Study of the protein distribution in the pig lens cross section by Raman spectroscopy

The distribution of proteins in the cross section of a normal pig lens was studied by near-infrared Raman spectroscopy. The Raman spectra were measured in the visual and equatorial axes of this cross section and the protein peak intensities were determined. It was found that along each axis the protein intensities fluctuate. They have a considerable increment along the visual axis with the exception of the C-N bond peak intensities at 1087.2 cm(-1), which decrease, and along the equatorial axis the increment is slight. This increment in protein distribution along the visual axis is related with the refractive gradient of the lens. The classification of pig lens spectra in these axes was performed using principal component analysis (PCA) and linear discriminant analysis (LDA). Cross-validation shows an excellent group separation.     

Raman Scattering Activities for Uniaxially Oriented Molecules

Raman scattering activities were derived for uniaxially oriented molecules. The unique axis of the molecules is assumed to rotate around one of the axes of space-fixed coordinate in a fixed orientation angle with respect to the axis, while the other two principal axes of the molecules are randomly oriented. Expressions for Raman scattering activities in terms of the elements of derived polarizability tensor are given as the function of orientation angle and are tabulated for various symmetries of point groups.     

Hybrid rylene arrays via combination of Stille coupling and C-H transformation as high-performance electron transport materials

Hybrid rylene arrays have been prepared via a combination of Stille coupling and C-H transformation. The ability to extend the π system along the equatorial axis of rylenes not only leads to broadened light absorption but also increases the electron affinity, which can facilitate electron injection and transport with ambient stability.     

Adsorbed anthranilic acid molecules cause charge reversal of nonionic micelles

The effect of anthranilic acid, an aromatic amino acid, on the structural characteristics of nonionic micelles of Triton X-100 at different pH values was investigated by light scattering and small-angle neutron scattering (SANS) measurements. The scattered light intensity decreases as pH is increased or decreased on either side of the isoelectric point (IEP = 3.4) of the amino acid. Analysis of the SANS data using a sticky hard-sphere model shows that the micelles are oblate ellipsoids with an axial ratio of approximately 2.3. No significant change could be observed in the size of the micelles with a change in the pH, while the stickiness parameter (tau), which is related to the interaction potential (u(0)) increases on either side of the IEP. As tau increases, u(o) becomes less negative, indicating a decrease in the attractive interaction between nonionic micelles. This can be explained in terms of the changes in the surface charge of the micelles resulting from a shift in the acid-base equilibrium of the adsorbed amino acid. The variation of the intermicellar interaction as calculated from the stickiness parameter is consistent with the picture of reversal of charge of amino acids with pH. This is further supported by the observed variation of the cloud point of the solutions at different pH values. The change in the interparticle interaction is also reflected in the diffusion coefficient of the micelles measured by dynamic light scattering.     

Raman spectra of amino acids and their aqueous solutions

Amino acids are the basic "building blocks" that combine to form proteins and play an important physiological role in all life-forms. Amino acids can be used as models for the examination of the importance of intermolecular bonding in life processes. Raman spectra serve to obtain information regarding molecular conformation, giving valuable insights into the topology of more complex molecules (peptides and proteins). In this paper, amino acids and their aqueous solution have been studied by Raman spectroscopy. Comparisons of certain values for these frequencies in amino acids and their aqueous solutions are given. Spectra of solids when compared to those of the solute in solution are invariably much more complex and almost always sharper. We present a collection of Raman spectra of 18 kinds of amino acids (L-alanine, L-arginine, L-aspartic acid, cystine, L-glutamic acid, L-glycine, L-histidine, L-isoluecine, L-leucine, L-lysine, L-phenylalanine, L-methionone, L-proline, L-serine, L-threonine, L-tryptophan, L-tyrosine, L-valine) and their aqueous solutions that can serve as references for the interpretation of Raman spectra of proteins and biological materials.     

The structures of Langmuir-Blodgett films of fatty acids and their salts

Recent advances in several experimental techniques have enabled detailed structural information to be obtained for floating (Langmuir) monolayers and Langmuir-Blodgett films. These techniques are described briefly and their application to the study of films of fatty acids and their salts is discussed. Floating monolayers on aqueous subphases have been shown to possess a complex polymorphism with phases whose structures may be compared to those of smectic mesophases. However, only those phases that exist at high surface pressures are normally used in Langmuir-Blodgett (LB) deposition. In single LB monolayers of fatty acids and fatty acid salts the acyl chains are in the all-trans conformation with their long axes normal to the substrate. The in-plane molecular packing is hexagonal with long-range bond orientational order and short-range positional order: known as the hexatic-B structure. This structure is found irrespective of the phase of the parent floating monolayer. The structures of multilayer LB films are similar to the structures of their bulk crystals, consisting of stacked bilayer lamellae. Each lamella is formed from two monolayers of fatty acid molecules or ions arranged head to head and held together by hydrogen bonding between pairs of acids or ionic bonding through the divalent cations. With acids the acyl chains are tilted with respect to the substrate normal and have a monoclinic structure, whereas the salts with divalent cations may have the chains normal to the substrate or tilted. The in-plane structures are usually centred rectangular with the chains in the trans conformation and packed in a herringbone pattern. Multilayer films of the acids show only a single-step order-disorder transition at the melting point. This temperature tends to rise as the number of layers increases. Complex changes occur when multilayer films of the salts are heated. Disorder of the chains begins at low temperatures but the arrangement of the head groups does not alter until the melting temperature is reached. Slow heating to a temperature just below the melting temperature gives, with some salts, a radical change in phase. The lamellar structure disappears and a new phase consisting of cylindrical rods lying parallel to the substrate surface and stacked in a hexagonal pattern is formed. In each rod the cations are aligned along the central axis surrounded by the disordered acyl chains.     

ANALYSIS OF PHOTO-OXIDIZED AMINO ACIDS IN TRYPTIC PEPTIDES OF CALF LENS γ-II CRYSTALLIN

Insoluble and crosslinked proteins and increased pigmentation in the eye lens are features of aging and cataracts. Determining the amino acids which are involved in insolubilization, crosslinking and visible light scattering will shed light on the mechanisms by which cataracts form. Calf lens γ-II crystallin was irradiated at 295 nm, digested and separated into tryptic peptides. Additional tryptic peptides were found in the digest of irradiated γ-II which were not present in the dark control digest. These peptides were identified by amino acid sequencing and shown to correspond to expected tryptic fragments of the protein, indicating more facile digestion in the UV-irradiated protein than in dark controls. Amino acid analysis of the irradiated protein and peptides showed losses of histidine. methionine and cysteine residues as compared to control samples. Tryptophan, which is not detected by amino acid analysis, was also found to be reactive since losses in its fluorescence intensity were observed after irradiation. Some of the photochemically active amino acids had lower than expected responses in amino acid sequencing experiments. This suggested specific sites of photochemical activity in the various peptides. The evidence for peptide crosslinks is also discussed.     

Analysis of photo-oxidized amino acids in tryptic peptides of calf lens gamma-II crystallin.

Insoluble and crosslinked proteins and increased pigmentation in the eye lens are features of aging and cataracts. Determining the amino acids which are involved in insolubilization, crosslinking and visible light scattering will shed light on the mechanisms by which cataracts form. Calf lens gamma-II crystallin was irradiated at 295 nm, digested and separated into tryptic peptides. Additional tryptic peptides were found in the digest of irradiated gamma-II which were not present in the dark control digest. These peptides were identified by amino acid sequencing and shown to correspond to expected tryptic fragments of the protein, indicating more facile digestion in the UV-irradiated protein than in dark controls. Amino acid analysis of the irradiated protein and peptides showed losses of histidine, methionine and cysteine residues as compared to control samples. Tryptophan, which is not detected by amino acid analysis, was also found to be reactive since losses in its fluorescence intensity were observed after irradiation. Some of the photochemically active amino acids had lower than expected responses in amino acid sequencing experiments. This suggested specific sites of photochemical activity in the various peptides. The evidence for peptide crosslinks is also discussed.     

Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus

Vision begins when light is absorbed by visual pigments. It is commonly believed that the absorption spectra of visual pigments are modulated by interactions between the retinal and amino acids within or near 4.5 angstroms of the retinal in the transmembrane (TM) segments. However, this dogma has not been rigorously tested. In this study, we show that the retinal-opsin interactions extend well beyond the retinal binding pocket. We found that, although it is positioned outside of TM segments, the C-terminus of the rhodopsin in the rockfish longspine thornyhead (Sebastolobus altivelis) modulates its lambda(max) by interacting mainly with the last TM segment. Our results illustrate how amino acids in the C-terminus are likely to interact with the retinal. We anticipate our analyses to be a starting point for viewing the spectral tuning of visual pigments as interactions between the retinal and key amino acids that are distributed throughout the entire pigment.     

Development of probe electrospray using a solid needle

Electrospray using a solid needle probe for the analysis of liquid samples was developed. The needle was moved up and down a vertical axis by a motor-driven system. At the lowest position of the needle, the tip of the needle touched the surface of the liquid sample and a small amount of liquid was picked up by the needle. At the highest position, a high voltage of approximately 3 kV was applied to the needle and the sample loaded on the tip of the needle was electrosprayed. The ions formed were measured by an orthogonal time-of-flight mass spectrometer. A single sample loading by the needle gave reasonably strong ion signals for amino acids, peptides, proteins and polyethylene glycol (PEG) in aqueous solution. The addition of salts or acids to aqueous solution led to dramatic enhancement of the ion signals. Copyright (c) 2007 John Wiley & Sons, Ltd.     

Hydro­gen‐bonding patterns in cis‐4‐ammonio­cyclo­hexane­carboxyl­ate hemihydrate

In the title compound, C₇H₁₃NO₂·0.5H₂O, cis‐4‐amino­cyclo­hexane­carboxylic acid exists as a zwitterion and co‐crystallizes with water mol­ecules in a 2:1 amino acid–water ratio. The cyclo­hexane ring adopts a chair conformation, with the carboxyl­ate and ammonium groups in axial and equatorial positions, respectively. The basic motif in the crystal structure is a sandwich structure, formed by two amino acid units linked by head‐to‐tail hydrogen bonds. Hydro­gen bonds of the type N⁺—H⋯O—C—O⁻ link these motifs, forming helicoidally extended chains running along the c axis. The water molecule lies on a twofold axis and interacts with the chains by means of O—H⋯O hydrogen bonds.     

Au nanorod arrays tailored for surface-enhanced Raman spectroscopy.

We have demonstrated surface-enhanced Raman spectroscopy (SERS) on arrays of Au nanorods aligned in line by a dynamic oblique deposition technique. For light polarized along the major axes of the nanorods, the plasma resonance of the Au nanorods has been tuned to a wavelength suitable for Raman spectroscopy. Raman scattering on the discrete nanorods is significantly enhanced compared with that on semicontinuous Au films. Since the preparation process is physically bottom-up, it is robust in its selection of the materials and is useful for providing SERS sensors at low cost.     

Ibotenic acid analogues. Synthesis and biological testing of two bicyclic 3-isoxazolol amino acids

The bicyclic 3-isoxazolol amino acids (RS)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[4,5-c]pyridine-4-carboxylic acid (5, 4-HPCA) and (RS)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[4,5-c]pyridine-6-carboxylic acid (11, 6-HPCA) were synthesized as model compounds for studies of the structural requirements of central excitatory amino acid neurotransmitter receptors. 4-HPCA was synthesized via introduction of a methoxycarbonyl group into the 4-position of the lithiated N-nitroso intermediate 1. The key reaction in the synthesis of 6-HPCA is an intramolecular N-alkylation of the appropriately substituted acetamidomalonate derivative 7 using sodium hydride as a base. On the basis of the pKA values for 4-HPCA the existence of an intramolecular hydrogen bond in the zwitterionic form of this amino acid is proposed. 6-HPCA was shown by 1H NMR spectroscopy to adopt preferentially a conformation with the carboxylate group in an equatorial position. 4- and 6-HPCA were tested as agonists and antagonists at excitatory amino acid receptors on neurones in the cat spinal cord using microelectrophoretic techniques. Neither compound showed significant effects at these receptors.     

Reduction potential tuning at a type 1 copper site does not compromise electron transfer reactivity

Type 1 (T1) copper sites promote biological electron transfer (ET) and typically possess a weakly coordinated thioether sulfur from an axial Met [Cu(II)-Sdelta approximately 2.6 to 3.3 A] along with the conserved His2Cys equatorial ligands. A strong axial bond [Cu(II)-Oepsilon1 approximately 2.2 A] is sometimes provided by a Gln (as in the stellacyanins), and the axial ligand can be absent (a Val, Leu or Phe in the axial position) as in ceruloplasmin, Fet3p, fungal laccases and some plantacyanins (PLTs). Cucumber basic protein (CBP) is a PLT which has a relatively short Cu(II)-S(Met89) axial bond (2.6 A). The Met89Gln variant of CBP has an electron self-exchange (ESE) rate constant (k(ese), a measure of intrinsic ET reactivity) approximately 7 times lower than that of the wild-type protein. The Met89Val mutation to CBP results in a 2-fold increase in k(ese). As the axial interaction decreases from strong Oepsilon1 of Gln to relatively weak Sdelta of Met to no ligand (Val), ESE reactivity is therefore enhanced by approximately 1 order of magnitude while the reduction potential increases by approximately 350 mV. The variable coordination position at this ubiquitous ET site provides a mechanism for tuning the driving force to optimize ET with the correct partner without significantly compromising intrinsic reactivity. The enhanced reactivity of a three-coordinate T1 copper site will facilitate intramolecular ET in fungal laccases and Fet3p.     

Color vision: "OH-site" rule for seeing red and green

Eyes gather information, and color forms an extremely important component of the information, more so in the case of animals to forage and navigate within their immediate environment. By using the ONIOM (QM/MM) (ONIOM = our own N-layer integrated molecular orbital plus molecular mechanics) method, we report a comprehensive theoretical analysis of the structure and molecular mechanism of spectral tuning of monkey red- and green-sensitive visual pigments. We show that interaction of retinal with three hydroxyl-bearing amino acids near the β-ionone ring part of the retinal in opsin, A164S, F261Y, and A269T, increases the electron delocalization, decreases the bond length alternation, and leads to variation in the wavelength of maximal absorbance of the retinal in the red- and green-sensitive visual pigments. On the basis of the analysis, we propose the "OH-site" rule for seeing red and green. This rule is also shown to account for the spectral shifts obtained from hydroxyl-bearing amino acids near the Schiff base in different visual pigments: at site 292 (A292S, A292Y, and A292T) in bovine and at site 111 (Y111) in squid opsins. Therefore, the OH-site rule is shown to be site-specific and not pigment-specific and thus can be used for tracking spectral shifts in any visual pigment.     

Study by Raman spectromicroscopy of the effect of tensile deformation on the molecular structure of Bombyx mori silk

The effect of mechanical deformation on the polarized Raman spectra of a silk monofilament of the silkworm Bombyx mori has been studied in order to detect tensile stress-induced changes of the fibroin conformation and reorientation up to the breaking point. For this study, a motorized mechanical stretcher has been specifically designed to fit under the Raman microscope, thus allowing the simultaneous recording of the stress, strain and polarized Raman spectra. Due to its twin drive screw design, this stretcher allows to stretch the silk fiber symmetrically and thus to probe the same area of the fiber during the entire elongation procedure. The results obtained have allowed to clarify the assignment of some vibrational bands of silk. They also show that the intensity of some Raman bands is affected by tensile deformation. In particular, the amide III/amide I intensity ratio decreases as the strain increases and the variation is proportional to the stress applied on the fiber. These variations in intensity suggest that the alignment of the protein chains decreases with strain which might be due to the reorganization of the amorphous phase. The Raman spectra also show that several bands shift toward low wavenumbers as the strain applied increases indicating that the force constant and/or dihedral angles of the peptide bonds, in particular those involved in the β-sheets, are affected by drawing. Therefore, a local stress is directly applied on the β-sheets and the wavenumber shift observed is proportional to the stress applied on the fiber.     

A two-dimensional iron(II) carboxylate linear chain polymer that exhibits a metamagnetic spin-canted antiferromagnetic to single-chain magnetic transition

A two-dimensional iron(II) carboxylate coordination polymer, [Fe(pyoa)2]infinity, where pyoa is 2-(pyridin-3-yloxy)acetate, has been prepared by hydrothermal synthesis. Its crystal structure reveals a single iron(II) site with an elongated octahedral coordination environment containing four equatorial carboxylate oxygens and two axial pyridyl nitrogens; the iron(II) sites are linked by syn-anti micro-carboxylates to form chains along the b axis that have an Fe...Fe separation of 4.910 A. The shortest interchain and interlayer Fe...Fe distances are 6.453 and 11.125 A, respectively. The 4.2-295 K M?ssbauer spectra of [Fe(pyoa) 2] infinity consist of a single paramagnetic high-spin iron(II) quadrupole doublet. The axial Fe-N bond direction defines the Jahn-Teller axis at an iron(II) site and, consequently, the orientation of the single-ion magnetic anisotropy. Thus, along the b axis in a given chain, the spins are collinear and parallel to the Jahn-Teller axis. The Jahn-Teller axes of adjacent intralayer chains have different orientations with an angle of 79.2 degrees between the axes in adjacent chains in a bc layer. [Fe(pyoa)2]infinity exhibits field-induced metamagnetic behavior such that, in an applied field smaller than the critical field, the iron(II) spin-canted moments experience intrachain ferromagnetic interactions and weak interchain antiferromagnetic interactions; the spin canting yields weak ferromagnetism. In an applied field larger than the critical field, the weak antiferromagnetic interchain interactions are overwhelmed to yield superparamagnetic-like slow-magnetic relaxation with an energy barrier of 23(3) K. Single-crystal magnetic studies reveal a quasi-uniaxial magnetic anisotropy with the a axis as the easy-magnetic axis and the b axis as the hard-magnetic axis; the susceptibility measured along the easy a axis may be fit with the Glauber model to yield an effective intrachain exchange coupling constant of 2.06(8) K. A dynamic analysis of the susceptibility yields a 6.3(1) K energy barrier for intrachain domain wall creation. The observed field-assisted superparamagnet-like behavior is consistent with the dynamics of a single-chain magnet. Thus, [Fe(pyoa)2]infinity is best considered as a "metamagnetic-like" single-chain magnet.     

Interlayer water molecules in vanadium pentoxide hydrate. IX. Anisotropic translational diffusion leading to anisotropic ac conductivity

The anisotropy of the dynamic properties of interlayer water molecules along the a and b axes of vanadium pentoxide hydrate, orthorhombic V2O5.nH2O, was studied using quasielastic neutron scattering (QENS) in relation to the anisotropy of the ac conductivity. The QENS spectra were analyzed using a stretched exponential function and a Lorentzian function. Both methods showed that the double-layer water molecules along the b axis are more mobile than those along the a axis. The difference in mobility between the two axes is more pronounced using a Lorentzian function analysis. These facts suggest that the diffusion coefficient of water molecules along the b axis is larger than that along the a axis, which is closely related to the ac conductivity originating from proton hopping. The anisotropy of the dynamic motion of water molecules can be attributed to the shorter b-axis length (b=3.60 A), with respect to the longer and less regular repetition of the atomic arrangements along the a axis (42.34 A).     

Effects of hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil

The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.