Dynamical structure of αB-crystallin

The human small heat-shock protein αB-crystallin is an extremely difficult molecule to study, with its inherent structural dynamics posing unique challenges to all biophysical and structural biology techniques. Here we highlight how the polydispersity and quaternary dynamics of αB-crystallin are intrinsically inter-twined, and how this can impact on measurements of the oligomeric distribution. We show that, in spite of these difficulties, considerable understanding of the varied fluctuations αB-crystallin undergoes at equilibrium has emerged in the last few years. By reporting on data obtained from a variety of biophysical techniques, we demonstrate how the αB-crystallin solution ensemble is governed by molecular motions of varying amplitude and time-scales spanning several orders of magnitude. We describe how these diverse measurements are being used to construct an integrated view of the dynamical structure of αB-crystallin, and highlight areas that require further interrogation. With its study motivating the refinement of experimental techniques, and the development of new approaches to combine the hybrid datasets, we conclude that αB-crystallin continues to represent a paradigm for dynamical biology.     

Denaturation of β-sheet structure

A two-dimensional Ising model is used to study the thermal denaturation of parallel β-sheet structures in biomolecules.The fraction of intact hydrogen bonds and the excess heat capacity are evaluated as a function of the temperature.     

On the computation of the tertiary structure of globular proteins—IV. Use of secondary structure information

The distance geometry approach for computing the tertiary structure of globular proteins emphasized in this series of papers (Goelet al., J. theor. Biol. 99, 705–757, 1982) is developed further. This development includes incorporation of some secondary structure information—the location of alpha helices in the primary sequence—in the algorithm to compute the tertiary structure of alpha helical globular proteins. An algorithm is developed which estimates the interresidue distances between chain-proximate helices. These distances, in conjunction with the global statistical average distances obtainable from a database of real proteins and determined by the primary sequence of the protein under study, are used to determine the tertiary structure. Five proteins, parvalbumin, hemerythrin, human hemoglobin, lamprey hemoglobin, and sperm whale myoglobin, are investigated. The root mean square (RMS) errors between the calculated structures and those determined by X-ray diffraction range from 4.78 to 7.56 Å. These RMSs are 0.21–2.76 Å lower than those estimated without the secondary structure information. Contact maps and three-dimensional backbone representations also show considerable improvements with the introduction of secondary structure information.     

Secondary structure of Qβ RNA

The complete set of possible secondary structures of a variant Qβ RNA sequenced by Schaffner has been found using a computer program which allows G-U pairing as well as the usual Watson-Crick A-U and G-C pairing. Of special interest are those secondary structures with the highest double-strandedness. Omitting G-U pairing, we find the structure with the maximum double-strandedness has a pairing of 62% and exhibits a similarity to the clover leaf structure of tRNA. Including G-U pairing, the complementary strands of RNA are asymmetrical. We find maximum pairings of 71% for both the plus and minus strands. These structures also exhibit a cloverleaf structure. A similar analysis has been carried out for the secondary structure of a larger Qβ variant sequenced by Mills, Kramer and Spiegelman, but in this case there are a large number of secondary structures with the same maximum number of pairs and it is therefore not possible to select a unique structure with the maximum double-strandedness.     

Evolutionary modifications of molecular structure of ATP-synthase γ-subunit

The ATP-synthase γ-subunit (FoF1) belongs to the rotor part of this oligomeric complex. Catalytic hydrolysis of adenosine triphosphate (ATP) is accompanied by rotation of γ-polypeptide inside the sphere formed by six subunits (αβ)₃ of the enzyme. The γ-subunit regulates ATPase and ATP-synthase activities of the FoF1. In the present work, evolutionary and reverse changes of this regulatory polypeptide and their effect on properties of the enzyme are studied. It is suggested that elongation of the γ-subunit globular part had resulted from the atpC intragene duplication in the process of adaptive evolution. The evolved fragment participates in light regulation of the chloroplast ATP-synthase.     

Intramolecular distortion of the α-helical structure of polypeptides

Broadening of the infrared amide A, amide I and amide II bands of α-helical polypeptides has been observed for thermodynamically unstable α-helices. This spectroscopic fact can be explained now by the geometrical distortions of the backbone of the helical structure. Two models for distorted helices which include regular or irregular distortions of the angles of internal rotation of the main polypeptide chain have been considered. It is pointed out that the instability of α-helix is associated with irregular distortions of the polypeptide backbone.     

The structure of the α-keratin microfibril

Quantitative measurements of the intensity of the meridional reflections in the X-ray-diffraction pattern of alpha-keratin are shown to be consistent with a microfibril structure in which a surface lattice with an axially projected period around 200 A is subject to a periodic interruption with an axially projected period of 470 A. Taken in conjunction with recent evidence on the chemical structure of alpha-keratin and other intermediate filaments this finding enables an elaboration to be made of a model proposed earlier by RDB Fraser, TP MacRae, & E Suzuki (J. Mol. Biol. 108, 435-452, 1976) for the alpha-helical framework of the microfibril. The disposition and connectivity of the helical segments suggested here provides a straightforward explanation of a number of recent physicochemical and electron-microscopical observations on intermediate filaments and provides a starting point for the development of models for the framework of other intermediate filaments.     

Strength and structure of spiders’ silks

Spider silks are composite materials with often complex microstructures. They are spun from liquid crystalline dope using a complicated spinning mechanism which gives the animal considerable control. The material properties of finished silk are modified by the effects of water and other solvents, and spiders make use of this to produce fibres with specific qualities. The surprising sophistication of spider silks and spinning technologies makes it imperative for us to understand both material and manufacturing in nature before embarking on the commercialization of biotechnologically modified silk dope.     

Morphological structure and optical properties of the wings of Morphidae

The morphological structure and optical properties of the wings of 14 species of Morphidae have been investigated. Most of the scales of the iridescent species of Morphidae （Lepidoptera） present a very particular structure. The ground scales, responsible for the major part of the optical properties, are covered by a very regular set of longitudinal ridges. The ridges themselves are constituted by a superposition of lamellae that act locally as a multilayered structure. This very specific morphology leads to both interferences and diffraction effects. The first one is responsible of the brilliant blue coloration of the males, while the second one diffracts this colored light at a very large angle. These two phenomena give to the butterfly a very effective long-range communication system. The morphological characteristics of the scales of the various species are presented in detail. Two types of optical measurement were performed on the iridescent wings of 14 different species of Morphidae： spectroscopic measurements under various incidences and gonioscopic measurements for a given incidence angle and wavelength. The first allows a determination of the index of refraction of the cuticular material. The second leads to the drawing of spatial diffraction maps. It shows that most of the reflected light is diffracted laterally over a very large angle （90° 〈 0 〈 120°, according to the different species） and that this repartition depends of the polarization of incident light. As predicted by previous calculations, the dissymmetric structure of the ridge is responsible for the separation of the polarization modes in the various diffraction orders.     

Primary structure of the major β-chain of rat haemoglobins

The amino acid sequence of the major β-chain, ^IIβ, from rat haemoglobins was established with an automated sequencer. Amino acid heterogeneities were found that appear to result from allelic variation at particular residues. We applied several new or unusual techniques in determining the sequence: (1) reaction of the polypeptide with dansylaziridine for detection of cysteine; (2) blockage of the N-terminal residue and the ε-amino group of lysine residues with 1-fluoro-2-nitro-4-trimethylammoniobenzene iodide and subsequent identification of the modified lysine phenylthiohydantoin by absorbance at 420nm; (3) identification of histidine phenylthiohydantoin by its blue fluorescence under long-wave u.v. light; (4) cleavage of the chain into two or three fragments and subsequent sequencing without purification [a detailed statement giving the major phenylthiohydantoins assigned at each step for each sequence run before their alignment in individual sequences has been deposited as Supplementary Publication SUP 50084 (10 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1978) 169, 5]; (5) separation of fragments produced by CNBr cleavage by cation-exchange chromatography; (6) peptide sequencing after attachment of the peptide to cytochrome c. The amino acid sequence was confirmed by amino acid compositions of the complete chain, of CNBr fragments 1 and 3, and of 11 purified tryptic peptides.     

Studies on solution NMR structure of brazzein——Secondary structure and molecular scaffold

Brazzein is a sweet-tasting protein isolated from the fruit of West African plant Pentadiplandra brazzeana Baillon. It is the smallest and the most water-soluble sweet protein discovered so far and is highly thermostable. The proton NMR study of brazzein at 600 MHz (pH 3.5, 300 K) is presented. The complete sequence specific assignments of the individual backbone and sideehain proton resonances were achieved using through-bond and through-space eonneetivities obtained from standard two-dimensional NMR techniques. The secondary structure of brazzein contains one α-helix (residues 21—29), one short 3_(10)-helix (residues 14—17), two strands of antiparallel β-sheet (residues 34—39, 44—50) and probably a third strand (residues 5—7) near the N-terminus. A comparative analysis found that brazzein shares a so-called 'eysteine-stabilized alpha-beta' (CSαβ) motif with scorpion neurotoxins, insect defensins and plant γ-thionins. The significance of this multi-function motif, the possible active sites an     

Studies on solution NMR structure of brazzein——Secondary structure and molecular scaffold

Brazzein is a sweet-tasting protein isolated from the fruit of West African plantPentadiplandra brazzeana Baillon. It is the smallest and the most water-soluble sweet protein discovered so far and is highly thermostable. The proton NMR study of brazzein at 600 MHz (pH 3.5, 300 K) is presented. The complete sequence specific assignments of the individual backbone and sidechain proton resonances were achieved using through-bond and through-space connectivities obtained from standard two-dimensional NMR techniques. The secondary structure of brazzein contains one alpha-helix (residues 21-29), one short 3(10)-helix (residues 14-17), two strands of antiparallel beta-sheet (residues 34-39, 44-50) and probably a third strand (residues 5-7) near the N-terminus. A comparative analysis found that brazzein shares a so-called 'cysteine-stabilized alpha-beta' (CSalphabeta) motif with scorpion neurotoxins, insect defensins and plant gamma - thionins. The significance of this multi-function motif, the possible active sites and the structural basis of themostability were discussed.     

Effects of Hofmeister ions on the α-helical structure of proteins

The molecular conformation of proteins is sensitive to the nature of the aqueous environment. In particular, the presence of ions can stabilize or destabilize (denature) protein secondary structure. The underlying mechanisms of these actions are still not fully understood. Here, we combine circular dichroism (CD), single-molecule Förster resonance energy transfer, and atomistic computer simulations to elucidate salt-specific effects on the structure of three peptides with large α-helical propensity. CD indicates a complex ion-specific destabilization of the α-helix that can be rationalized by using a single salt-free computer simulation in combination with the recently introduced scheme of ion-partitioning between nonpolar and polar peptide surfaces. Simulations including salt provide a molecular underpinning of this partitioning concept. Furthermore, our single-molecule Förster resonance energy transfer measurements reveal highly compressed peptide conformations in molar concentrations of NaClO₄ in contrast to strong swelling in the presence of GdmCl. The compacted states observed in the presence of NaClO₄ originate from a tight ion-backbone network that leads to a highly heterogeneous secondary structure distribution and an overall lower α-helical content that would be estimated from CD. Thus, NaClO₄ denatures by inducing a molten globule-like structure that seems completely off-pathway between a fully folded helix and a coil state.     

Crystal structure of a hemojuvelin-binding fragment of neogenin at 1.8Å

Neogenin is a type I transmembrane glycoprotein with a large ectodomain containing tandem immunoglobulin-like and fibronectin type III (FNIII) domains. Closely related to the tumor suppressor gene DCC, neogenin functions in critical biological processes through binding to various ligands, including netrin, repulsive guidance molecules, and the iron regulatory protein hemojuvelin. We previously reported that neogenin binds to hemojuvelin through its membrane-proximal fifth and sixth FNIII domains (FN5-6), with domain 6 (FN6) contributing the majority of critical binding interactions. Here we present the crystal structure of FN5-6, the hemojuvelin-binding fragment of human neogenin, at 1.8?. The two FNIII domains are orientated nearly linearly, a domain arrangement most similar to that of a tandem FNIII-containing fragment within the cytoplasmic tail of the β4 integrin. By mapping surface-exposed residues that differ between neogenin FN5-6 and the comparable domains from DCC, which does not bind hemojuvelin, we identified a potential hemojuvelin-binding site on neogenin FN6. Neogenin FN5, which does not bind hemojuvelin in isolation, exhibits a highly electropositive surface, which may be involved in interactions with negatively-charged polysaccharides or phospholipids in the membrane bilayer. The neogenin FN5-6 structure can be used to facilitate a molecular understanding of neogenin's interaction with hemojuvelin to regulate iron homeostasis and with hemojuvelin-related repulsive guidance molecules to mediate axon guidance.     

The structure of dopamine induced α-synuclein oligomers

Inclusions of aggregated α-synuclein (α-syn) in dopaminergic neurons are a characteristic histological marker of Parkinson’s disease (PD). In vitro, α-syn in the presence of dopamine (DA) at physiological pH forms SDS-resistant non-amyloidogenic oligomers. We used a combination of biophysical techniques, including sedimentation velocity analysis, small angle X-ray scattering (SAXS) and circular dichroism spectroscopy to study the characteristics of α-syn oligomers formed in the presence of DA. Our SAXS data show that the trimers formed by the action of DA on α-syn consist of overlapping worm-like monomers, with no end-to-end associations. This lack of structure contrasts with the well-established, extensive β-sheet structure of the amyloid fibril form of the protein and its pre-fibrillar oligomers. We propose on the basis of these and earlier data that oxidation of the four methionine residues at the C- and N-terminal ends of α-syn molecules prevents their end-to-end association and stabilises oligomers formed by cross linking with DA-quinone/DA-melanin, which are formed as a result of the redox process, thus inhibiting formation of the β-sheet structure found in other pre-fibrillar forms of α-syn.     

Computational exploration of metal–organic frameworks: examples of advances in crystal structure predictions and electronic structure tuning

The purpose of this article is to consider some recent developments in the area of the computational chemistry of metal–organic frameworks (MOFs), and more specifically on their crystal structure prediction and electronic structures. We intend here to illustrate how computational approaches might be powerful tool for the discovery of new families of hybrid frameworks, helping to understand their often complex energy landscapes. Also, MOFs have attracted a lot of attention due to their potential use for photocatalysis and optoelectronic, making it necessary to develop strategies to control their electronic structures. We will show how recent computational studies in this area have allowed a better understanding of their electronic properties and their potential tunability, highlighting when they have given successful guidelines for the discovery of novel MOFs with targeted properties.     

Specific recognition in the tertiary structure of β-sheets of proteins

The frequency of occurrence of nearest neighbour residue pairs on adjacent antiparallel (β_A) and parallel (β_P) strands is obtained from 30 known protein structures. The specificity of interstrand recognition due to such pairing as a factor in the folding of β-sheets is studied by statistical methods. Residues of sufficiently high count for statistical analysis are treated individually while the rest are combined into small groups of similar size, polarity, and/or genetic exchangeability. The hypothesis of specific recognition between individuals and small groups is contrasted with the alternative hypothesis of non-specific recognition between broad classes (hydrophobia, neutral, polar) of residues. A χ² test of pair correlations favours specific recognition against non-specific recognition with a high level of confidence. The largest and most significant correlations are: Ser/Thr (1.9 ± 0.3), Ile/Val (1.7 ± 0.3) and Lys-Arg/Asp-Gln (1.8 ± 0.3) in β_A, and Ile/Leu (1.9 ± 0.4) in β_P. The pair Gly/Gly never occurs in any β-sheet. The specific residue-pair correlations derived here may be useful in statistical prediction methods of protein tertiary structure.