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C Levinthal

Publications and source records attributed to C Levinthal.

At least 19 recordsLinked to original sources
PubMed1991

FASTRUN: a special purpose, hardwired computer for molecular simulation.

We describe the design, construction, and performance of a special purpose, hardwired accelerator for molecular mechanical calculations called FASTRUN. The processor was designed at Columbia University in 1984, constructed in the Instrumentation Division of Brookhaven National Laboratory, and delivered to Columbia in final form in 1989. It was rendered functional for molecular mechanics in early 1990. Together with its host Star array processor, FASTRUN has a measured performance for molecular dynamics simulations which compares favorably with present day supercomputers. The hardware replication cost of FASTRUN is on the order of $100,000.00.

Computer Simulation↗
PubMed1991

A single tryptic fragment of colicin E1 can form an ion channel: stoichiometry confirms kinetics.

The molecularity of the ion channel formed by peptide fragments of colicin has taken on particular significance since the length of the active peptide has been shown to be less than 90 amino acids and the lumen size at least 8 A. Cell survival experiments show that killing by colicin obeys single-hit statistics, and ion leakage rates from phospholipid vesicles are first order in colicin concentration. However, interpretation in molecular terms is generally complicated by the requirement of large numbers of colicin molecules per cell or vesicle. We have measured the discharge of potential across membranes of small phospholipid vesicles by following the changes in binding of potential sensitive spin labeled phosphonium ions as a function of the number of colicin fragments added. Because of the sensitivity of the method, it was possible to reliably investigate the effect of colicin in a range where there was no more than 0.2 colicins per vesicle. The quantitative results of these experiments yield a direct molecular stoichiometry and demonstrate that one C-terminal fragment of the colicin molecule per one vesicle is sufficient to induce a rapid ion flux in these vesicles. In addition, the experiments confirm earlier findings that the colicin fragments do not migrate from one vesicle to another at pH 4.5. Similar results are obtained with large unilamellar vesicles.

Colicins↗
PubMed1989

Site-directed mutagenesis of colicin E1 provides specific attachment sites for spin labels whose spectra are sensitive to local conformation.

Colicin E1 is an E. coli plasmid-encoded water-soluble protein that spontaneously inserts into lipid membranes to form a voltage-gated ion channel. We have employed a novel approach in which site-directed mutagenesis is used to provide highly specific attachment points for nitroxide spin labels. A series of colicin mutants, differing only by the position of a single cysteine residue, were prepared and selectively labeled at that cysteine. A hydrophilic sequence (398-406) within the C-terminal domain of the water-soluble form of the protein was investigated and exhibited an electron paramagnetic resonance (EPR) spectral periodicity strongly suggesting an amphiphilic alpha-helix. After removal of the N-terminus of the protein with trypsin, the spectra for this sequence indicate increased label mobility and a more flexible structure.

Amino Acid Sequence↗
PubMed1988

A Purkinje cell differentiation marker shows a partial DNA sequence homology to the cellular sis/PDGF2 gene.

To search for genes involved in determining the morphology of individual neuronal types, a cDNA library was constructed from postnatal day 13 mouse cerebellum. From this library, 2 clones, L7 and L19, were isolated by a differential hybridization procedure and shown by in situ hybridization to be Purkinje cell-specific within the cerebellum. Both RNAs appear between postnatal days 4 and 8 and continue into adulthood, coinciding with terminal differentiation of the Purkinje cells. L7 seems to be expressed exclusively in the cerebellum, whereas L19 is expressed throughout the brain. Consistent with the RNA localization, L7 protein is found only in the cerebellum and is confined to the Purkinje cells. The L7 amino acid sequence has been deduced from the cDNA sequence, and a pseudo-repeat within the L7 protein sequence is homologous to the amino acids sequence in the primary translation product of the gene for human sis/PDGF.

Amino Acid Sequence↗
PubMed1988

Infancy and early childhood follow-up of neonates with periventricular or intraventricular hemorrhage or isolated ventricular dilation: a case controlled study.

Survivors of periventricular or intraventricular hemorrhage and isolated ventricular dilation showed a higher incidence of major developmental problems in the motor areas than matched control subjects in infancy. This effect is still seen, but less evident in early childhood. Problems were mainly related to grades III and IV periventricular or intraventricular hemorrhage and isolated ventricular dilation. The outcome of newborns with grades I and II hemorrhage was benign.

Cerebral Hemorrhage↗
PubMed1986

"Dry" enzymes.

Explore the source record for details and available documents.

Enzymes↗
PubMed1986

A very short peptide makes a voltage-dependent ion channel: the critical length of the channel domain of colicin E1.

Cleavage of colicin E1 molecules with a variety of proteases or with cyanogen bromide (CNBr) generates COOH-terminal fragments which have channel-forming activity similar to that of intact colicin in planar lipid bilayer membranes. The smallest channel-forming fragment obtained by CNBr cleavage of the wild-type molecule consists of the C-terminal 152 amino acids. By the use of oligonucleotide-directed mutagenesis, we have made nine mutants along this 152 amino acid peptide, in which an amino acid was replaced by methionine in order to create a new CNBr cleavage site. The smallest of the CNBr-cleaved C-terminal fragments with channel-forming activity, in planar bilayer membranes, was generated by cleavage at new Met position 428 and has 94 amino acids, whereas a 75 amino acid peptide produced by cleavage of a new Met at position 447 did not have channel activity. The NH2-terminus of the channel-forming domain of colicin E1 appears therefore to lie between residues 428 and 447. Since, however, the last six C-terminal residues of the colicin can be removed without changing activity, the number of amino acids necessary to form the channel is 88 or less. In addition, the unique Cys residue in colicin E1 was replaced by Gly, and nine mutants were then made with Cys placed at sequential locations along the peptide for eventual use as sulfhydryl attachment sites to determine the local environment of the replaced amino acid. In the course of making 21 mutants, eight charged residues have been replaced by uncharged Met or Cys without changing the biological activity of the intact molecule. It has been proposed previously that the conformation of the colicin E1 channel is a barrel formed from five or six alpha-helices, each having 20 amino acids spanning the membrane and two to four residues making the turn at the boundary of the membrane. Our finding that 88 amino acids can make an active channel, combined with recently reported stoichiometric evidence that the channel is a monomer excludes this model and adds significant constraints which can be used in building a molecular model of the channel.

Amino Acid Sequence↗
PubMed1986

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations.

We describe a method for predicting the conformations of loops in proteins and its application to four of the complementarity determining regions [CDRs] in the crystallographically determined structure of MCPC603. The method is based on the generation of a large number of randomly generated conformations for the backbone of the loop being studied, followed by either minimization or molecular dynamics followed by minimization starting from these random structures. The details of the algorithm for the generation of the loops are presented in the first paper in this series (Shenkin et al. [submitted]). The results of minimization and molecular dynamics applied to these loops is presented here. For the two shortest CDRs studied (H1 and L2, which are five and seven amino acids long), minimizations and dynamics simulations which ignore interactions of the loop amino acids beyond the carbon beta replicate the conformation of the crystal structure closely. This suggests that these loops fold independently of sequence variation. For the third CDR (L3, which is nine amino acids), those portions of the CDR near its base which are hydrogen bonded to framework are well replicated by our procedures, but the top of the loop shows significant conformational variability. This variability persists when side chain interactions for the MCPC603 sequence are included. For a fourth CDR (H3, which is 11 amino acids long), new low-energy backbone conformations are found; however, only those which are close to the crystal are compatible with the sequence when side chain interactions are taken into account. Results from minimization and dynamics on single CDRs with all other CDRs removed are presented. These allow us to explore the extent to which individual CDR conformations are determined by interactions with framework only.

Binding Sites, Antibody↗
PubMed1986

Gating of a voltage-dependent channel (colicin E1) in planar lipid bilayers: translocation of regions outside the channel-forming domain.

C-terminal fragments of colicin E1, ranging in mol wt from 14.5 to 20 kD, form channels with voltage dependence and ion selectivity qualitatively similar to those of whole E1, placing an upper limit on the channel-forming domain. Under certain conditions, however, the gating kinetics and ion selectivity of channels formed by these different E1 peptides can be distinguished. The differences in channel behavior appear to be correlated with peptide length. Enzymatic digestion with trypsin of membrane-bound E1 peptides converts channel behavior of longer peptides to that characteristic of channels formed by shorter fragments. Apparently trypsin removes segments of protein N-terminal to the channel-forming region, since gating behavior of the shortest fragment is little affected by the enzyme. The success of this conversion depends on the side of the membrane to which trypsin is added and on the state, open or closed, of the channel. Trypsin modifies only closed channels from the cis side (the side to which protein has been added) and only open channels from the trans side. These results suggest that regions outside the channel-forming domain affect ion selectivity and gating, and they also provide evidence that large protein segments outside the channel-forming domain are translocated across the membrane with channel gating.

Colicins↗
PubMed1976

Conformational flexibility and protein folding: rigid structural fragments connected by flexible joints in subtilisin BPN.

Conformational energy calculations are used to analyze the interactions of structural substructures in subtilisin BPN. These substructures are kept fixed or "rigid" so that the only variables in the calculations are the backbone segments that separate them. The flexible segments are assumed to be free turns. Using this representation of the protein it is possible to predict both a likely order of events along a folding pathway and preferred modes of conformational changes of the native protein. Moreover, when the native structure has been perturbed by moving the substructures apart, it is possible to assess the range of interactions that return the protein, upon energy minimization, to its original conformation. These results suggest an approach to the folding problem based on the piecemeal formation of tertiary structure from smaller prefolded fragments.

Computers↗
PubMed1975

Hemoglobin interaction in sickle cell fibers. I: Theoretical approaches to the molecular contacts.

Computerized molecular model building has been used to deduce the arrangement of sickle cell hemoglobin molecules (Hb-S) in the tubular fibers which form within sickling cells and in concentrated cell-free solutions of deoxygenated Hb-S. A "best" solution has been found which satisfies all of the reported properties of these fibers. In the proposed arrangement the contact between adjacent Hb-S molecules in the direction parallel to the fiber axis is primarily hydrophobic and in addition contains two salt bridges between the molecules. This contact would be disrupted with the Glu of Hb-A at the beta6 position instead of the Val of Hb-S, and it would not make a long fiber with oxygenated Hb-S. Residues in the A helix and the GH corner of the beta2 chain of one molecule are in contact with residues of the A, B, and E helices and the GH corner of the alpha1 chain of its neighbor. The intermolecular contact in the direction perpendicular to the fiber axis is mainly between the end of the E helix and the EF corner of the beta1 chain on the first molecule and the F helix and FG corner of the alpha2 chain of its neighbor. Some of the implications of these contacts are reported here, and others will be presented in subsequent papers.

Binding Sites↗
PubMed1974

Structure and development of neuronal connections in isogenic organisms: transient gap junctions between growing optic axons and lamina neuroblasts.

We previously showed that the growth of each bundle of eight optic fibers from one ommatidium into the optic lamina of Daphnia occurs in such a way that one of the eight fibers precedes the others into the lamina. The growth cone of this lead fiber makes surface contact with undifferentiated neuroblasts near the midplane. This is followed by a glial-like wrapping of each neuroblast around the fiber. In this report, gap junctions are shown to form for a short period of time between the growing lead fiber and the neuroblast that is wrapping around it. It is proposed that these junctions may represent a morphological correlate of informational exchange between axon and neuroblast. This signaling would then reflect the fact that the sequence of axon proliferation by the lamina neuroblasts within an optic cartrdige, ultimately composed of five lamina neurons and eight optic fibers, parallels the order in which the neuroblasts undergo the wrapping reaction with the lead fiber.

Animals↗