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Query: UMLS:C0344329 (collapse)
 28,634 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We have shown previously that mutations in nuclear genes, termed MGI, for mitochondrial genome integrity, can convert the petite-negative yeast Kluyveromyces lactis into a petite-positive form with the ability to produce mitochondrial genome deletion mutants (Chen and Clark-Walker, Genetics, 133, 517-525, 1993). Here we describe that two genes, MGI2 and MGI5, encode the alpha- and gamma-subunits of mitochondrial F1-ATPase. Specific mutations, Phe443-->Ser and Ala333-->Val in MGI2, and Thr275-->Ala in MGI5, confer on cells the ability to produce petite mutants spontaneously with deletions in mitochondrial (mt) DNA and the capacity to lose their mitochondrial genomes upon treatment with ethidium bromide. Structural integrity of the F1 complex seems to be needed for expression of the Mgi- phenotype as null mutations in MGI2 and MGI5 remove the ability to form mtDNA deletions. It is suggested that mgi mutations allow petites to survive because an aberrant F1 complex prevents collapse of the mitochondrial inner membrane potential that normally occurs on loss of mtDNA-encoded F0 subunits.
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PMID:Specific mutations in alpha- and gamma-subunits of F1-ATPase affect mitochondrial genome integrity in the petite-negative yeast Kluyveromyces lactis. 762 39

Computer analysis of the crystallographic structure of the A subunit of Escherichia coli heat-labile toxin (LT) was used to predict residues involved in NAD binding, catalysis and toxicity. Following site-directed mutagenesis, the mutants obtained could be divided into three groups. The first group contained fully assembled, non-toxic new molecules containing mutations of single amino acids such as Val-53-->Glu or Asp, Ser-63-->Lys, Val-97-->Lys, Tyr-104-->Lys or Asp, and Ser-114-->Lys or Glu. This group also included mutations in amino acids such as Arg-7, Glu-110 and Glu-112 that were already known to be important for enzymatic activity. The second group was formed by mutations that caused the collapse or prevented the assembly of the A subunit: Leu-41-->Phe, Ala-45-->Tyr or Glu, Val-53-->Tyr, Val-60-->Gly, Ser-68-->Pro, His-70-->Pro, Val-97-->Tyr and Ser-114-->Tyr. The third group contained those molecules that maintained a wild-type level of toxicity in spite of the mutations introduced: Arg-54-->Lys or Ala, Tyr-59-->Met, Ser-68-->Lys, Ala-72-->Arg, His or Asp and Arg-192-->Asn. The results provide a further understanding of the structure-function of the active site and new, non-toxic mutants that may be useful for the development of vaccines against diarrhoeal diseases.
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PMID:Probing the structure-activity relationship of Escherichia coli LT-A by site-directed mutagenesis. 783 May 60

Hypomagnesaemia with magnesuria are common findings in cyclosporin-(CsA)-treated patients and have been proposed as both a cause and a consequence of nephrotoxicity. To investigate the role of Mg depletion in the pathogenesis of acute CsA nephrotoxicity, rats kept on a low-salt diet were maintained on plain water (Mg(-)group) or water supplemented with 2% MgCl2 (Mg(+)group) and randomly assigned to treatment with CsA 15 mg/kg (CsA) or vehicle (VH) s.c. for 7 days. Water and food ingestion in VH animals was adjusted to the intake of CsA animals. CsAMg(-) group showed a significant plasma magnesium (PMg) reduction as compared to baseline (1.13 versus 1.53 mg/dl, P < 0.001) or VH values (versus 1.60 mg/dl, P < 0.001) and a significantly greater posttreatment fractional excretion of magnesium (FeMg) as compared to VH (9.4 versus 5.4%, P < 0.01). Magnesium supplementation increased PMg (2.11 versus 1.57 mg/dl P < 0.001) and FeMg (13.6 versus 6.2%, P < 0.001) but did not prevent a reduction in GFR with CsA treatment. Alanine aminopeptidase (AAP) excretion at 7 days was significantly greater than baseline (130 versus 44 IU/gCr, P < 0.05) or VH (36 IU/gCr, P < 0.05) values only in the CsAMg(-) rats. No differences were observed in intraerythrocyte Mg, blood pressure, and urinary excretion of N-acetyl-beta-D-glucosaminidase among groups. Renal histology was similar in CsA rats independent of magnesium supplementation: mild vacuolization and tubular collapse in proximal tubules.(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:Effects of oral magnesium supplementation on acute experimental cyclosporin nephrotoxicity. 817 71

We have solved the 2.0-A resolution crystal structures of four cavity-creating Ile/Leu-->Ala mutations in the hydrophobic core of barnase and compare and contrast the structural responses to mutation with those found for Leu-->Ala mutations in T4 lysozyme. First, there are rearrangements of structure of barnase that cause the cavities to collapse partly, and there is an approximately linear relationship between the changes in stability and the volume of the cavity similar to that found for the mutants of T4 lysozyme. Second, although it is currently accepted that hydrophobic cavities formed on the mutation of large hydrophobic side chains to smaller ones are not occupied by water molecules, we found a buried water molecule in the crystal structure of the barnase mutant Ile76-->Ala. A single hydrogen bond is formed between the water molecule and a polar atom, the carbonyl oxygen of Phe7, in the hydrophobic cavity that is formed on mutation. A survey of hydrophobic cavities produced by similar mutations in different proteins reveals that they all contain a proportion of polar atoms in their linings. The availability of such polar sites has implications for understanding folding pathways because a solvated core is presumed present in the transition state for folding and unfolding. Notably, the hydrogen bond between the cavity-water and the carbonyl group of Phe7 is also a marked early feature of very recent molecular dynamics simulations of barnase denaturation [Caflisch, A., & Karplus, M. (1995) J. Mol. Biol. 252, 672-708]. It is possible that cavities engineered into the hydrophobic cores of other proteins may contain water molecules, even though they cannot be detected by crystallographic analysis.
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PMID:Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities. 860 78

The structure of a metastable folding intermediate of human insulin-like growth factor I (IGF-I) and an engineered model are investigated by circular dichroism and two-dimensional 1H NMR spectroscopy. The intermediate, which contains two of three native disulfide bonds, was trapped by acid quenching and isolated by reverse-phase HPLC. The reduced cysteine residues were mapped to residues 47 and 52 (corresponding to A6-A11 in insulin). In the native state this disulfide bridge anchors an adjoining amphipathic alpha-helix (helix 2; residues 42 to 49) against the hydrophobic core. Comparison of CD and 1H-NMR spectra demonstrates that the acid-quenched intermediate is partially folded and contains elements of native secondary and tertiary structure. Spectra are similar to those of an equilibrium model in which the reduced cysteine residues are replaced by alanine. Complete 1H-NMR sequential assignment of the alanine model has been obtained and demonstrates that removal of the disulfide bond is associated with local unfolding of the adjoining alpha-helix. Native secondary structure (including helices 1 and 3) is otherwise retained and defines a folded subdomain. Long-range nuclear Overhauser effects (NOE) within this subdomain are similar to those of native IGF-I; no non-native NOE is observed. Our results support the hypothesis that folding of the insulin motif is directed by a subset of native structural elements and that these elements form at an early step in the pathway. Formation of helix 2, despite its prominence in the native state, is likely to represent a late step. Hydrophobic collapse of this segment appears to precede helix formation.
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PMID:Native and non-native structure in a protein-folding intermediate: spectroscopic studies of partially reduced IGF-I and an engineered alanine model. 865 30

The hydrophobic effect is the major factor that drives a protein molecule toward collapse and folding. In this process, residues with apolar side chains associate to form a solvent-shielded hydrophobic core. Often, this hydrophobic contribution to folding is quantified by measuring buried apolar surface area, reckoned as the difference in area between hydrophobic groups in the folded protein and in a standard state. Typically, the standard state area of a residue is obtained from tripeptide models, with the results taken to implicitly represent values appropriate for the unfolded state. Here, we show that a tripeptide is a poor descriptor of the unfolded state, and its widespread use has prompted erroneous conclusions about folding. As an alternative, we explore two limiting models, chosen to bracket the expected behavior of the unfolded chain between reliable extremes. One extreme is represented by simulated hard-sphere peptides and shown to behave like a homopolymer with excluded volume in a good solvent. The other extreme is represented by fragments excised from folded proteins and conjectured to approximate the time-average behavior of a thermally denatured protein at Tm, the midpoint of the unfolding transition. Using these models, it is shown that the area buried by apolar side chains upon folding is considerably less than earlier estimates. For example, upon transfer from the unfolded state to the middle of an alpha-helix, an alanine side chain buries negligible area and, surprisingly, a valine side chain actually gains area. Among other applications, an improved model of the unfolded state can be used to better evaluate the driving force for helix formation in peptides and proteins.
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PMID:Modeling unfolded states of peptides and proteins. 884 48

Bcl-2 belongs to a family of apoptosis-regulatory proteins which incorporate into the outer mitochondrial as well as nuclear membranes. The mechanism by which the proto-oncogene product Bcl-2 inhibits apoptosis is thus far elusive. We and others have shown previously that the first biochemical alteration detectable in cells undergoing apoptosis, well before nuclear changes become manifest, is a collapse of the mitochondrial inner membrane potential (delta psi m), suggesting the involvement of mitochondrial products in the apoptotic cascade. Here we show that mitochondria contain a pre-formed approximately 50-kD protein which is released upon delta psi m disruption and which, in a cell-free in vitro system, causes isolated nuclei to undergo apoptotic changes such as chromatin condensation and internucleosomal DNA fragmentation. This apoptosis-inducing factor (AIF) is blocked by N-benzyloxycarbonyl-Val-Ala-Asp.fluoromethylketone (Z-VAD.fmk), an antagonist of interleukin-1 beta-converting enzyme (ICE)-like proteases that is also an efficient inhibitor of apoptosis in cells. We have tested the effect of Bcl-2 on the formation, release, and action of AIF. When preventing mitochondrial permeability transition (which accounts for the pre-apoptotic delta psi m disruption in cells), Bcl-2 hyperexpressed in the outer mitochondrial membrane also impedes the release of AIF from isolated mitochondria in vitro. In contrast, Bcl-2 does not affect the formation of AIF, which is contained in comparable quantities in control mitochondria and in mitochondria from Bcl-2-hyperexpressing cells. Furthermore, the presence of Bcl-2 in the nuclear membrane does not interfere with the action of AIF on the nucleus, nor does Bcl-2 hyperexpression protect cells against AIF. It thus appears that Bcl-2 prevents apoptosis by favoring the retention of an apoptogenic protease in mitochondria.
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PMID:Bcl-2 inhibits the mitochondrial release of an apoptogenic protease. 887 5

To investigate the molecular mechanisms of the 'gain of toxic function' of mutant Cu/Zn superoxide dismutase (SOD) associated with familial amyotrophic lateral sclerosis (FALS), mutant (Ala 4 --> Thr, Gly 85 --> Arg, Gly 93 --> Ala, and two base-pair deletion in the 126th codon), as well as wild-type (wt), Cu/Zn SODs were expressed in COS7 cells. The formation of granular cytoplasmic aggregates accompanied by collapse of the cytoplasm was observed in cells expressing mutant (mt) Cu/Zn SODs, but not in cells expressing wt Cu/Zn SOD. The aggregates contained ribosome-like particles and endoplasmic reticulum. These results suggest the possibility that mt Cu/Zn SODs promote the formation of aggregates which are toxic to cells.
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PMID:Formation of granular cytoplasmic aggregates in COS7 cells expressing mutant Cu/Zn superoxide dismutase associated with familial amyotrophic lateral sclerosis. 985 58

Monte Carlo simulations were applied to beta-hairpin folding of a valine-based peptide. Two valine residues in the middle of the peptide were substituted with glycine, to serve as turn residues. Unlike lattice model simulations, structure prediction methods, and unfolding simulations, our simulations used an atom-based model, constant temperature (274 K), and non-beta-hairpin initial conformations. Based on the concept of solvent reference, the effective energy function simplified the solvent calculation and overcame the multiple minima problem. Driven by the hydrophobic interaction, the peptide first folded into a compact U-shaped conformation with a central turn, in analogy to the initial collapse with simultaneous nucleation in protein folding. The peptide units in the U-shaped conformation then reoriented, gradually forming hydrogen bonds in the beta-hairpin pattern from the beta-turn to the ends of the strands. With the same energy function, an alanine-based peptide folded into helix-dominated structures. The basic structure types (alpha-helix or beta-hairpin) that formed during the simulations depended upon the amino acid sequence. Compared with helix, beta-hairpin folding is driven mainly by the hydrophobic interaction. Hydrogen bonding is necessary to maintain the ordered secondary structure.
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PMID:Monte Carlo simulations of beta-hairpin folding at constant temperature. 987 31

The hydrophobic core packing in four-alpha-helical bundles appears to be crucial for stabilizing the protein structure. To examine the structural basis of hydrophobic stabilization, the crystal structures of the Leu-->Val (L41V) and Leu-->Ala (L41A) substitutions of the core residue Leu41 of the ROP protein have been determined. Both substitutions are destabilizing and lead to formation of cavities. The main responses to mutations are the collapse of the central part of the alpha-helix containing the site of mutation, shifts of internal water molecules, and in L41A, the trapping of a water molecule in a cavity engineered by the mutation. For both mutants, these effects limit the increase in cavity size to less than 10 A3, while an increase of 37 A3 and 100 A3 is expected for L41V and L41A, respectively, in the absence of any cavity size reducing effects. The mobility of internal side-chains is increased and in L41A, it reaches values typical for exposed residues. A parameter (Deltanh) is introduced as a measure of the number of van der Waals contacts lost. For ROP, barnase and T4 lysozyme mutants, there is a good correlation between Deltanh and the free energy of unfolding DeltaDeltaG relative to wild-type protein. The Deltanh value turns out to be more suitable for analysing structural and energetic responses to mutation than other parameter, such as cavity volumes and packing densities. Possible evolutionary implications of the DeltaDeltaG versus Deltanh relationship are discussed.
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PMID:A correlation between the loss of hydrophobic core packing interactions and protein stability. 987 46


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