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M S Weiss

Publications and source records attributed to M S Weiss.

At least 37 records · Page 2Linked to original sources
PubMed1997

Charges, hydrogen bonds, and correlated motions in the 1 A resolution refined structure of the mating pheromone Er-1 from Euplotes raikovi.

A detailed description is given of the structure of the small protein mating pheromone Er-1 at atomic resolution. Emphasis is placed on the locations of charges and hydrogen bonds. The model includes all the protein atoms, anisotropic displacement parameters, four disordered side chains, 22 water molecules, a disordered ethanol, and "riding" hydrogen atoms. Analysis of the model revealed that this dense crystal is perfused by hydrogen-bonding networks of solvent and protein atoms. The termini of helices are capped by hydrogen bonding to solvent and protein atoms, and to symmetry-related molecules. An examination of the valencies and charges of the hydrogen-bonding groups suggests that three of the "water" molecules capping the C termini of two helices, and one other, may instead be NH4 ions. Water molecules mediate all but one of the interhelical hydrogen bonds, and many of the lattice interactions. Regions of the molecule where the atomic vibrations deviate from isotropy are identified. There is almost no overall libration of the molecule allowed by the packing, but the side-chains vibrate relative to the backbone. Four side-chains display alternate conformations. Indirect evidence is presented that the switches between their conformations are correlated and driven by protonation of acidic side-chains. These structural features are discussed in the context of function and stability. Equipped with the analysis of the model, we review the course and results of the refinement of the model against 1 A X-ray diffraction data to a crystallographic R-factor of 12.92%.

Amino Acid Sequence↗
PubMed1997

The crystal structure of the designed trimeric coiled coil coil-VaLd: implications for engineering crystals and supramolecular assemblies.

The three-dimensional structure of the 29-residue designed coiled coil having the amino acid sequence acetyl-E VEALEKK VAALESK VQALEKK VEALEHG-amide has been determined and refined to a crystallographic R-factor of 21.4% for all data from 10-A to 2.1-A resolution. This molecule is called coil-VaLd because it contains valine in the a heptad positions and leucine in the d heptad positions. In the trigonal crystal, three molecules, related by a crystallographic threefold axis, form a parallel three-helix bundle. The bundles are stacked head-to-tail to form a continuous coiled coil along the c-direction of the crystal. The contacts among the three helices within the coiled coil are mainly hydrophobic: four layers of valine residues alternate with four layers of leucine residues to form the core of the bundle. In contrast, mostly hydrophilic contacts mediate the interaction between trimers: here a total of two direct protein--protein hydrogen bonds are found. Based on the structure, we propose a scheme for designing crystals of peptides containing continuous two-, three-, and four-stranded coiled coils.

Amino Acid Sequence↗
PubMed1996

A challenging case for protein crystal structure determination: the mating pheromone Er-1 from Euplotes raikovi.

Four different phasing methods have been applied to the determination of the crystal structure of the 40 amino-acid mating pheromone of the unicellular ciliated protozoan Euplotes raikovi. The difficulties, failures and successes in attempts to solve the structure by: (1) molecular replacement, (2) direct phasing using the 'Shake and Bake' algorithm, (3) isomorphous replacement, and (4) multiple-wavelength anomalous dispersion are described. The structure was first solved by molecular replacement, and then was the first successful structure determination by 'Shake and Bake' without the direct involvement of its authors. A description of the current status of the high-resolution refinement of the structure is also given. The model is refined against 1 A resolution data to an R factor of 12.9%, and includes H atoms and discretely disordered side chains.

Journal Article↗
PubMed1996

Unusual trigonal-planar copper configuration revealed in the atomic structure of yeast copper-zinc superoxide dismutase.

The three-dimensional structure of yeast copper-zinc superoxide dismutase (CuZnSOD) has been determined in a new crystal form in space group R32 and refined against X-ray diffraction data using difference Fourier and restrained crystallographic refinement techniques. The unexpected result is that the copper ion has moved approximately 1 angstrom from its position in previously reported CuZnSOD models, the copper-imidazolate bridge is broken, and a roughly trigonal planar ligand geometry characteristic of Cu(I) rather than Cu(II) is revealed. Final R values for the two nearly identical room temperature structures are 18.6% for all 19 149 reflections in the 10.0-1.7 angstrom resolution range and 18. 2% for 17 682 reflections (F > 2 sigma) in the 10.0-1.73 angstrom resolution range. A third structure has been determined using X-ray data collected at -180 degrees C. The final R value for this structure is 19.0% (R(free) = 22.9%) for all 24 356 reflections in the 10.0-1.55 angstrom resolution range. Virtually no change in the positions of the ligands to the zinc center is observed in these models. The origin of the broken bridge and altered Cu-ligand geometry is discussed.

Crystallography, X-Ray↗
PubMed1995

A cooperative model for receptor recognition and cell adhesion: evidence from the molecular packing in the 1.6-A crystal structure of the pheromone Er-1 from the ciliated protozoan Euplotes raikovi.

The crystal structure of the pheromone Er-1 from the unicellular eukaryotic organism Euplotes raikovi was determined at 1.6 A resolution and refined to a crystallographic R factor of 19.9%. In the tightly packed crystal, two extensive intermolecular helix-helix interactions arrange the Er-1 molecules into layers. Since the putative receptor of the pheromone is a membrane-bound protein, whose extracellular C-terminal domain is identical in amino acid sequence to the soluble pheromone, the interactions found in the crystal may mimic the pheromone-receptor interactions as they occur on a cell surface. Based on this, we propose a model for the interaction between soluble pheromone molecules and their receptors. In this model, strong pheromone-receptor binding emerges as a consequence of the cooperative utilization of several weak interactions. The model offers an explanation for the results of binding studies and may also explain the adhesion between cells that occurs during mating.

Amino Acid Sequence↗
PubMed1995

Structure of the isolated catalytic domain of diphtheria toxin.

The structure of the isolated catalytic domain of diphtheria toxin at pH 5.0 was determined by X-ray crystallography at 2.5 A resolution and refined to an R-factor of 19.7%. The domain is bound to its endogenous inhibitor adenylyl(3'-->5')uridine 3'-monophosphate (ApUp). The structure of this 190-residue domain, which was expressed in and isolated from Escherichia coli, is essentially identical to the structure of the catalytic domain within whole diphtheria toxin determined at pH 7.5. However, there are two adjacent surface loops (loop 66-78 and loop 169-176) that exhibit clear differences when compared to the structure of the catalytic domain in whole diphtheria toxin. Although both loops are at the surface of the protein and are relatively flexible, the chain trace is well-defined in the electron density. The main structural difference is the closer approach of loops 66-78 and 169-176. We ascribe this structural change mainly to the absence of the neighboring transmembrane domain in the isolated catalytic domain as compared to whole diphtheria toxin. We suggest that this change represents the first step of the structural transition from the catalytic domain in whole diphtheria toxin to the translocated form of the domain. The changes are described in detail, and their implications for membrane translocation are discussed.

Binding Sites↗
PubMed1993

Porin conformation in the absence of calcium. Refined structure at 2.5 A resolution.

The crystal structure of porin from Rhodobacter capsulatus in the absence of divalent calcium ions has been refined to convergence at a resolution of 2.5 A using the simulated annealing refinement method. The final model consists of all 301 amino acid residues, 77 solvent molecules, one tris(hydroxymethyl)-aminomethane molecule and one unknown ligand modeled as n-octyltetraoxyethylene. A superposition with the previously described model containing three calcium ions showed structural changes at the segment 108-116 of the inner loop beta 5-beta 6, and at loops beta 8-beta 9 and beta 11-beta 12 at the extracellular side of the porin molecule. Evidence is presented that the conformational changes depend on the presence or absence of calcium ions. A possible influence on porin function is discussed.

Amino Acid Sequence↗
PubMed1992

Structure of porin refined at 1.8 A resolution.

The crystal structure of porin from Rhodobacter capsulatus has been refined using the simulated annealing method. The final model consists of all 301 amino acid residues well obeying standard geometry, three calcium ions, 274 solvent molecules, three detergent molecules and one unknown ligand modeled as a detergent molecule. The final crystallographic R-factor is 18.6% based on 42,851 independent reflections in the resolution range 10 to 1.8 A. The model is described in detail.

Amino Acid Sequence↗
PubMed1991

Molecular architecture and electrostatic properties of a bacterial porin.

The integral membrane protein porin from Rhodobacter capsulatus consists of three tightly associated 16-stranded beta barrels that give rise to three distinct diffusion channels for small solutes through the outer membrane. The x-ray structure of this porin has revealed details of its shape, the residue distributions within the pore and at the membrane-facing surface, and the location of calcium sites. The electrostatic potential has been calculated and related to function. Moreover, potential calculations were found to predict the Ca2+ sites.

Bacterial Outer Membrane Proteins↗
PubMed1991

Prediction of the general structure of OmpF and PhoE from the sequence and structure of porin from Rhodobacter capsulatus. Orientation of porin in the membrane.

By comparing the hydrophilicity profiles and sequences of porin from Rhodobacter capsulatus with those of OmpF and PhoE from Escherichia coli, a set of insertions and deletions for alignment of the sequences has been deduced. With this alignment a similar folding of OmpF and PhoE has been predicted as found by X-ray structure analysis of porin from Rhodobacter capsulates. Furthermore, the orientation of the porin trimer in the outer membrane was inferred from topological data on PhoE. According to this result a single channel of approx. 30 A diameter starts at the outer surface. Near the middle of the outer membrane bilayer this channel branches out into three separate channels, each running within a single porin monomer to the periplasmic surface.

Amino Acid Sequence↗
PubMed1991

The structure of porin from Rhodobacter capsulatus at 1.8 A resolution.

The structure of the porin from Rhodobacter capsulatus was determined at a resolution of 1.8 A. The analysis started from a closely related crystal structure that had been solved at a medium resolution of 3 A using multiple isomorphous replacement and solvent flattening. The new structure contains the complete sequence of 301 amino acid residues. Refinement of the model is under way; the present R-factor is 22% with good geometry. Except for the lengths of several loops, the resulting chain fold corresponds to the medium resolution model. The membrane channel is lined by a large number of ionogenic side chains with characteristic segregation of differently charged groups.

Amino Acids↗
PubMed1991

Crystals of an integral membrane protein diffracting to 1.8 A resolution.

A new crystal form of porin from Rhodobacter capsulatus has been obtained. The crystals are rhombohedral, space group R3, with hexagonal axes a = b = 92.3 A, c = 146.2 A. They contain one monomer in the asymmetric unit and diffract to a resolution of at least 1.8 A.

Bacterial Outer Membrane Proteins↗
PubMed1991

A common channel-forming motif in evolutionarily distant porins.

Four new crystal packings of Escherichia coli porins are presented (phosphoporin, maltoporin, and two crystal forms of matrix porin). These were determined by molecular replacement methods using a polyalanine trial model acquired from the refined coordinates of porin from Rhodobacter capsulatus. The successful molecular replacement shows that the dominant motif found in R. capsulatus porin (a 16-stranded antiparallel beta-barrel) also applies to the E. coli porins, despite the lack of significant amino acid sequence homology. A 30 degrees-40 degrees tilt of the beta-strands with respect to the membrane normal was derived from the intensity distributions in the X-ray diffraction patterns for each porin studied, stressing their similarity. In view of the evolutionary distance between enteric and photosynthetic bacteria, the antiparallel beta-barrel may have significance as a basic structural motif for the formation of bacterial membrane channel structures.

Bacterial Outer Membrane Proteins↗
PubMed1990

The three-dimensional structure of porin from Rhodobacter capsulatus at 3 A resolution.

The crystal structure of porin from Rhodobacter capsulatus strain 37b4 has been solved at 3.0 A (1 A = 0.1 nm) resolution by multiple isomorphous replacement and solvent-flattening. The three pores of the trimer are well defined in the electron density map. Each pore consists of a 16-stranded beta-barrel which traverses the membrane as a tube. Near its center the tube is narrowed by chain segments protruding from the inner wall of the barrel that form an eye-let with an irregular cross-section of about 6 A by 10 A. The eye-let has an axial length of about 10 A; it defines the exclusion limit for diffusing particles.

Bacterial Outer Membrane Proteins↗
PubMed1987

Progressive resistive exercise in weaning high quadriplegics from the ventilator.

Acutely high level quadriplegics may experience neuromuscular respiratory insufficiency secondary to loss of use of intercostal and abdominal muscles as well as partial involvement of the phrenic nerve. Frequently, these patients will require mechanical ventilation in the initial stages of their treatment. These patients may present difficulty with weaning off the ventilator. In addition, poor respiratory reserve increases the risk of episodic decompensation. We have instituted a progressive resistive exercise protocol (PRE) analogous to PRE commonly used in training skeletal muscle, to wean patients off the ventilator. This involves determining the patient's endurance to the development of fatigue while off the ventilator. Patients are re-evaluated weekly until they are weaned from the ventilator. Three case studies are reported in which this protocol was used. In addition to our standard respiratory therapy and physical therapy protocols, values for vital capacity and maximum inspiratory force at admission and post-weaning were recorded. After completion of the programme, none of the patients required re-intubation or subsequent mechanical ventilation. This method of diaphragm training may be useful in weaning high level quadriplegics from the ventilator.

Adult↗
PubMed1985

Electrolaryngeal speech produced by laryngectomized subjects: perceptual characteristics.

The purpose of this study was to investigate the perceptual confusions individuals experience while listening to the speech of laryngectomized persons who used electrolarynges. Six talkers generated speech samples using two different models of electrolarynges. Intelligibility was evaluated from phonetic transcriptions of the speech samples. Confusion matrices were generated from the transcriptions. Talkers varied considerably in their intelligibility, but there was little difference in intelligibility for a given talker using either model of electrolarynx. The perceptual confusions revealed that most errors occurred on the voicing feature.

Humans↗
PubMed1983

Neurophysiological effects of -X impact acceleration.

In 19 experiments, eight unanesthetized Rhesus monkeys, with torsos restrained in a seated position, and with head and neck free to move, were subjected to peak sled accelerations in the -X direction ranging from 42 m/s2 to 963 m/s2. Recordings of cortical somatosensory evoked potentials were made using recording electrodes chronically implanted over the somatosensory cortex. Electrical pulse stimuli were delivered at a rate of 5 Hz through spinal electrodes located at L1-L2. Evoked potentials were recorded prior to impact, through the impact event, and subsequent to impact, then subjected to quantitative analysis procedures which included normalized cross-correlation and exponential regression. The results of this analysis suggest a neurophysiological effect which holds promise as an indicator of a pre-injurious central nervous system condition. This effect is a transient increase of 2% to 5% in the latency of the primary surface positive peak of the cortical evoked potential. There appears to be a threshold for these increases in latency at peak sled accelerations in the region of 600 m/s2. This is consistent with previous findings and provides the basis for applying these techniques to human volunteer experiments.

Acceleration↗