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A Bax

Publications and source records attributed to A Bax.

At least 73 records · Page 4Linked to original sources
PubMed1995

Sequential backbone assignment of isotopically enriched proteins in D2O by deuterium-decoupled HA(CA)N and HA(CACO)N.

It is demonstrated that sequential resonance assignment of the backbone 1H alpha and 15N resonances of proteins can be obtained without recourse to the backbone amide protons, an approach which should be useful for assignment of regions with rapidly exchanging backbone amide protons and for proteins rich in proline residues. The method relies on the combined use of two 2D experiments, HA(CA)N and HA(CACO)N or their 3D analogs, which correlate 1H alpha with the intraresidue 15N and with the 15N resonance of the next residue. The experiments are preferably conducted in D2O, where very high resolution in the 15N dimension can be achieved by using 2H decoupling. The approach is demonstrated for a sample of human ubiquitin, uniformly enriched in 13C and 15N. Complete backbone and 13C beta/1H beta resonance assignments are presented.

Amino Acid Sequence↗
PubMed1995

NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.

Magnetic Resonance Spectroscopy↗
PubMed1995

Spin-locked multiple quantum coherence for signal enhancement in heteronuclear multidimensional NMR experiments.

For methine sites the relaxation rate of 13C-1H two-spin coherence is generally slower than the relaxation rate of the individual 13C and 1H single spin coherences. The slower decay of two-spin coherence can be used to increase the sensitivity and resolution in heteronuclear experiments, particularly those that require correlation of H alpha and C alpha chemical shifts. To avoid dephasing of the two-spin coherence caused by 1H-1H J-couplings, the 1H spin is locked by the application of a weak rf field, resulting in a spin-locked multiple quantum coherence. For a sample of calcium-free calmodulin, use of the multiple quantum approach yields significant signal enhancement over the conventional constant-time 2D HSQC experiment. The approach is applicable to many multidimensional NMR experiments, as demonstrated for a 3D 13C-separated ROESY CT-HMQC spectrum.

Animals↗
PubMed1995

Flexibility and function in HIV-1 protease.

HIV protease is a homodimeric protein whose activity is essential to viral function. We have investigated the molecular dynamics of the HIV protease, thought to be important for proteinase function, bound to high affinity inhibitors using NMR techniques. Analysis of 15N spin relaxation parameters, of all but 13 backbone amide sites, reveals the presence of significant internal motions of the protein backbone. In particular, the flaps that cover the proteins active site of the protein have terminal loops that undergo large amplitude motions on the ps to ns time scale, while the tips of the flaps undergo a conformational exchange on the microsecond time scale. This enforces the idea that the flaps of the proteinase are flexible structures that facilitate function by permitting substrate access to and product release from the active site of the enzyme.

Amino Acid Sequence↗
PubMed1995

Solution structure of calcium-free calmodulin.

The three-dimensional structure of calmodulin in the absence of Ca2+ has been determined by three- and four-dimensional heteronuclear NMR experiments, including ROE, isotope-filtering combined with reverse labelling, and measurement of more than 700 three-bond J-couplings. In analogy with the Ca(2+)-ligated state of this protein, it consists of two small globular domains separated by a flexible linker, with no stable, direct contacts between the two domains. In the absence of Ca2+, the four helices in each of the two globular domains form a highly twisted bundle, capped by a short anti-parallel beta-sheet. This arrangement is qualitatively similar to that observed in the crystal structure of the Ca(2+)-free N-terminal domain of troponin C.

Animals↗
PubMed1994

1H, 13C, 15N nuclear magnetic resonance backbone assignments and secondary structure of human calcineurin B.

The calmodulin- and calcium-stimulated protein phosphatase calcineurin, PP2B, consists of two subunits: calcineurin B, which binds Ca2+, and calcineurin A, which contains the catalytic site and a calmodulin binding site. Heteronuclear 3D and 4D NMR experiments were carried out on a recombinant human calcineurin B which is a 170-residue protein of molecular mass 19.3 kDa, uniformly labeled with 15N and 13C. The nondenaturing detergent CHAPS was used to obtain a monomeric form of calcineurin B. Three-dimensional triple resonance experiments yielded complete sequential assignment of the backbone nuclei (1H, 13C, and 15N). This assignment was verified by a 4D HN(COCA)NH experiment carried out with 50% randomly deuteriated and uniformly 15N- and 13C-enriched calcineurin B. The secondary structure of calcineurin B has been determined on the basis of the 13C alpha and 13C beta secondary chemical shifts, J(HNH alpha) couplings, and NOE connectivities obtained from 3D 15N-separated and 4D 13C/15N-separated NOESY spectra. Calcineurin B has eight helices distributed in four EF-hand, helix-loop-helix [Kretsinger, R. H. (1980) CRC Crit. Rev. Biochem. 8, 119-174] calcium binding domains. The secondary structure of calcineurin B is highly homologous to that of calmodulin. In comparison to calmodulin, helices B and C are shorter while helix G is considerably longer. As was observed for calmodulin in solution, calcineurin B does not have a single long central helix; rather, helices D and E are separated by a six-residue sequence in a flexible nonhelical conformation.

Amino Acid Sequence↗
PubMed1994

Localization of bound water in the solution structure of a complex of the erythroid transcription factor GATA-1 with DNA.

BACKGROUND: The erythroid specific transcription factor GATA-1 is responsible for the regulation of transcription of erythroid-expressed genes and is an essential component required for the generation of the erythroid lineage. GATA-1 binds specifically as a monomer to the asymmetric consensus target sequence (T/A)GATA-(A/G) found in the cis-regulatory elements of all globin genes and most other erythroid specific genes that have been examined. We have previously determined the solution structure of the complex of the zinc-containing DNA-binding domain of chicken GATA-1 with its cognate DNA target site by multidimensional heteronuclear NMR. From previous studies of complexes between proteins and DNA, water appears to play an important role in DNA-protein recognition by mediating bridging hydrogen bonds between functional groups on the protein and DNA bases. Solvation free energy calculations, however, suggest that hydrophobic interactions should exclude water from parts of the GATA-1:DNA interface. RESULTS: Using water-selective two-dimensional heteronuclear magnetic resonance spectroscopy, we have identified the location of bound water molecules in the specific complex of chicken GATA-1 with DNA. A number of water molecules could be detected between the protein and the phosphate backbone, as well as at the solvent exposed surface of the protein. However, no water molecules could be observed at the interface of the protein with the bases of the DNA. With only one exception, the bound water molecules have a residency time > 200-300 ps. CONCLUSIONS: Unlike other protein-DNA complexes, the majority of specific interactions between GATA-1 and the DNA bases in the major groove are hydrophobic in nature. The exclusion of water from the protein-DNA base interface in the major groove supports the view that the specific binding energy is indeed dominated by hydrophobic effects.

Animals↗
PubMed1994

NMR evidence for similarities between the DNA-binding regions of Drosophila melanogaster heat shock factor and the helix-turn-helix and HNF-3/forkhead families of transcription factors.

Heteronuclear multidimensional NMR experiments of residues 33-163 of the DNA-binding domain of Drosophila heat shock factor, dHSF(33-163), were recorded, using only 3 mg of uniformly 15N-labeled or 2 mg of uniformly 15N/13C-labeled protein. The polypeptide consists of a structured part comprising three helices, a three-stranded antiparallel beta-sheet, with the first two strands connected by a four-residue type I tight turn. The second helix is disrupted at its C-terminal end by a proline residue and is followed by an extended turn, leading to the third helix. The dHSF(33-163) protein is unstructured at its N- and C-termini, and a third unstructured region is found from Thr113 to Arg124. Exchange broadening of the 15N-1H correlations upon titration of 15N labeled HSF with a 13-base-pair DNA duplex suggests a DNA-binding motif in which the third helix acts as the recognition helix. Both the secondary structure and DNA-binding pattern of dHSF(33-163) suggest that the overall topology resembles that the helix-turn-helix bacterial activator CAP [Weber, I. T., & Steitz, T. A. (1987) J. Mol. Biol. 198, 311-326] and the liver-specific transcription factor HNF-3 gamma, the prototype of the HNF-3/forkhead protein family [Clark, K. L., Halay, E. D., Lai, E., & Burley, S. K. (1993) Nature 364, 412-420].

Amino Acid Sequence↗
PubMed1994

Measurement of four-bond HN-H alpha J-couplings in staphylococcal nuclease.

Quantitative J-correlation and triple-resonance ECOSY-type experiments are used to unambiguously establish the presence of four-bond sequential HN-H alpha J-couplings in the protein staphylococcal nuclease. Substantially negative 4JH alpha HN values, ranging from -0.8 to -2.3 Hz, are observed when the psi angle is near +120 degrees, and the following phi angle near +60 degrees. For other conformations, the four-bond HN-H alpha J-couplings fall between -0.5 and +0.5 Hz.

Amino Acid Sequence↗
PubMed1994

Resonance assignment of methionine methyl groups and chi 3 angular information from long-range proton-carbon and carbon-carbon J correlation in a calmodulin-peptide complex.

Several simple 3D experiments are used to provide J correlations between methionine C epsilon methyl carbons and either the C gamma H2 protons or C beta and C gamma. The intensity of the J correlations provides information on the size of the three-bond J couplings and thereby on the chi 3 torsion angle. In addition, a simple 3D version of the HMBC experiment provides a sensitive link between the C epsilon H3 methyl protons and C gamma. The methods are demonstrated for a 20 kDa complex between calmodulin and a 26-residue peptide fragment of skeletal muscle myosin light chain kinase.

Amino Acid Sequence↗
PubMed1994

Measurement of HN-H alpha J couplings in calcium-free calmodulin using new 2D and 3D water-flip-back methods.

Two new methods are described for the measurement of three-bond JHNH alpha couplings in proteins isotopically enriched with 15N. Both methods leave the water magnetization in an unsaturated state, parallel to the z-axis, and therefore offer significant enhancements in sensitivity for rapidly exchanging backbone amide protons. The J couplings can be measured either from a set of constant-time 2D 1H-15N HMQC spectra, which are modulated in intensity by JHNH alpha, or from a water-flip-back version of the 3D HNHA experiment. The method is demonstrated for a sample of calcium-free calmodulin. Residues Lys75-Asp80 have JHNH alpha values in the 6-7 Hz range, suggesting that a break in the 'central helix' occurs at the same position as previously observed in solution NMR studies of Ca(2+)-ligated calmodulin.

Calmodulin↗
PubMed1994

Solution structure of the DNA-binding domain of Drosophila heat shock transcription factor.

The solution structure of the DNA-binding domain of the Drosophila heat shock transcription factor, as determined by multidimensional multinuclear NMR, resembles that of the helix-turn-helix class of DNA-binding proteins. The domain comprises a four-stranded antiparallel beta-sheet, packed against a three-helix bundle. The second helix is significantly distorted and is separated from the third helix by an extended turn which is subject to conformational averaging on an intermediate time scale. Helix 3 forms a classical amphipathic helix with polar and charged residues exposed to the solvent. Upon titration with DNA, resonance shifts in the backbone and Asn and Gln side-chain amides indicate that helix 3 acts as the recognition helix of the heat shock transcription factor.

Amino Acid Sequence↗
PubMed1993

Transforming growth factor beta 1: NMR signal assignments of the recombinant protein expressed and isotopically enriched using Chinese hamster ovary cells.

The transforming growth factor beta s are a homologous family of multifunctional cytokines that regulate cell growth and differentiation. As a prelude to studies of the solution structure and dynamics of TGF-beta 1, we report virtually complete assignment of 1H and 15N resonances for this 25-kDa homodimeric protein. Recombinant TGF-beta 1 was expressed in Chinese hamster ovary cells. The cells were grown either in a completely 15N-enriched medium or in a medium containing selectively 13C, 15N-labeled amino acids to obtain either uniformly or specifically labeled protein, respectively. Two- and three-dimensional heteronuclear edited magnetic resonance spectra of the uniformly 15N-labeled protein and three samples selectively labeled with 13C and 15N yielded assignments for 96% of the backbone amide and C alpha protons and 87% of the side chain protons. To our knowledge, this is the first report of the use of an animal cell expression system to obtain extensive isotopic enrichment in order to sequentially assign a protein. The methodology described herein for the isotopic enrichment and resonance assignments of TGF-beta 1 should be generally applicable to other eukaryotic proteins expressed by animal cells.

Amino Acid Sequence↗
PubMed1993

Transforming growth factor beta 1: secondary structure as determined by heteronuclear magnetic resonance spectroscopy.

Virtually complete backbone NMR signal assignments have been reported for transforming growth factor beta 1 (TGF-beta 1) [Archer et al. (1993) Biochemistry (preceding paper in this issue)]. Herein we report the secondary structure of the protein in solution on the basis of these assignments and proton NOE's observed in a variety of 2D and 3D heteronuclear NMR spectra. Regular elements of secondary structure derived from the NOE data consist of (a) three helices spanning residues Y58-H68, F24-G29, and N5-F8 and (b) several pairs of two-stranded antiparallel beta-sheets. The longest two-stranded sheet runs from residue L83 to V106 with a type II reverse turn at G93-R94 and a chain twist at residue N103-M104. These elements of regular structure were confirmed by hydrogen exchange, chemical shift, and coupling constant data. With the exception of residues G46-S53, which exhibit relatively few and weak intraresidue NOE's, residues in the rest of the protein adopt an irregular but well-defined structure. All peptide bonds are trans except for a cis peptide bond between Glu35 and Pro36. The structural characteristics observed for TGF-beta 1 in solution generally agree closely with the recently derived crystal structures of TGF-beta 2 [Daopin et al. (1992) Science 257, 369-374; Schlunegger & Grütter (1992) Nature 358, 430-434]. Several noteworthy differences were observed that may be related to function.

Amino Acid Sequence↗
PubMed1993

A simple and sensitive experiment for measurement of JCC couplings between backbone carbonyl and methyl carbons in isotopically enriched proteins.

A simple 2D difference experiment is described that allows quantitative measurement of 13C-13C J couplings between backbone carbonyl and side-chain carbons. Precise 3JCC values were measured from data recorded in just 2 h for a 1-mM solution of the 20-kD complex between the protein calmodulin and a 26-residue synthetic peptide. The J couplings aid in determining the chi 1 angles of valine, isoleucine and threonine residues, and in making stereospecific assignments of the Val C gamma methyl groups. Error analysis indicates that the uncertainty in the derived J couplings is generally less than ca. 0.3 Hz.

Amino Acids↗
PubMed1993

Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins.

Experiments and procedures are described that greatly alleviate the sequential assignment process of uniformly 13C/15N-enriched proteins by determining the type of amino acid from experiments that correlate side chain with backbone amide resonances. A recently proposed 3D NMR experiment, CBCA(CO)NH, correlates C alpha and C beta resonances to the backbone amide 1H and 15N resonances of the next residue (Grzesiek, S. and Bax, A. (1992) J. Am. Chem. Soc., 114, 6291-6293). An extension of this experiment is described which correlates the proton H beta and H alpha resonances to the amide 1H and 15N resonances of the next amino acid, and a detailed product operator description is given. A simple 2D-edited constant-time HSQC experiment is described which rapidly identifies H beta and C beta resonances of aromatic or Asn/Asp residues. The extent to which combined knowledge of the C alpha and C beta chemical shift values determines the amino acid type is investigated, and it is demonstrated that the combined C alpha and C beta chemical shifts of three or four adjacent residues usually are sufficient for defining a unique position in the protein sequence.

Algorithms↗
PubMed1993

Measurement of amide proton exchange rates and NOEs with water in 13C/15N-enriched calcineurin B.

A rapid and sensitive 2D approach is presented for measuring amide proton exchange rates and the NOE interaction between amide protons and water. The approach is applicable to uniformly 13C/15N-enriched proteins and can measure magnetization exchange rates in the 0.02 to > 20 s-1 range. The experiments rely on selective excitation of the water resonance, coupled with purging of underlying H alpha resonances, followed by NOESY- or ROESY-type transfer to amide protons, which are dispersed by the amide 15N frequencies in an HSQC-type experiment. Two separate but interleaved experiments, with and without selective inversion of the H2O resonance, yield quantitative results. The method is demonstrated for a sample of the calcium-binding protein calcineurin B. Results indicate rapid amide exchange for the five calcineurin B residues that are analogous to the five rapidly exchanging residues in the 'central helix' of the homologous protein calmodulin.

Amides↗