Search

Shape and dimensions of the newly discovered Streptomyces alpha-chitin-bonding protein, CHB1 have been investigated. It has two domains, a main elongated globule of about 4 nm and a domain somewhat like a foot in shape and about 2 nm wide. Disulfide bonds are important to the structural/functional properties. The affinity to chitin is lost when they are reduced.

Platinum nanoparticles embedded in hybrid matrixes were studied using anomalous and conventional small-angle x-ray scattering.

Researchers used 11.5 Angstrom cryo-electron microscopy to map the E. coli 70S ribosome. This technique allows the ribosome to be visualized without the need for crystallization.

Research was conducted to examine a ligand-binding protein (SIS2) of a glutamate receptor ion channel (GluR) via solution scattering studies to investigate GluR-binding and signal-transduction mechanisms. The solution scattering properties of the free and agonist-bound states of a ligand-binding domain of the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate receptor subunit GluRD were compared. Results indicate a molecular envelope for the construct in solution.

Research was conducted to examine the properties of a mutant hexokinase I, in which residues critical to the stability of the dimer have been changed by directed mutation. The resulting mutant was shown to exist in solution as a monomer at elevated concentrations of enzyme, either in the presence or absence of ligands. Results indicate that the allosteric regulation of catalysis in monomeric hexokinase I probably involves an interface between the N- and C-terminal halves, similar to ones defined by crystal structures.

Small‐angle X‐ray scattering (SAXS) is an established technique for structural analysis of biological macromolecules in solution. During the last decade, inline chromatography setups coupling SAXS with size exclusion (SEC‐SAXS) or ion exchange (IEC‐SAXS) have become popular in the community. These setups allow one to separate individual components in the sample and to record SAXS data from isolated fractions, which is extremely important for subsequent data interpretation, analysis, and structural modeling. However, in case of partially overlapping elution peaks, inline chromatography SAXS may still yield scattering profiles from mixtures of components. The deconvolution of these scattering data into the individual fractions is nontrivial and potentially ambiguous. We describe a cross‐platform computer program, EFAMIX, for restoring the scattering and concentration profiles of the components based on the evolving factor analysis (EFA). The efficiency of the program is demonstrated in a number of simulated and experimental SEC‐SAXS data sets. Sensitivity and limitations of the method are explored, and its applicability to IEC‐SAXS data is discussed. EFAMIX requires minimal user intervention and is available to academic users through the program package ATSAS as from release 3.1. [ABSTRACT FROM AUTHOR]

The quaternary structure of the V1 ATPase from the tobacco hornworm Manduca sexta and the F1 ATPase from Escherichia coli was characterized using small-angle X-ray scattering. The radii of gyration of the V1 and F1 complexes as well as the shape of the V1 ATPase were also determined. Experimental results showed that a seventh mass, which is thought to be the stalk that links V1 with the membrane domain V0 in the intact V1V0-ATPase, extends perpendicularly to the center of the hexameric unit.

A study was conducted to analyze the quarternary structures of the thiamine diphosphate dependent enzyme pyruvate decarboxylase from Saccharomyces cerevisiae, Zymomonas mobilis and Pisum sativuum. X-ray solution scattering was carried out to perform the analysis while solutions were prepared from enzyme stock solutions. Results indicated that mutant E51 is a critical component in cofactor binding and catalytic activity.

A new method for evaluating linear prolate functions (LPF) is examined. The method solves the eigensystem of the corresponding differential equation. A concise algorithm is introduced to generate LPFs without the Bouwkamp procedure. The eigenvectors of the system generate coefficients of the representation of the required functions into a series of spherical Bessel functions. The algorithm has been initially implemented on a FORTRAN 77 program CALCPRO running on an IBM-PC.

The pH dependence of the three-dimensional quarternary structure of yeast pyruvate decarboxylase (PDC) was examined in the pH range from 6.2 to 8.4 by a synchroton radiation solution x-ray scattering study. The equilibrium between tetramers and dimers occurs at about pH 7.5 and the PDC's catalytic activity is dependent on the volume fraction of tetramer. The experimental observations of an equilibrium shift and formation of octamers were further analyzed. These observations were found to indicate that the dimers must undergo a conformational change when forming the tetramer, as suggested by earlier studies.

Two-component systems (TCS) are widespread signaling systems present in all domains of life. TCS typically consist of a signal receptor/transducer and a response regulator. The receptors (histidine kinases, chemoreceptors and photoreceptors) are often embedded in the membrane and have a similar modular structure. Chemoreceptors were shown to function in highly ordered arrays, with trimers of dimers being the smallest functional unit. However, much less is known about photoreceptors. Here, we use small-angle scattering (SAS) to show that detergent-solubilized sensory rhodopsin II in complex with its cognate transducer forms dimers at low salt concentration, which associate into trimers of dimers at higher buffer molarities. We then fit an atomistic model of the whole complex into the SAS data. The obtained results suggest that the trimer of dimers is "tripod"-shaped and that the contacts between the dimers occur only through their cytoplasmic regions, whereas the transmembrane regions remain unconnected. [ABSTRACT FROM AUTHOR]

The eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. The canonical Alu domain consists of the SRP9/14 protein heterodimer and a tRNA-like folded Alu RNA that adopts a strictly 'closed' conformation involving a loop-loop pseudoknot. Here, we study the structure of the Alu domain from Plasmodium falciparum (PfAlu), a divergent apicomplexan protozoan that causes human malaria. Using NMR, SAXS and cryo-EM analyses, we show that, in contrast to its prokaryotic and eukaryotic counterparts, the PfAlu domain adopts an 'open' Y-shaped conformation. We show that cytoplasmic P. falciparum ribosomes are non-discriminative and recognize both the open PfAlu and closed human Alu domains with nanomolar affinity. In contrast, human ribosomes do not provide high affinity binding sites for either of the Alu domains. Our analyses extend the structural database of Alu domains to the protozoan species and reveal species-specific differences in the recognition of SRP Alu domains by ribosomes. The SRP Alu domain is involved in co-translational protein targeting. Soni et al. investigate the Alu domain of Plasmodium falciparum, the agent of malaria, and find that unlike any other it adopts an open conformation. [ABSTRACT FROM AUTHOR]

During clathrin-mediated endocytosis, a complex and dynamic network of protein-membrane interactions cooperate to achieve membrane invagination. Throughout this process in yeast, endocytic coat adaptors, Sla2 and Ent1, must remain attached to the plasma membrane to transmit force from the actin cytoskeleton required for successful membrane invagination. Here, we present a cryo-EM structure of a 16-mer complex of the ANTH and ENTH membrane-binding domains from Sla2 and Ent1 bound to PIP2 that constitutes the anchor to the plasma membrane. Detailed in vitro and in vivo mutagenesis of the complex interfaces delineate the key interactions for complex formation and deficient cell growth phenotypes demonstrate its biological relevance. A hetero-tetrameric unit binds PIP2 molecules at the ANTH-ENTH interfaces and can form larger assemblies to contribute to membrane remodeling. Finally, a time-resolved small-angle X-ray scattering study of the interaction of these adaptor domains in vitro suggests that ANTH and ENTH domains have evolved to achieve a fast subsecond timescale assembly in the presence of PIP2 and do not require further proteins to form a stable complex. Together, these findings provide a molecular understanding of an essential piece in the molecular puzzle of clathrin-coated endocytic sites. During clathrin-mediated endocytosis in yeast, endocytic coat adaptors, Sla2 and Ent1, must remain attached to the plasma membrane to transmit force from the actin cytoskeleton required for membrane invagination. Here authors present a cryo-EM structure of a 16-mer complex of the ANTH and ENTH membrane-binding domains from Sla2 and Ent1 bound to PIP2 that constitutes the anchor to the plasma membrane. [ABSTRACT FROM AUTHOR]

Small‐angle X‐ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element‐specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X‐rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline. [ABSTRACT FROM AUTHOR]