Structure of the CAP-DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface

The crystallographic structure of the CAP-DNA complex at 3.0 Å resolution has been reported previously. For technical reasons, the reported structure had been determined using a gapped DNA molecule lacking two phosphates important for CAP-DNA interaction. In this work, we report the crystallographic structure of the CAP-DNA complex at 2.5 Å resolution using a DNA molecule having all phosphates important for CAP-DNA interaction. The present resolution permits unambiguous identification of amino acid-base and amino acid-phosphate hydrogen bonded contacts in the CAP-DNA complex. In addition, the present resolution permits accurate definition of the kinked DNA conformation in the CAP-DNA complex.     

A New Crystal Form of the Fab Fragment of a Monoclonal Antibody to Human Interleukin-2: The Three-Dimensional Structure at 2.7 Å Resolution

The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 in a new crystal form (space group P2₁2₁2₁; unit cell parameters: a = 42.82 Å, b = 90.68 Å, and c = 139.82 Å) was determined by the X-ray molecular replacement method at the resolution of 2.7 Å. The protein folding and the stereochemistry of its antigen-binding site were comparatively analyzed.     

Elucidation of the Molecular Basis for Arabinoxylan-Debranching Activity of a Thermostable Family GH62 α-l-Arabinofuranosidase from Streptomyces thermoviolaceus

Xylan-debranching enzymes facilitate the complete hydrolysis of xylan and can be used to alter xylan chemistry. Here, the family GH62 α-l-arabinofuranosidase from Streptomyces thermoviolaceus (SthAbf62A) was shown to have a half-life of 60 min at 60°C and the ability to cleave α-1,3 l-arabinofuranose (l-Araf) from singly substituted xylopyranosyl (Xylp) backbone residues in wheat arabinoxylan; low levels of activity on arabinan as well as 4-nitrophenyl α-l-arabinofuranoside were also detected. After selective removal of α-1,3 l-Araf substituents from disubstituted Xylp residues present in wheat arabinoxylan, SthAbf62A could also cleave the remaining α-1,2 l-Araf substituents, confirming the ability of SthAbf62A to remove α-l-Araf residues that are (1→2) and (1→3) linked to monosubstituted β-d-Xylp sugars. Three-dimensional structures of SthAbf62A and its complex with xylotetraose and l-arabinose confirmed a five-bladed β-propeller fold and revealed a molecular Velcro in blade V between the β1 and β21 strands, a disulfide bond between Cys27 and Cys297, and a calcium ion coordinated in the central channel of the fold. The enzyme-arabinose complex structure further revealed a narrow and seemingly rigid l-arabinose binding pocket situated at the center of one side of the β propeller, which stabilized the arabinofuranosyl substituent through several hydrogen-bonding and hydrophobic interactions. The predicted catalytic amino acids were oriented toward this binding pocket, and the catalytic essentiality of Asp53 and Glu213 was confirmed by site-specific mutagenesis. Complex structures with xylotetraose revealed a shallow cleft for xylan backbone binding that is open at both ends and comprises multiple binding subsites above and flanking the l-arabinose binding pocket.     

Structure of AAV-DJ, a Retargeted Gene Therapy Vector: Cryo-Electron Microscopy at 4.5 Å Resolution

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Highlights? The 4.5 Å cryo-EM structure of AAV-DJ fully resolves the polypeptide backbone ? Liver tropism selected for in AAV-DJ has not changed the heparin binding site ? Changed conformation in an antigenic loop blocks binding of a neutralizing mAb ? Changed in vivo tropism may result from changed immune interactions     

Insight into the environment of a pre-Roman Iron Age hillfort at Vladař, Czech Republic, using a multi-proxy approach

The large fortified hilltop site of Vladař, northwest Bohemia, Czech Republic (50°05′N, 13°13′E), has recently been studied intensively by way of environmental archaeology, in which palaeoecological methods have played a crucial role. The latter include the analyses of pollen, green algae, Cladocera, other microfossils, plant macro-remains (including charcoal and wood) and chemical composition, carried out on the wet sediments from an artificial cistern/pond situated in the middle of the large citadel, supplemented by charcoal and wood analysis on material from dry situations. The continuous palaeoecological record consists of well-preserved biological remains and covers the period from ca. 400 b.c. to recent times. The chronology is primarily based on radiocarbon dating, supplemented by archaeological finds. The main focus is on the La Tène period of the Iron Age. During the early to middle La Tène the hillfort had a considerable number of permanent inhabitants and woodland was almost completely replaced by an agricultural landscape. The site became partly abandoned by the end of the 3rd century b.c. and completely abandoned around the birth of Christ, after which it reverted to natural woodland communities.     

The Molecular Basis of Voltage-gated Ca2+ Channel Diversity: Is It Time for T?

The existence of diversity in the voltage activated Ca²⁺ channel populations of vertebrate cells has been long recognized. More recently, the molecular cloning of a considerable number of Ca²⁺ channel subunits from cDNA libraries has indicated that the range of possible Ca²⁺ channel phenotypes a cell can express may be even greater than was previously appreciated. A challenge of recent years has been to resolve how the properties of recombinant channels correspond with their counterparts experimentally characterized in native cells. In this short review I will outline the properties of both native and recombinant Ca²⁺ channels, and will then describe the current agreements and controversies concerning their relationships to each other. Received: 14 July 1997/Revised: 4 November 1997     

The Structure and Stability of the Disulfide-Linked γS-Crystallin Dimer Provide Insight into Oxidation Products Associated with Lens Cataract Formation

The reducing environment in the eye lens diminishes with age, leading to significant oxidative stress. Oxidation of lens crystallin proteins is the major contributor to their destabilization and deleterious aggregation that scatters visible light, obscures vision, and ultimately leads to cataract. However, the molecular basis for oxidation-induced aggregation is unknown. Using X-ray crystallography and small-angle X-ray scattering, we describe the structure of a disulfide-linked dimer of human γS-crystallin that was obtained via oxidation of C24. The γS-crystallin dimer is stable at glutathione concentrations comparable to those in aged and cataractous lenses. Moreover, dimerization of γS-crystallin significantly increases the protein’s propensity to form large insoluble aggregates owing to non-cooperative domain unfolding, as is observed in crystallin variants associated with early-onset cataract. These findings provide insight into how oxidative modification of crystallins contributes to cataract and imply that early-onset and age-related forms of the disease share comparable development pathways.     

Molecular analysis of the gene encoding α-lytic protease: evidence for a preproenzyme

A 1.7-kb EcoRI fragment containing the structural gene for α-lytic protease has been cloned from Lysobacter enzymogenes 495 chromosomal DNA: the first example of a gene cloned from this organism. The protein sequence deduced from the nucleotide sequence encoding this serine protease matches the published amino acid sequence [Olson et al., Nature 228 (1970) 438–442] precisely. Sequence analysis and S 1 mapping indicate that, like subtilisin [e.g. Wells et al., Nucleic Acids Res. 11 (1983) 7911–7925] α-lytic protease is synthesized as a pre-pro protein (41 kDa) that is subsequently processed to its mature extracellular form (20 kDa). This first finding of a large N-terminal protease precursor in a Gram-negative bacterial protease strengthens the hypothesis that large precursors may be a general property of extracellular bacterial proteases, and suggests that the N- or C-terminal location of the precursor segment may be significant.     

Catalytically Dead αCaMKII K42M Mutant Acts as a Dominant Negative in the Control of Synaptic Strength

During long-term potentiation (LTP) of excitatory synapses, Ca²⁺/calmodulin-dependent protein kinase II (CaMKII) is activated by Ca²⁺ influx through NMDA receptors that potentiate AMPA receptor currents by insertion of additional GluR1-containing receptors at the synapse and by increasing AMPA channel conductance, as well as by stimulating structural changes. CaMKII is also involved in the maintenance of LTP and contributes to maintenance of behavioral sensitization by cocaine or amphetamine. Recent studies show that transient expression of catalytically dead αCaMKII K42M mutant after exposure to amphetamine persistently reverses the behavioral effects of the addiction. A suggested interpretation is that this mutant acts as a dominant negative in the control of synaptic strength, but this interpretation has not been physiologically tested. Here we investigate the effect of αCaMKII K42M mutant expressed in single CA1 pyramidal neurons on basal excitatory neurotransmission in cultured rat hippocampal organotypic slices. The mutant caused nearly 50% reduction in the basal CA3–CA1 transmission, while overexpression of the wild-type αCaMKII had no effect. This result is consistent with the dominant negative hypothesis, but there are complexities. We found that the decrease in basal transmission did not occur when activity in the slices was suppressed after transfection by TTX or when NMDA receptors were blocked by APV. Thus, the dominant negative effect requires neural activity for its expression.     

Structure of the Mtb CarD/RNAP β-Lobes Complex Reveals the Molecular Basis of Interaction and Presents a Distinct DNA-Binding Domain for Mtb CarD

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The Primary Structure of Water Buffalo αs1- and β-Casein: Identification of Phosphorylation Sites and Characterization of a Novel β-Casein Variant

The primary structure of water buffalo α_s1-casein and of β-casein A and B variants has been determined using a combination of mass spectrometry and Edman degradation procedures. The phosphorylated residues were localized on the tryptic phosphopeptides after performing a β-elimination/thiol derivatization. Water buffalo α_s1-casein, resolved in three discrete bands by isoelectric focusing, was found to consist of a single protein containing eight, seven, or six phosphate groups. Compared to bovine α_s1-casein C variant, the water buffalo α_s1-casein presented ten amino acid substitutions, seven of which involved charged amino acid residues. With respect to bovine βA₂-casein variant, the two water buffalo β-casein variants A and B presented four and five amino acid substitutions, respectively. In addition to the phosphoserines, a phosphothreonine residue was identified in variant A. From the phylogenetic point of view, both water buffalo β-casein variants seem to be homologous to bovine βA₂-casein.     

Variants of the α6 β1 Laminin Receptor in Early Murine Development: Distribution,Molecular Cloning and Chromosomal Localization of the Mouse Integrin α6 Subunit

Laminin (A:B1:B2) is a major component of the first basement membrane to appear in the developing mouse embryo. Its effects on morphogenesis and differentiation are mediated by interaction with cell surface receptors that are members of the integrin family. We have studied the expression of the α₆ subunit of murine α₆β₁ and its ligand, laminin, in preimplantation mouse embryos, embryo outgrowths and in embryonic stem (ES) cells and embryonal carcinoma (EC) cells. The α₆ subunit is present in the oocyte and throughout preimplantation development. Laminin A chain appears later than α₆ and has a more restricted distribution until the late blastocyst stage. α₆β₁ is strongly expressed in ES and EC cells; the levels of mRNA expression are not altered by differentiation. Molecular cloning of cDNA for the murine integrin α₆ subunit from a mammary gland γt11 library showed, as in man, an open reading frame encoding two variants of α₆, α₆ and α_6B. The identity of the α₆ amino acid sequence to that in man and chicken is 93% and 73%, respectively. The gene for murine α₆ was mapped to chromosome 2. While undifferentiated ES and EC cells express only α_6B, α_6A is co-expressed in ES cells after differentiation is induced by retinoic acid. α_6B is also the only variant expressed in blastocyst stage embryos, but when blastocysts have grown out in culture both α_6A and α_6B are expressed reflecting the results in the cell lines. We suggest that the deposition of laminin in the embryo is a receptor-mediated process and that the shift in the expression of the variants, as the inner cell mass forms its first differentiated progeny, reflects a change in functional properties.     

Insight into the antimicrobial mechanism of action of β2,2-amino acid derivatives from molecular dynamics simulation: Dancing the can-can at the membrane surface

The development of antimicrobial agents that target and selectively disrupt biofilms is a pressing issue since, so far, no antibiotics have been developed that achieve this effectively. Previous experimental work has found a promising set of antibacterial peptides: β^2,2-amino acid derivatives, relatively small molecules with common structural elements composed of a polar head group and two non-polar hydrocarbon arms. In order to develop insight into possible mechanisms of action of these novel antibacterial agents, we have performed an in silico investigation of four leading β^2,2-amino acid derivatives, interacting with models of both bacterial (target) and eukaryotic (host) membranes, using molecular dynamics simulation with a model with all-atom resolution. We found an unexpected result that could shed light on the mechanism of action of these antimicrobial agents: the molecules assume a conformation where one of the hydrophobic arms is directed downward into the membrane core while the other is directed upwards, out of the membrane and exposed above the position of the membrane headgroups; we dubbed this conformation the “can-can pose”. Intriguingly, the can-can pose was most closely linked to the choice of headgroup. Also, the compound previously found to be most effective against biofilms displayed the strongest extent of this behavior and, additionally, this behavior was more pronounced for this compound in the bacterial than in the eukaryotic membrane. We hypothesize that adopting the can-can pose could possibly disrupt the protective peptidoglycan macronet found on the exterior of the bacterial membrane.