPL. Here, we use a fluorescence polarization activity-based protein profiling (fluopol-ABPP) assay to discover selective small-molecule inhibitors of PREPL. Fluopol-ABPP is a substrate-free approach that is ideally suited for studying serine hydrolases for which no substrates are known, such as PREPL. After screening over 300,000 compounds using fluopol-ABPP, we employed a number of secondary assays to confirm assay hits and characterize a group of 3-oxo-1-phenyl-2,3,5,6,7,8-hexahydroisoquinoline-4-carbonitrile and 1-alkyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile PREPL inhibitors that are able to block PREPL activity in cells. Moreover, when administered to mice, 1-isobutyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile distributes to the brain, indicating that it may be useful for in vivo studies. The application of fluopol-ABPP has led to the first reported PREPL inhibitors, and these inhibitors will be of great value in studying the biochemistry of PREPL and in eventually understanding the link between PREPL and HCS.     

Highly hydrophilic surfaces from polyglycidol grafts with dual antifouling and specific protein recognition properties

Homopolymer grafts from α-tert-butoxy-ω-vinylbenzyl-polyglycidol (PGL) were prepared on gold and stainless steel (SS) substrates modified by 4-benzoyl-phenyl (BP) moieties derived from the electroreduction of the parent salt 4-benzoyl benzene diazonium tetrafluoroborate. The grafted BP aryl groups efficiently served to surface-initiate photopolymerization (SIPP) of PGL. In similar conditions, SIPP of hydroxyethyl methacrylate (HEMA) permitted the production of PHEMA grafts as model surfaces. Water contact angles were found to be 66°, 15°, and 0° for SS-BP, SS-PHEMA, and SS-PPGL, respectively. The spontaneous spreading of water drops on SS-PPGL was invariably observed with 1.5 μL water drops. PPGL thus appears as a superhydrophilic polymer. Resistance to nonspecific adsorption of proteins of PPGL and PHEMA grafts on gold was evaluated by surface plasmon resonance (SPR) using antibovine serum albumin (anti-BSA). The results conclusively show that PPGL-grafts exhibit enhanced resistance to anti-BSA adsorption compared to the well-known hydrophilic PHEMA. PPGL grafts were further modified with BSA through the carbonyldiimidazole activation of the OH groups providing immunosensing surfaces. The so-prepared PPGL-grafted BSA hybrids specifically interacted with anti-BSA in PBS as compared to antimyoglobin. It is clear that the superhydrophilic character of PPGL grafts opens new avenues for biomedical applications where surfaces with dual functionality, namely, specific protein grafting together with resistance to biofouling, are required.     

Spectroscopic and electronic structure studies of a dimethyl sulfoxide reductase catalytic intermediate: implications for electron- and atom-transfer reactivity

The electronic structure of a genuine paramagnetic des-oxo Mo(V) catalytic intermediate in the reaction of dimethyl sulfoxide reductase (DMSOR) with (CH(3))(3)NO has been probed by electron paramagnetic resonance (EPR), electronic absorption, and magnetic circular dichroism (MCD) spectroscopies. EPR spectroscopy reveals rhombic g- and A-tensors that indicate a low-symmetry geometry for this intermediate and a singly occupied molecular orbital that is dominantly metal centered. The excited-state spectroscopic data were interpreted in the context of electronic structure calculations, and this has resulted in a full assignment of the observed MCD and electronic absorption bands, a detailed understanding of the metal-ligand bonding scheme, and an evaluation of the Mo(V) coordination geometry and Mo(V)-S(dithiolene) covalency as it pertains to the stability of the intermediate and electron-transfer regeneration. Finally, the relationship between des-oxo Mo(V) and des-oxo Mo(IV) geometric and electronic structures is discussed relative to the reaction coordinate in members of the DMSOR enzyme family.     

Quantitative detection of C-deuterated drugs by CARS microscopy and Raman microspectroscopy

The introduction of carbon-deuterium (C-D) bonds into drug compounds by organic synthesis is a non-invasive labelling approach, which does not alter the chemical and physiological properties of the drug itself. C-deuterated drugs exhibit characteristic vibrational signatures in the C-D stretching region around 2100-2300 cm(-1), which avoids spectral interference with contributions from a complex biological environment. In this paper, the quantitative detection of C-deuterated drugs by Raman microspectroscopy and single-band CARS microscopy is examined. Concentration-dependent studies on drugs with aliphatic and aromatic C-D moieties were performed in a two-channel microfluidic chip, using the corresponding non-deuterated (C-H) isotopologues as an internal reference.