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C Sander

Publications and source records attributed to C Sander.

At least 37 records · Page 2Linked to original sources
PubMed1991

GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites.

GTPase domains are functional and structural units employed as molecular switches in a variety of important cellular functions, such as growth control, protein biosynthesis, and membrane traffic. Amino acid sequences of more than 100 members of different subfamilies are known, but crystal structures of only mammalian ras p21 and bacterial elongation factor Tu have been determined. After optimal superposition of these remarkably similar structures, careful multiple sequence alignment, and calculation of residue-residue interactions, we analyzed the two subfamilies in terms of structural conservation, sequence conservation, and residue contact strength. There are three main results. (i) A structure-based alignment of p21 and elongation factor Tu. (ii) The definition of a common conserved structural core that may be useful as the basis of model building by homology of the three-dimensional structure of any GTPase domain. (iii) Identification of sequence regions, other than the effector loop and the nucleotide binding site, that may be involved in the functional cycle: they are loop L4, known to change conformation after GTP hydrolysis; helix alpha 2, especially Arg-73 and Met-67 in ras p21; loops L8 and L10, including ras p21 Arg-123, Lys-147, and Leu-120; and residues located spatially near the N and C termini. These regions are candidate sites for interaction either with the GTP/GDP exchange factor, with a GTPase-affected function, or with a molecule delivered to a destination site with the aid of the GTPase domain.

Amino Acid Sequence↗
PubMed1991

Identification by computer sequence analysis of transcriptional regulator proteins in Dictyostelium discoideum and Serratia marcescens.

We have performed computer searches in the database of known protein sequences for proteins similar in sequence to bacteriophage regulatory proteins of known 3-D structure. The searches are more selective than other methods due to the use of a length-dependent threshold in sequence similarity, above which structural homology is implied with high certainty. Two probable DNA binding proteins were identified which are predicted to have a three-dimensional structure very similar to bacteriophage cro and repressor proteins. Approximate three-dimensional model coordinates are available from the authors. Both proteins contain the helix-turn-helix sequence motif typical of a wide class of DNA binding proteins and their function is deduced by analogy to sequence-similar proteins of known function. We predict that the Y.Smal protein in the restriction-modification enzyme gene locus of the enterobacterium serratia marcescens is a regulator of endonuclease expression; and, that the vegetative specific gene VSH7 of the slime mold dictyostelium discoideum codes for a regulator of gene expression specific for the slime mold growth phase before the onset of the developmental program. Point mutations that would have a strong effect on growth regulation phenotype are suggested. The VSH7 protein would be the first eukaryotic representative of the cro/phage repressor class.

Amino Acid Sequence↗
PubMed1991

Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.

The problem of constructing all-atom model co-ordinates of a protein from an outline of the polypeptide chain is encountered in protein structure determination by crystallography or nuclear magnetic resonance spectroscopy, in model building by homology and in protein design. Here, we present an automatic procedure for generating full protein co-ordinates (backbone and, optionally, side-chains) given the C alpha trace and amino acid sequence. To construct backbones, a protein structure database is first scanned for fragments that locally fit the chain trace according to distance criteria. A best path algorithm then sifts through these segments and selects an optimal path with minimal mismatch at fragment joints. In blind tests, using fully known protein structures, backbones (C alpha, C, N, O) can be reconstructed with a reliability of 0.4 to 0.6 A root-mean-square position deviation and not more than 0 to 5% peptide flips. This accuracy is sufficient to identify possible errors in protein co-ordinate sets. To construct full co-ordinates, side-chains are added from a library of frequently occurring rotamers using a simple and fast Monte Carlo procedure with simulated annealing. In tests on X-ray structures determined at better than 2.5 A resolution, the positions of side-chain atoms in the protein core (less than 20% relative accessibility) have an accuracy of 1.6 A (r.m.s. deviation) and 70% of chi 1 angles are within 30 degrees of the X-ray structure. The computer program MaxSprout is available on request.

Algorithms↗
PubMed1991

A structure-derived sequence pattern for the detection of type I copper binding domains in distantly related proteins.

A structure-based approach to the definition of sequence patterns characteristic of protein domains is presented by example. The approach requires a multiple sequence alignment of a family (or set of related families) as well as at least one three-dimensional structure. The pattern derived does not merely summarize the information in the known sequences but attempts to generalize the pattern specifications based on structural insight. In this example, the pattern-driven database search identified correctly most of the known type I copper-binding domains and detected the presence of a homologous domain in a previously unknown case (CopA protein). The significance of these results is discussed.

Amino Acid Sequence↗
PubMed1991

Database of homology-derived protein structures and the structural meaning of sequence alignment.

The database of known protein three-dimensional structures can be significantly increased by the use of sequence homology, based on the following observations. (1) The database of known sequences, currently at more than 12,000 proteins, is two orders of magnitude larger than the database of known structures. (2) The currently most powerful method of predicting protein structures is model building by homology. (3) Structural homology can be inferred from the level of sequence similarity. (4) The threshold of sequence similarity sufficient for structural homology depends strongly on the length of the alignment. Here, we first quantify the relation between sequence similarity, structure similarity, and alignment length by an exhaustive survey of alignments between proteins of known structure and report a homology threshold curve as a function of alignment length. We then produce a database of homology-derived secondary structure of proteins (HSSP) by aligning to each protein of known structure all sequences deemed homologous on the basis of the threshold curve. For each known protein structure, the derived database contains the aligned sequences, secondary structure, sequence variability, and sequence profile. Tertiary structures of the aligned sequences are implied, but not modeled explicitly. The database effectively increases the number of known protein structures by a factor of five to more than 1800. The results may be useful in assessing the structural significance of matches in sequence database searches, in deriving preferences and patterns for structure prediction, in elucidating the structural role of conserved residues, and in modeling three-dimensional detail by homology.

Amino Acid Sequence↗
PubMed1991

Detection of common three-dimensional substructures in proteins.

We present a fully automatic algorithm for three-dimensional alignment of protein structures and for the detection of common substructures and structural repeats. Given two proteins, the algorithm first identifies all pairs of structurally similar fragments and subsequently clusters into larger units pairs of fragments that are compatible in three dimensions. The detection of similar substructures is independent of insertion/deletion penalties and can be chosen to be independent of the topology of loop connections and to allow for reversal of chain direction. Using distance geometry filters and other approximations, the algorithm, implemented in the WHAT IF program, is so fast that structural comparison of a single protein with the entire database of known protein structures can be performed routinely on a workstation. The method reproduces known non-trivial superpositions such as plastocyanin on azurin. In addition, we report surprising structural similarity between ubiquitin and a (2Fe-2S) ferredoxin.

Algorithms↗
PubMed1991

The structure of ColE1 rop in solution.

The structure of the ColE1 repressor of primer (rop) protein in solution was determined from the proton nuclear magnetic resonance data by a combined use of distance geometry and restrained molecular dynamics calculations. A set of structures was determined with low internal energy and virtually no violations of the experimental distance restraints. Rop forms homodimers: Two helical hairpins are arranged as an antiparallel four helix bundle with a left-handed rope-like twist of the helix axes and with left-handed bundle topology. The very compact packing of the side chains in the helix interfaces of the rop coiled-coil structure may well account for its high stability. Overall, the solution structure is highly similar to the recently determined X-ray structure (Banner, D.W., Kokkinidis, M. and Tsernoglou, D. (1987) J. Mol. Biol., 196, 657-675), although there are minor differences in regions where packing forces appear to influence the crystal structure.

Bacterial Proteins↗
PubMed1991

The role of heat-shock and chaperone proteins in protein folding: possible molecular mechanisms.

Recently some heat-shock proteins have been linked to functions of 'chaperoning' protein folding in vivo. Here current experimental evidence is reviewed and possible requirements for such an activity are discussed. It is proposed that one mode of chaperone action is to actively unfold misfolded or badly aggregated proteins to a conformation from which they could refold spontaneously; that improperly folded proteins are recognized by excessive stretches of solvent-exposed backbone, rather than by exposed hydrophobic patches; and that the molecular mechanism for unfolding is either repeated binding and dissociation ('plucking') or translocation of the protein backbone through a binding cleft ('threading'), allowing the threaded chain to refold spontaneously. The observed hydrolysis of ATP would provide the energy for active unfolding. These hypotheses can be applied to both monomeric folding and oligomeric assembly and are sufficiently detailed to be open to directed experimental verification.

Heat-Shock Proteins↗
PubMed1991

Interactions between megakaryocytes and sinus wall. An ultrastructural study on bone marrow tissue in primary (essential) thrombocythemia.

An ultrastructural study was performed on bone marrow tissue in primary (essential) thrombocythemia to evaluate possible interactions between megakaryocytes and sinusoids. In addition to a preferential localization of megakaryocytes in the subendothelial space, two different kinds of cytoplasmic processes could be discriminated penetrating the sinus wall. Serial sections disclosed that megakaryocytes developed multiple pseudopod-like plump projections derived from their peripheral zone and devoid of organelles. It is tempting to speculate that these ameboid features could serve as anchors to keep the cell in a subendothelial position and to monitor changes occurring in circulation. The second type of cytoplasmic processes reaching into the vascular lumen consisted of tentacle-like elongated protrusions rich in organelles, apparently originating from the intermediate zone. These projections were thought to present either the beginning of megakaryocytes egress into circulation or putative platelets. Frequently, there was an intrasinusoidal localization of megakaryocytes which revealed numerous so-called platelet territories and apparently an enforced platelet shedding. Generally, these features are comparable with aspects obtained from animal studies, following excessively stimulated megakaryo- and thrombocytopoiesis by application of anti-platelet serum.

Bone Marrow↗
PubMed1991

Ultrastructure of bone marrow tissue in so-called primary (idiopathic) myelofibrosis-osteomyelosclerosis (agnogenic myeloid metaplasia). II. The myeloid stroma (hematopoietic microenvironment).

An ultrastructural study was performed on bone marrow tissue in 8 patients revealing early and late stages of so-called primary (idiopathic) myelofibrosis - osteomyelosclerosis (agnogenic myeloid metaplasia) to evaluate the constituents of the hematopoietic microenvironment (myeloid stroma). A survey of the stroma cells disclosed an overall increase, particularly in so-called undifferentiated (primitive - pluripotent), but also in transitional (fibroblastic) reticular cells and myofibroblasts. The most primitive reticular cells were characterized by their stellate aspect with elongated slender cytoplasmic processes traversing the interstitial space, and by the scarcity of organelles. The transition into a fibroblast was preceded by the appearance of branching cisternal structures of the rough endoplasmic reticulum, extensively developed Golgi fields and an abundance in mitochondria. Frequently, so-called myofibroblasts were encountered displaying bundles of filaments along the subplasmalemmal region. Extracellularly fibrillar material with an irregular cross-banding as well as microfibrils could be observed. The many vascular structures (sinusoids and capillaries) exhibited a multilayered basement membrane-like material including many fibrils and adventitial cells (pericytes, smooth muscle and transitional reticular cells) with numerous cytoplasmic processes. Undifferentiated and transitional reticular cells as well as myofibroblasts seem to form an integral part of the hematopoietic microenvironment in OMF and are assumed to play an important role for the evolution of the disease-specific myelofibrosis in this disorder.

Bone Marrow↗
PubMed1991

Ultrastructure of bone marrow tissue in so-called primary (idiopathic) myelofibrosis-osteomyelosclerosis (agnogenic myeloid metaplasia). I. Abnormalities of megakaryopoiesis and thrombocytes.

An electron microscopic study was conducted with the aim to analyze abnormalities of the megakaryopoiesis in bone marrow tissue of patients suffering from so-called primary (idiopathic) myelofibrosis-osteomyelosclerosis. In comparison with control specimens and in confirmation of light microscopical findings, a pronounced pleomorphism of the megakaryocytic cell line could be observed consisting of giant forms, micromegakaryocytes and naked (pyknotic) nuclei. Further atypias were expressed by a dissociation of nuclear-cytoplasmic maturation. These included particularly the amount of dense granules, and the development of the demarcation membrane system as well as the occurrence of emperipolesis (i.e. internalization of hematopoietic cells) already in immature or megakaryoblastic elements. In these specimens there was a striking variety in the appearance of dense granules of the alpha or bull's eye type revealing frequent elongated roll- and dumbbell-like shapes and a doubling of the nucleoids. Thrombocytes showed giant forms with either hypertrophy of the open canalicular system or abundance of dense granules and beta-glycogen accumulation. Remarkable was a focal sponge-like proliferation of the open canalicular system in many of the large platelets and giant and fused granules of the alpha and osmiophilic type. The abnormalities disclosed in megakaryo- and thrombocytes may have certain functional implications, i.e. to hemorrhage and thrombosis which are often encountered out of proportion to the platelet counts in this disorder. Moreover, those anomalies indicate a disorganization of megakaryopoiesis which may contribute to the abnormal release of factors (platelet-derived growth factor and factor 4) predominantly involved in the process of myelofibrosis.

Blood Platelets↗
PubMed1990

Proton nuclear magnetic resonance assignments and secondary structure determination of the ColE1 rop (rom) protein.

The complete resonance assignment of the ColE1 rop (rom) protein at pH 2.3 was obtained by two-dimensional (2D) proton nuclear magnetic resonance spectroscopy (1H NMR) at 500 and 600 MHz using through-bond and through-space connectivities. Sequential assignments and elements of regular secondary structure were deduced by analysis of nuclear Overhauser enhancement spectroscopy (NOESY) experiments and 3JHN alpha coupling constants. One 7.2-kDa monomer of the homodimer consists of two antiparallel helices connected by a hairpin loop at residue 31. The C-terminal peptide consisting of amino acids 59-63 shows no stable conformation. The dimer forms a four-helix bundle with opposite polarization of neighboring elements in agreement with the X-ray structure.

Amino Acid Sequence↗
PubMed1990

Immunohistochemical localization of rhodanese.

The role of rhodanese in the detoxication of acute cyanide exposure is controversial. The debate involves questions of the availability of rhodanese to cyanide in the peripheral circulation. Blood-borne cyanide will distribute to the brain and may induce lesions or even death. The present study addresses the dispute by determining the distribution of rhodanese in tissues considered to have the highest rhodanese activity and thought to serve as major detoxication sites. The results indicate that rhodanese levels are highest in (1) hepatocytes that are in close proximity to the blood supply of the liver (2) epithelial cells surrounding the bronchioles (a major entry route for gaseous cyanide) and (3) proximal tubule cells of the kidney (serving to facilitate cyanide detoxication and elimination as thiocyanate). Rhodanese activity in the brain is low compared with liver and kidney (Mimori et al., 1984; Drawbaugh & Marrs, 1987); the brain is not considered to be a major site of cyanide detoxication. The brain, however, is the target for cyanide toxicity. In this study our goal was also to differentiate the distribution of rhodanese in an area of the brain. We found that the enzyme level is highest in fibrous astrocytes of the white matter. Cyanide-induced brain lesions may thus occur in areas of the brain lacking sufficient sites for detoxication.

Animals↗
PubMed1990

Excluded volume approximation to protein-solvent interaction. The solvent contact model.

Important properties of globular proteins, such as the stability of its folded state, depend sensitively on interactions with solvent molecules. Existing methods for estimating these interactions, such as the geometrical surface model, are either physically misleading or too time consuming to be applied routinely in energy calculations. As an alternative, we derive here a simple model for the interactions between protein atoms and solvent atoms in the first hydration layer, the solvent contact model, based on the conservation of the total number of atomic contacts, a consequence of the excluded-volume effect. The model has the conceptual advantage that protein-protein contacts and protein-solvent contacts are treated in the same language and the technical advantage that the solvent term becomes a particularly simple function of interatomic distances. The model allows rapid calculation of any physical property that depends only on the number and type of protein-solvent nearest-neighbor contacts. We propose use of the method in the calculation of protein solvation energies, conformational energy calculations, and molecular dynamics simulations.

Amino Acids↗
PubMed1990

Molecular cloning of YPT1/SEC4-related cDNAs from an epithelial cell line.

Molecular analysis of Saccharomyces cerevisiae secretion mutants has led to the identification of two Ras-like GTP-binding proteins, Ypt1p and Sec4p, which are essential for transport along the exocytic route. To study the regulation of membrane traffic in epithelial cells, a set of 11 clones encoding proteins similar to the YPT1/SEC4 products were isolated from an MDCK (Madin-Darby canine kidney) cell cDNA library. Four of these proteins, Rab8, -9, -10, and -11, are novel members of this subfamily of Ras-like proteins, and two of them are closely related to Ypt1p and Sec4p. The ratio of the number of clones isolated over the total number screened reveals a high level of complexity for this subfamily of GTP-binding proteins. This diversity supports their proposed function in controlling different steps in membrane traffic.

Amino Acid Sequence↗
PubMed1990

[Fine structure of megakaryocyte precursor cells (promegakaryoblasts) derived from smears and sections of bone marrow tissue in patients with chronic myeloid leukemia and so-called primary osteomyelofibrosis with accompanying thrombocythemia].

An immunomorphometric study (antiglycoprotein III a - Y2/51) was performed on routinely processed trephine biopsies in 24 patients with chronic myeloid leukemia (CML) as well as so-called primary osteomyelofibrosis (OMF) to determine the frequency and fine structure of promegakaryoblasts (PMB). With respect to controls, there was a significant increase in megakaryocytes in both entities with an orderly expansion of the precursor subpopulation in CML, but a relative decrease in OMF. In comparison with smears of aspirates, sizes of PMB were reduced by about 25% (factor 1.4) in the corresponding bone marrow sections.

Bone Marrow↗
PubMed1990

[Advantages of biplane transesophageal echocardiography].

Biplane transesophageal echocardiography (BTEE) was intraoperatively performed on 27 patients; ten patients with coronary artery bypass graft surgery, ten with aortic valve replacement, five with mitral valve replacement, one with reconstruction of complete AV-canal, and one with surgical repair of dissecting aortic aneurysm. Compared with the transverse views of the monoplane TEE, BTEE permits the following additional images of the heart: 1) Longitudinal "two-chamber-view" for assessment of left ventricular (LV) anterior, apical, and posterior wall motion, and for assessment of mitral valve anatomy and function (e.g., grading of color flow regurgitation). 2) Imaging of the right-ventricular outflow tract (RVOT) for evaluation of RVOT obstruction, including a crosswise imaging of aortic valve. 3) Proximal two-thirds of the aorta ascendens for the diagnosis of dissecting aortic aneurysm (de Bakey Types I and II). 4) Imaging of the superior vena cava, helpful for detecting transposition of pulmonary veins. 5) Apex of left ventricle, advantageous for detecting thrombus. 6) Longitudinal view of the descending aorta: from the origin of the left subclavian artery down to the origin of the coeliac artery (origins of both vessels, inclusively). We prepared post mortem sections of the heart corresponding to the longitudinal echocardiographic views and documented them by photography. In conclusion, the second plane provides an important improvement in semi-invasive imaging of the heart.

Adult↗