Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 A˚, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced "leopard skin"-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism.

Models of protein linear molecular motors for dynamic nanodevices

Protein molecular motors are natural nano-machines that convert the chemical energy from the hydrolysis of adenosine triphosphate into mechanical work. These efficient machines are central to many biological processes, including cellular motion, muscle contraction and cell division. The remarkable energetic efficiency of the protein molecular motors coupled with their nano-scale has prompted an increasing number of studies focusing on their integration in hybrid micro- and nanodevices, in particular using linear molecular motors. The translation of these tentative devices into technologically and economically feasible ones requires an engineering, design-orientated approach based on a structured formalism, preferably mathematical. This contribution reviews the present state of the art in the modelling of protein linear molecular motors, as relevant to the future design-orientated development of hybrid dynamic nanodevices. © 2009 The Royal Society of Chemistry.

Protein Molecular Surface Mapped at Different Geometrical Resolutions

Many areas of biochemistry and molecular biology, both fundamental and applications-orientated, require an accurate construction, representation and understanding of the protein molecular surface and its interaction with other, usually small, molecules. There are however many situations when the protein molecular surface gets in physical contact with larger objects, either biological, such as membranes, or artificial, such as nanoparticles. The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties. The relevance of the molecular surface-derived properties has been demonstrated through the calculation of the statistical strength of the prediction of protein adsorption. It is expected that the extension of this methodology to other phenomena involving proteins near solid surfaces, in particular the protein interaction with nanoparticles, will result in important benefits in the understanding and design of protein-specific solid surfaces. © 2013 Nicolau et al.

Assessment of the molecular structure of an intermediate member of the triplite-zwieselite mineral series: A raman and infrared study

The mineral series triplite-zwieselite with theoretical formula (Mn2+)2(PO4)(F)-(Fe2+)2(PO4)(F) from the El Criolo granitic pegmatite, located in the Eastern Pampean Ranges of Córdoba Province, was studied using electron microprobe, thermogravimetry, and Raman and infrared spectroscopy. The analysis of the mineral provided a formula of (Fe1.00, Mn0.85, Ca0.08, Mg0.06)∑2.00(PO4)1.00(F0.80, OH0.20)∑1.00. An intense Raman band at 981 cm−1 with a shoulder at 977 cm−1 is assigned to the ν1 symmetric stretching mode. The observation of two bands for the phosphate symmetric stretching mode offers support for the concept that the phosphate units in the structure of triplite-zwieselite are not equivalent. Low-intensity Raman bands at 1012, 1036, 1071, 1087, and 1127 cm−1 are assigned to the ν3 antisymmetric stretching modes. A set of Raman bands at 572, 604, 639, and 684 cm−1 are attributed to the ν4 out-of-plane bending modes. A single intense Raman band is found at 3508 cm−1 and is assigned to the stretching vibration of hydroxyl units. Infrared bands are observed at 3018, 3125, and 3358 cm−1 and are attributed to water stretching vibrations. Supplemental materials are available for this article. Go to the publisher's online edition of Spectroscopy Letters to view the supplemental file.

Soluble NSF attachment protein receptor molecular mimicry by a Legionella pneumophila Dot/Icm effector

Upon infection, Legionella pneumophila uses the Dot/Icm type IV secretion system to translocate effector proteins from the Legionella-containing vacuole (LCV) into the host cell cytoplasm. The effectors target a wide array of host cellular processes that aid LCV biogenesis, including the manipulation of membrane trafficking. In this study, we used a hidden Markov model screen to identify two novel, non-eukaryotic soluble NSF attachment protein receptor (SNARE) homologs: the bacterial Legionella SNARE effector A (LseA) and viral SNARE homolog A proteins. We characterized LseA as a Dot/Icm effector of L. pneumophila, which has close homology to the Qc-SNARE subfamily. The lseA gene was present in multiple sequenced L. pneumophila strains including Corby and was well distributed among L. pneumophila clinical and environmental isolates. Employing a variety of biochemical, cell biological and microbiological techniques, we found that farnesylated LseA localized to membranes associated with the Golgi complex in mammalian cells and LseA interacted with a subset of Qa-, Qb- and R-SNAREs in host cells. Our results suggested that LseA acts as a SNARE protein and has the potential to regulate or mediate membrane fusion events in Golgi-associated pathways.

Identification of the sources of primary organic aerosols at urban schools : a molecular marker approach

Children are particularly susceptible to air pollution and schools are examples of urban microenvironments that can account for a large portion of children’s exposure to airborne particles. Thus this paper aimed to determine the sources of primary airborne particles that children are exposed to at school by analyzing selected organic molecular markers at 11 urban schools in Brisbane, Australia. Positive matrix factorization analysis identified four sources at the schools: vehicle emissions, biomass burning, meat cooking and plant wax emissions accounting for 45%, 29%, 16% and 7%, of the organic carbon respectively. Biomass burning peaked in winter due to prescribed burning of bushland around Brisbane. Overall, the results indicated that both local (traffic) and regional (biomass burning) sources of primary organic aerosols influence the levels of ambient particles that children are exposed at the schools. These results have implications for potential control strategies for mitigating exposure at schools.

Crystal structures of the co-crystalline adduct 5-(4-bromophenyl)-1,3,4-thiadiazol-2-amine--4-nitrobenzoic acid (1/1) and the salt 2-amino-5-(4-bromophenyl)-1,3,4-thiadiazol-3-ium 2-carboxy-4,6-dinitrophenolate

The structures of the 1:1 co-crystalline adduct C8H6BrN3S . C7H5NO4 (I) and the salt C8H7BrN3S+ C7H3N2O7- (II) from the interaction of 5-(4-bromophenyl)-1,3,4-thiadiazol-2-amine with 4-nitrobenzoic acid and 3,5-dinitrosalicylic acid, respectively, have been determined. The primary inter-species association in both (I) and (II) is through duplex R2/2(8) (N-H...O/O-H...O) or (N-H...O/N-H...O) hydrogen bonds, respectively, giving heterodimers. In (II), these are close to planar [dihedral angles between the thiadiazole ring and the two phenyl rings are 2.1(3)deg. (intra) and 9.8(2)deg. (inter)], while in (I) these angles are 22.11(15) and 26.08(18)deg., respectively. In the crystal of (I), the heterodimers are extended into a one-dimensional chain along b through an amine N-...N(thiadiazole) hydrogen bond but in (II), a centrosymmetric cyclic heterotetramer structure is generated through N-H...O hydrogen bonds to phenol and nitro O-atom acceptors and features, together with the primary R2/2(8) interaction, conjoined R4/6(12), R2/1(6) and S(6) ring motifs. Also present in (I) are pi--pi interactions between thiadiazole rings [minimum ring centroid separation, 3.4624(16)deg.] as well as short Br...O(nitro) interactions in both (I) and (II) [3.296(3)A and 3.104(3)A, respectively].

Crystal structures and hydrogen bonding in the proton transfer salts of nicotine with 3,5-dinitrosalicylic acid and 5-sulfosalicylic acid

The structures of the 1:1 anhydrous salts of nicotine (NIC) with 3,5-dinitrosalicylic acid (DNSA) and 5-sulfosalicylic acid (5-SSA), namely (1R,2S)-1-methyl-2-(3-pyridyl)-1H-pyrrolidin-1-ium 2-carboxy-4,6-dinitrophenolate, C10H15N2+ C7H3N2O7-, (I) and (1R,2S)-1-methyl-2-(3-pyridyl)-1H-pyrrolidin-1-ium 3-carboxy-4-hydroxybenzenesulfonate, C10H15N2+ C7H5O6S-, (II) are reported. The asymmetric units of both (I) and (II) comprise two independent nicotinium cations (C and D) and either two DNSA or two 5-SSA anions (A and B), respectively. One of the DNSA anions shows a 25% rotational disorder in the benzene ring system. In the crystal of (I), inter-unit pyrrolidinium N-H...N(pyridine) hydrogen bonds generate zigzag NIC cation chains which extend along a while the DNSA anions are not involved in any formal inter-species hydrogen bonding but instead form pi--pi associated stacks which parallel the NIC chains along a [ring centroid separation, 3.857(2)A]. Weak C-H...O interactions between chain substructures give an overall three-dimensional structure. With (II), A and B anions form independent zigzag chains with C and D cations, respectively, through carboxylic acid O-H...N(pyridine) hydrogen bonds. These chains, which extend along b are pseudo-centrosymmetrically related and give pi--pi interactions between the benzene rings of anions A and B and the pyridine rings of the NIC cations C and D, respectively [ring centroid separations, 3.6422(19) and 3.7117(19)A]. Present also are weak intermolecular C-H...O hydrogen-bonding interactions between the chains, giving an overall three-dimensional structure.

Raman and infrared spectroscopic studies of phurcalite from Red Canyon, Utah, USA – Implications for the molecular structure

Raman and infrared spectra of the uranyl mineral phurcalite, Ca2(UO2)3O2(PO4)2⋅7H2O, from Red Canyon, Utah, USA, were studied and tentatively interpreted. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (PO4)3− units and to the stretching and bending vibrations and libration modes of water molecules. Approximate lengths of U–O in (UO2)2+ and O–H⋯O hydrogen bond lengths were inferred from observed stretching vibrations. The presence of structurally nonequivalent U6+ and P5+ was inferred from the number of corresponding stretching bands of (UO2)2+ and (PO4)3− units observed in the Raman and infrared spectra..

A vibrational spectroscopic study of the borate mineral ezcurrite Na4B10O17·7H2O – Implications for the molecular structure

We have studied the boron containing mineral ezcurrite Na4B10O17·7H2O using electron microscopy and vibrational spectroscopy. Both tetrahedral and trigonal boron units are observed. The nominal resolution of the Raman spectrometer is of the order of 2 cm−1 and as such is sufficient enough to identify separate bands for the stretching bands of the two boron isotopes. The Raman band at 1037 cm−1 is assigned to BO stretching vibration. Raman bands at 1129, 1163, 1193 cm−1 are attributed to BO stretching vibration of the tetrahedral units. The Raman band at 947 cm−1 is attributed to the antisymmetric stretching modes of tetrahedral boron. The sharp Raman peak at 1037 cm−1 is from the 11-B component such a mode, then it should have a smaller 10-B satellite near (1.03) × (1037) = 1048 cm−1, and indeed a small peak at 1048 is observed. The broad Raman bands at 3186, 3329, 3431, 3509, 3547 and 3576 cm−1 are assigned to water stretching vibrations. Broad infrared bands at 3170, 3322, 3419, 3450, 3493, 3542, 3577 and 3597 cm−1 are also assigned to water stretching vibrations. Infrared bands at 1330, 1352, 1389, 1407, 1421 and 1457 cm−1 are assigned to the antisymmetric stretching vibrations of trigonal boron. The observation of so many bands suggests that there is considerable variation in the structure of ezcurrite. Infrared bands at 1634, 1646 and 1681 cm−1 are assigned to water bending modes. The number of water bending modes is in harmony with the number of water stretching vibrations.

A vibrational spectroscopic study of the silicate mineral plumbophyllite Pb2Si4O10⋅H2O

Raman spectroscopy complimented with infrared spectroscopy has been used to study the molecular structure of the mineral of plumbophyllite. The Raman spectrum is dominated by a very intense sharp peak at 1027 cm−1, assigned to the SiO stretching vibrations of (SiO3)n units. A very intense Raman band at 643 cm−1 is assigned to the bending mode of (SiO3)n units. Raman bands observed at 3215, 3443, 3470, 3494 and 3567 cm−1 are assigned to water stretching vibrations. Multiple water stretching and bending modes are observed showing that there is much variation in hydrogen bonding between water and the silicate surfaces. Because of the close similarity in the structure of plumbophyllite and apophyllite, a comparison of the spectra with that of apophyllites is made. By using vibrational spectroscopy an assessment of the molecular structure of plumbophyllite has been made.

Thermal behavior of kaolinite–urea intercalation complex and molecular dynamics simulation for urea molecule orientation

The thermal behavior of kaolinite–urea intercalation complex was investigated by thermogravimetry–differential scanning calorimetry (TG–DSC), X-ray diffraction (XRD), and fourier transform infrared spectroscopy (FTIR). In addition, the interaction mode of urea molecules intercalated into the kaolinite gallery was studied by means of molecular dynamics simulation. Three main mass losses were observed at 136 °C, in the range of 210–270 °C, and at 500 °C in the TG–DSC curves, which were, respectively, attributed to (1) melting of the surface-adsorbed urea, (2) removal of the intercalated urea, and (3) dehydroxylation of the deintercalated kaolinite. The three DSC endothermic peaks at 218, 250, and 261 °C were related to the successive removals of intercalated urea with three different distribution structures. Based on the angle between the dipole moment vector of urea and the basal surface of kaolinite, the three urea models could be described as follows: (1) Type A, the dipole moment vector is nearly parallel to the basal surface of kaolinite; (2) Type B, the dipole moment vector points to the silica tetrahedron with the angle between it and the basal surface of kaolinite ranging from 20°to 40°; and (3) Type C, the dipole moment vector is nearly perpendicular to the basal surface of kaolinite. The three distribution structures of urea molecules were validated by the results of the molecular dynamics simulation. Furthermore, the thermal behavior of the kaolinite–urea intercalation complex investigated by TG–DSC was also supported by FTIR and XRD analyses.

Vibrational spectroscopic characterization of the arsenate mineral barahonaite: Implications for the molecular structure

The mineral barahonaite is in all probability a member of the smolianinovite group. The mineral is an arsenate mineral formed as a secondary mineral in the oxidized zone of sulphide deposits. We have studied the barahonaite mineral using a combination of Raman and infrared spectroscopy. The mineral is characterized by a series of Raman bands at 863 cm−1 with low wavenumber shoulders at 802 and 828 cm−1. These bands are assigned to the arsenate and hydrogen arsenate stretching vibrations. The infrared spectrum shows a broad spectral profile. Two Raman bands at 506 and 529 cm−1 are assigned to the triply degenerate arsenate bending vibration (F 2, ν4), and the Raman bands at 325, 360, and 399 cm−1 are attributed to the arsenate ν2 bending vibration. Raman and infrared bands in the 2500–3800 cm−1 spectral range are assigned to water and hydroxyl stretching vibrations. The application of Raman spectroscopy to study the structure of barahonaite is better than infrared spectroscopy, probably because of the much higher spatial resolution.