UMLS:C0344329 - FACTA Search

Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Target Concepts:

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

We have solved and analysed the crystal structures of five mutants in the hydrophobic core of barnase to investigate the structural basis for the contribution of hydrophobic residues and side-chain packing to the stability of globular proteins. In case ease, an amino acid side-chain has been replaced with one of smaller volume. The overall structures of four Ile-->Val mutants (residues 51, 76, 88 and 96) and one Leu-->Val mutant (residue 89) are all isomorphous with the wild-type structure. The magnitude and nature of structural shifts in the three hydrophobic core regions of barnase depend on the local environment of the substitution site, but have some features in common. (1) Side-chain atoms move to a greater extent than do main-chain atoms. (2) Repacking at the substitution site is achieved by either a rigid body shift of side-chain atoms (for Ile-->Val76 and Ile-->Val96 mutants), or by a combination of a side-chain shift and rotation (for Ile-->Val51 and Ile-->Val88 mutants). The mutated residue moves to the greatest extent, and generally in the direction of the created cavity (the largest atomic shift is 0.9 A, for Ile-->Val51). The space left behind from such shifts is not seen to be filled by neighbouring side-chains. (3) Where a cavity remains after mutation, it does not contain any solvent molecules. (4) There is no correlation between the extent of structural movements and the atomic temperature factors of atoms that have moved. (5) Structural movements are not large enough to disrupt hydrogen bonding. Valine 88, in the Ile-->Val88 mutant, is disordered and the electron density suggests several side-chain conformations. The reduction in the volumes of the cavities introduced upon mutation, due to collapse of the surrounding structure, ranges from 11% (Ile-->Val96) to 90% (Ile-->Val51).
...
PMID:Crystal structural analysis of mutations in the hydrophobic cores of barnase. 825 77

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.
...
PMID:Modeling unfolded states of peptides and proteins. 884 48

The cause of dopaminergic cell death in Parkinson's disease (PD) remains unknown, but may involve oxidative stress and mitochondrial complex I deficiency. Opening of the permeability transition pore and disruption of the mitochondrial transmembrane potential are known to be common events in the apoptotic pathway. Cyclosporin A and its non-immunosuppressant analogue, N-methyl-4-valine cyclosporin inhibit the opening of the mitochondrial megachannel. Complex I inhibitors, including MPP+, are known to induce both apoptosis in cell culture and parkinsonism in man and other primates. The present study using propidium iodide and FITC-TUNEL staining to identify apoptotic cells, demonstrates that rotenone, MPP+ and tetrahydroisoquinoline induce apoptosis in PC12 cells. Apoptosis induced by these agents was decreased by cyclosporin A and N-methyl-4-valine cyclosporin. Thus, apoptosis induced by inhibitors of mitochondrial complex I is probably mediated by permeability pore opening and collapse of the mitochondrial membrane potential. This observation may allow the development of novel neuroprotective strategies in disorders that may involve mitochondrial dysfunction and apoptotic cell death.
...
PMID:Cyclosporin inhibition of apoptosis induced by mitochondrial complex I toxins. 979 6

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.
...
PMID:Monte Carlo simulations of beta-hairpin folding at constant temperature. 987 31

We have systematically mutated residues located in turns between beta-strands of the intestinal fatty acid binding protein (IFABP), and a glycine in a half turn, to valine and have examined the stability, refolding rate constants and ligand dissociation constants for each mutant protein. IFABP is an almost all beta-sheet protein exhibiting a topology comprised of two five-stranded sheets surrounding a large cavity into which the fatty acid ligand binds. A glycine residue is located in seven of the eight turns between the antiparallel beta-strands and another in a half turn of a strand connecting the front and back sheets. Mutations in any of the three turns connecting the last four C-terminal strands slow the folding and decrease stability with the mutation between the last two strands slowing folding dramatically. These data suggest that interactions between the last four C-terminal strands are highly cooperative, perhaps triggered by an initial hydrophobic collapse. We suggest that this trigger is collapse of the highly hydrophobic cluster of amino acids in the D and E strands, a region previously shown to also affect the last stage of the folding process (Kim et al., 1997). Changing the glycine in the strand between the front and back sheets also results in a unstable, slow folding protein perhaps disrupting the D-E strand interactions. For most of the other turn mutations there was no apparent correlation between stability and refolding rate constants. In some turns, the interaction between strands, rather than the turn type, appears to be critical for folding while in others, turn formation itself appears to be a rate limiting step. Although there is no simple correlation between turn formation and folding kinetics, we propose that turn scanning by mutagenesis will be a useful tool for issues related to protein folding.
...
PMID:Turn scanning by site-directed mutagenesis: application to the protein folding problem using the intestinal fatty acid binding protein. 1008 80

The intestinal fatty acid binding protein is one of a family of proteins that are composed of two beta-sheets surrounding a large interior cavity into which the ligand binds. Glycine residues occur in many of the turns between adjacent antiparallel beta-strands. In previous work, the effect of replacing these glycine residues with valine has been examined with stopped flow instrumentation using intrinsic tryptophan fluorescence spectroscopy [Kim and Frieden (1998) Protein Sci. 7, 1821-1828]. To resolve the burst phase missing in the stopped flow measurements, these valine mutants have been reexamined with sub-millisecond continuous flow instrumentation. Some of the glycine residues have also been replaced with proline, and the folding reactions of these proline mutants have been compared with those of their valine counterparts. In all cases, the stability of the protein is decreased, but some turns appear to be more critical for final structure stabilization than others. Surprisingly, the rate constants observed for all the mutants measured by sub-millisecond continuous flow methods are quite similar (1400-3000 s(-1)), and in all the mutants, there is a shift in the fluorescence emission maximum from that of the unfolded protein to lower wavelengths, suggesting some collapse of the unfolded state within 200 micros. In contrast to the rate constants observed for the initial folding events measured by the sub-millisecond continuous flow method, the rate constants for the slower phase observed in the stopped flow instrument vary widely for the different mutants. The latter step appears to be related to side chain stabilization rather than secondary structure formation. It is also shown that the ligand binds tightly only to the native protein and not to any intermediate forms.
...
PMID:The intestinal fatty acid binding protein: the role of turns in fast and slow folding processes. 1190 May 47

Mitochondrial permeability transition (mPT) is a crucial event in the progression to cell death in the setting of ischemia-reperfusion. We have used a model system in which mPT can be reliably and reproducibly induced to test the hypothesis that the profound protection associated with the phenomenon of myocardial preconditioning is mediated by suppression of the mPT. Adult rat myocytes were loaded with the fluorescent probe tetramethylrhodamine methyl ester, which generates oxidative stress on laser illumination, thus inducing the mPT (indicated by collapse of the mitochondrial membrane potential) and ATP depletion, seen as rigor contracture. The known inhibitors of the mPT, cyclosporin A (0.2 microM) and N-methyl-4-valine-cyclosporin A (0.4 microM), increased the time taken to induce the mPT by 1.8- and 2.9-fold, respectively, compared with control (P < 0.001) and rigor contracture by 1.5-fold compared with control (P < 0.001). Hypoxic preconditioning (HP) and pharmacological preconditioning, using diazoxide (30 microM) or nicorandil (100 microM), also increased the time taken to induce the mPT by 2.0-, 2.1-, and 1.5-fold, respectively (P < 0.001), and rigor contracture by 1.9-, 1.7-, and 1.5-fold, respectively, compared with control (P < 0.001). Effects of HP, diazoxide, and nicorandil were abolished in the presence of mitochondrial ATP-sensitive K(+) (K(ATP)) channel blockers glibenclamide (10 microM) and 5-hydroxydecanoate (100 microM) but were maintained in the presence of the sarcolemmal K(ATP) channel blocker HMR-1098 (10 microM). In conclusion, preconditioning protects the myocardium by reducing the probability of the mPT, which normally occurs during ischemia-reperfusion in response to oxidative stress.
...
PMID:Preconditioning protects by inhibiting the mitochondrial permeability transition. 1507 53

A class of peptides has been designed whose ability to self-assemble into hydrogel is dependent on their conformationally folded state. Under unfolding conditions aqueous peptide solutions are freely flowing having the viscosity of water. When folding is triggered by external stimuli, peptides adopt a beta-hairpin conformation that self-assembles into a highly crosslinked network of fibrils affording mechanically rigid hydrogels. MAX 1, a 20 residue, amphiphilic hairpin self-assembles via a mechanism which entails both lateral and facial self-assembly events to form a network of fibrils whose local structure consists of a bilayer of hairpins hydrogen bonded in the direction of fibril growth. Lateral self-assembly along the long axis of the fibril is mainly facilitated by intermolecular hydrogen bonding between the strands of distinct hairpins and the formation of hydrophobic contacts between residue side chains of laterally associating hairpins. Facial assembly is driven by the hydrophobic collapse of the valine-rich faces of the amphiphilic hairpins affording a bilayer laminate. The importance of forming lateral hydrophobic contacts during hairpin self-assembly and the relative contribution these interactions have towards nano-scale morphology and material rigidity is probed via the study of: MAX1, a hairpin designed to exploit lateral hydrophobic interactions; MAX 4, a peptide with reduced ability to form these interactions; and MAX5, a control peptide. CD spectroscopy and rheological experiments suggest that the formation of lateral hydrophobic interactions aids the kinetics of assembly and contributes to the mechanical rigidity of the hydrogel. Transmission electron microscopy (TEM) shows that these interactions play an essential role in the self-assembly process leading to distinct nano-scale morphologies.
...
PMID:Probing the importance of lateral hydrophobic association in self-assembling peptide hydrogelators. 1628 91

The rat intestinal fatty acid binding protein (IFABP) primarily comprises two beta-sheet structures surrounding a large internal cavity. The urea denatured WT protein folds within seconds after dilution to nondenaturing conditions. Replacing a glycine with valine in the turn between the last two beta-strands (Gly121Val) slows the folding process by more than three orders of magnitude. After incorporating 4-(19)F-phenylalanine into the mutant protein, we were able to directly monitor the behavior of the eight phenylalanine side chains in real time during folding using (19)F NMR. Specifically, there is a nonnative-like collapse in regions involving three phenylalanine residues (Phe-62, Phe-68, and Phe-93) within milliseconds. At least two distinct NMR peaks were observed, suggesting conformational fluctuations in this region. Formation of this site is followed by formation of native structure of Phe-2 and Phe-17, then by Phe-47, and finally by the cooperative rearrangement of the intermediate structures to the final native structure. It is proposed that the Gly121Val mutation slows the formation of a normal nucleating site, not only slowing overall folding, but also allowing intermediates in regions distant from the mutation to be experimentally observed. Because intermediates involved in protein folding are normally difficult to observe due to their marginal stability, the experimental approach used here may serve as a general method for determining the nature of both early and late steps in protein folding.
...
PMID:Observation of sequential steps in the folding of intestinal fatty acid binding protein using a slow folding mutant and 19F NMR. 1761 32

Ion flow in many voltage-gated K(+) channels (VGK), including the (human ether-a-go-go-related gene) hERG channel, is regulated by reversible collapse of the selectivity filter. hERG channels, however, exhibit low sequence homology to other VGKs, particularly in the outer pore helix (S5) domain, and we hypothesize that this contributes to the unique activation and inactivation kinetics in hERG K(+) channels that are so important for cardiac electrical activity. The S5 domain in hERG identified by NMR spectroscopy closely corresponded to the segment predicted by bioinformatics analysis of 676 members of the VGK superfamily. Mutations to approximately every third residue, from Phe(551) to Trp(563), affected steady state activation, whereas mutations to approximately every third residue on an adjacent face and spanning the entire S5 segment perturbed inactivation, suggesting that the whole span of S5 experiences a rearrangement associated with inactivation. We refined a homology model of the hERG pore domain using constraints from the mutagenesis data with residues affecting inactivation pointing in toward S6. In this model the three residues with maximum impact on activation (W563A, F559A, and F551A) face out toward the voltage sensor. In addition, the residues that when mutated to alanine, or from alanine to valine, that did not express (Ala(561), His(562), Ala(565), Trp(568), and Ile(571)), all point toward the pore helix and contribute to close hydrophobic packing in this region of the channel.
...
PMID:The pore domain outer helix contributes to both activation and inactivation of the HERG K+ channel. 1899 46

1 2 Next >>