Relative Solvent Exposure of the Alpha-Helix and Beta-Sheet in Water Determines the Initial Stages of Urea and Guanidinium Chloride-Induced Denaturation of Alpha/Beta Proteins

2019 ◽  
Vol 123 (42) ◽  
pp. 8889-8900 ◽  
Author(s):  
Sridip Parui ◽  
Biman Jana
Keyword(s):  
Alpha Helix ◽  
Beta Sheet ◽  
Guanidinium Chloride ◽  
Solvent Exposure ◽  
Beta Proteins ◽  
Alpha Beta

scholarly journals The secondary structure of protein G′, a robust molecule

1991 ◽  
Vol 274 (2) ◽  
pp. 503-507 ◽  
Author(s):  
C R Goward ◽  
L I Irons ◽  
J P Murphy ◽  
T Atkinson
Keyword(s):  
Biological Activity ◽  
Secondary Structure ◽  
Fluorescence Emission ◽  
Alpha Helix ◽  
Time Dependent ◽  
Protein G ◽  
Beta Sheet ◽  
Guanidinium Chloride ◽  
Streptococcal Protein G

The secondary structure of recombinant streptococcal Protein G' was predicted and compared with spectropolarimetric data. The predicted secondary structure consisted of 37 +/- 4% alpha-helix and 30 +/- 5% beta-sheet, whereas the values obtained from c.d. data were 29 +/- 2% alpha-helix and 41 +/- 3% beta-sheet. An alpha-helix-beta-sheet/turn-alpha-helix motif is conjectured to comprise the Fc-binding unit. The c.d. spectra in the near u.v. and far u.v. show that the Protein G' molecule is stable to heating at 100 degrees C and to extremes of pH (pH 1.5 to 11.0). The protein retained biological activity at these extremes. The molecule uncoils above pH 11.5 in a time-dependent fashion. Unfolding of the molecule in guanidinium chloride was monitored by c.d. and fluorescence emission; 3 M-guanidinium chloride was required to unfold the protein by 50%. The protein was completely unfolded in 5.5 M-guanidinium chloride and fully refolded with restoration of activity after removal of guanidinium chloride.

Biphasic effects of alcohols on the phase transition of poly(L-lysine) between .alpha.-helix and .beta.-sheet conformations

Biochemistry ◽  
1992 ◽  
Vol 31 (25) ◽  
pp. 5728-5733 ◽  
Author(s):  
Akira Shibata ◽  
Miharu Yamamoto ◽  
Takuya Yamashita ◽  
Jang Shing Chiou ◽  
Hiroshi Kamaya ◽  
...  
Keyword(s):  
Phase Transition ◽  
Alpha Helix ◽  
Beta Sheet

scholarly journals “In Silico” Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger

2017 ◽  
Vol 2017 ◽  
pp. 1-23 ◽  
Author(s):  
Doris C. Niño-Gómez ◽  
Claudia M. Rivera-Hoyos ◽  
Edwin D. Morales-Álvarez ◽  
Edgar A. Reyes-Montaño ◽  
Nury E. Vargas-Alejo ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Phytic Acid ◽  
Aqueous Media ◽  
Alpha Helix ◽  
Proton Donor ◽  
Van Der Waals Interactions ◽  
Beta Sheet ◽  
Instability Index ◽  
Bioinformatic Tools ◽  
Helix 12

Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of −0,304 and −0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H59 and H63 act as nucleophiles and that D339 and D319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions.

Alpha-Helix Self-Assembly of Oligopeptides Originated From Beta-Sheet Keratin

2012 ◽  
Vol 213 (24) ◽  
pp. 2628-2638 ◽  
Author(s):  
Qianjie Zhang ◽  
Bernd M. Liebeck ◽  
Kelu Yan ◽  
Dan E. Demco ◽  
Andrea Körner ◽  
...  
Keyword(s):  
Self Assembly ◽  
Alpha Helix ◽  
Beta Sheet

scholarly journals Precise assembly of complex beta sheet topologies from de novo designed building blocks

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Indigo Chris King ◽  
James Gleixner ◽  
Lindsey Doyle ◽  
Alexandre Kuzin ◽  
John F Hunt ◽  
...  
Keyword(s):  
De Novo ◽  
Computational Design ◽  
Building Blocks ◽  
Beta Sheets ◽  
Protein Domain ◽  
Beta Sheet ◽  
Design Models ◽  
Natural Protein ◽  
Complex Protein ◽  
Alpha Beta

Design of complex alpha-beta protein topologies poses a challenge because of the large number of alternative packing arrangements. A similar challenge presumably limited the emergence of large and complex protein topologies in evolution. Here, we demonstrate that protein topologies with six and seven-stranded beta sheets can be designed by insertion of one de novo designed beta sheet containing protein into another such that the two beta sheets are merged to form a single extended sheet, followed by amino acid sequence optimization at the newly formed strand-strand, strand-helix, and helix-helix interfaces. Crystal structures of two such designs closely match the computational design models. Searches for similar structures in the SCOP protein domain database yield only weak matches with different beta sheet connectivities. A similar beta sheet fusion mechanism may have contributed to the emergence of complex beta sheets during natural protein evolution.

scholarly journals Pocket 4 of the HLA-DR(α,β 1*0401) molecule is a major determinant of T cells recognition of peptide.

1995 ◽  
Vol 181 (3) ◽  
pp. 915-926 ◽  
Author(s):  
X T Fu ◽  
C P Bono ◽  
S L Woulfe ◽  
C Swearingen ◽  
N L Summers ◽  
...  
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
Peptide Binding ◽  
Alpha Helix ◽  
Single Amino Acid ◽  
Amino Acid Substitutions ◽  
Cell Recognition ◽  
T Cell Recognition ◽  
Hla Dr ◽  
Alpha Beta

To investigate the functional roles of individual HLA-DR residues in T cell recognition, transfectants expressing wild-type or mutant DR(alpha,beta 1*0401) molecules with single amino acid substitutions at 14 polymorphic positions of the DR beta 1*0401 chain or 19 positions of the DR alpha chain were used as antigen-presenting cells for five T cell clones specific for the influenza hemagglutinin peptide, HA307-19. Of the six polymorphic positions in the DR beta floor that were examined, mutations at only two positions eliminated T cell recognition: positions 13 (four clones) and 28 (one clone). In contrast, individual mutations at DR beta positions 70, 71, 78, and 86 on the alpha helix eliminated recognition by each of the clones, and mutations at positions 74 and 67 eliminated recognition by four and two clones, respectively. Most of the DR alpha mutations had minimal or no effect on most of the clones, although one clone was very sensitive to changes in the DR alpha chain, with loss of recognition in response to 10 mutants. Mutants that abrogated recognition by all of the clones were assessed for peptide binding, and only the beta 86 mutation drastically decreased peptide binding. Single amino acid substitutions at polymorphic positions in the central part of the DR beta alpha helix disrupted T cell recognition much more frequently than substitutions in the floor, suggesting that DR beta residues on the alpha helix make relatively greater contributions than those in the floor to the ability of the DR(alpha,beta 1*0401) molecule to present HA307-19. The data indicate that DR beta residues 13, 70, 71, 74, and 78, which are located in pocket 4 of the peptide binding site in the crystal structure of the DR1 molecule, exert a major and disproportionate influence on the outcome of T cell recognition, compared with other polymorphic residues.

scholarly journals Multiple native-like conformations trapped via self-association-induced hydrophobic collapse of the 33-residue β-sheet domain from platelet factor 4

1995 ◽  
Vol 306 (2) ◽  
pp. 407-419 ◽  
Author(s):  
E Ilyina ◽  
K H Mayo
Keyword(s):  
Electrostatic Interactions ◽  
Nuclear Overhauser Effect ◽  
Alpha Helix ◽  
Platelet Factor 4 ◽  
Random Coil ◽  
Beta Sheet ◽  
Platelet Factor ◽  
Hydrophobic Collapse ◽  
Low Dielectric ◽  
Self Association

Native platelet factor 4 (PF4) (70 residues) has a hydrophobic three-stranded anti-parallel beta-sheet domain on to which is folded an amphipathic C-terminal alpha-helix and an aperiodic N-terminal domain. The 33-amino acid beta-sheet domain from PF4 (residues 23-55) has been synthesized and studied by c.d. and n.m.r. At 10 degrees C and low concentration, peptide 23-55 appears to exist in aqueous solution in a random-coil distribution of highly flexible conformational states. Some preferred conformation, however, is observed, particularly within a relatively stable chain reversal from Leu-45 to Arg-49. As the peptide concentration and/or temperature is increased, a new conformational state(s) appears and intensifies as slowly exchanging (600 MHz 1H-n.m.r. chemical-shift time scale) random-coil resonances disappear. Hill plots of the concentration-dependence indicated mostly tetramer formation as found in native PF4. Although apparent resonance linewidths in aggregate state(s) are of the order of 100 Hz, sequence-specific assignments for most resonances could be made. N.m.r./nuclear Overhauser effect structural analysis indicates the formation of multiple native-like anti-parallel beta-sheet conformations, kinetically trapped via subunit-association-induced hydrophobic collapse and stabilized by low-dielectric electrostatic interactions among/between Gly-28 and Lys-50 in opposing subunits. Results are discussed in terms of protein folding.

scholarly journals Generating Bona Fide Mammalian Prions with Internal Deletions

2016 ◽  
Vol 90 (15) ◽  
pp. 6963-6975 ◽  
Author(s):  
Carola Munoz-Montesino ◽  
Christina Sizun ◽  
Mohammed Moudjou ◽  
Laetitia Herzog ◽  
Fabienne Reine ◽  
...  
Keyword(s):  
De Novo ◽  
Alpha Helix ◽  
Transmissible Spongiform Encephalopathies ◽  
Specific Information ◽  
Beta Sheet ◽  
Internal Deletion ◽  
C Terminus ◽  
Parkinson’S Diseases ◽  
Bona Fide ◽  
Mammalian Prions

ABSTRACTMammalian prions are PrP proteins with altered structures causing transmissible fatal neurodegenerative diseases. They are self-perpetuating through formation of beta-sheet-rich assemblies that seed conformational change of cellular PrP. Pathological PrP usually forms an insoluble protease-resistant core exhibiting beta-sheet structures but no more alpha-helical content, loosing the three alpha-helices contained in the correctly folded PrP. The lack of a high-resolution prion structure makes it difficult to understand the dynamics of conversion and to identify elements of the protein involved in this process. To determine whether completeness of residues within the protease-resistant domain is required for prions, we performed serial deletions in the helix H2 C terminus of ovine PrP, since this region has previously shown some tolerance to sequence changes without preventing prion replication. Deletions of either four or five residues essentially preserved the overall PrP structure and mutant PrP expressed in RK13 cells were efficiently converted into bona fide prions upon challenge by three different prion strains. Remarkably, deletions in PrP facilitated the replication of two strains that otherwise do not replicate in this cellular context. Prions with internal deletion were self-propagating andde novoinfectious for naive homologous and wild-type PrP-expressing cells. Moreover, they caused transmissible spongiform encephalopathies in mice, with similar biochemical signatures and neuropathologies other than the original strains. Prion convertibility and transfer of strain-specific information are thus preserved despite shortening of an alpha-helix in PrP and removal of residues within prions. These findings provide new insights into sequence/structure/infectivity relationship for prions.IMPORTANCEPrions are misfolded PrP proteins that convert the normal protein into a replicate of their own abnormal form. They are responsible for invariably fatal neurodegenerative disorders. Other aggregation-prone proteins appear to have a prion-like mode of expansion in brains, such as in Alzheimer's or Parkinson's diseases. To date, the resolution of prion structure remains elusive. Thus, to genetically define the landscape of regions critical for prion conversion, we tested the effect of short deletions. We found that, surprisingly, removal of a portion of PrP, the C terminus of alpha-helix H2, did not hamper prion formation but generated infectious agents with an internal deletion that showed characteristics essentially similar to those of original infecting strains. Thus, we demonstrate that completeness of the residues inside prions is not necessary for maintaining infectivity and the main strain-specific information, while reporting one of the few if not the only bona fide prions with an internal deletion.

scholarly journals The predicted secondary structures of class I fructose-bisphosphate aldolases

1988 ◽  
Vol 249 (3) ◽  
pp. 789-793 ◽  
Author(s):  
L Sawyer ◽  
L A Fothergill-Gilmore ◽  
P S Freemont
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Alpha Helix ◽  
Rabbit Muscle ◽  
X Ray Diffraction ◽  
Fructose Bisphosphate ◽  
Compact Structure ◽  
Alpha Beta ◽  
Surface Loops

The results of several secondary-structure prediction programs were combined to produce an estimate of the regions of alpha-helix, beta-sheet and reverse turns for fructose-bisphosphate aldolases from human and rat muscle and liver, from Trypanosoma brucei and from Drosophila melanogaster. All the aldolase sequences gave essentially the same pattern of secondary-structure predictions despite having sequences up to 50% different. One exception to this pattern was an additional strongly predicted helix in the rat liver and Drosophila enzymes. Regions of relatively high sequence variation generally were predicted as reverse turns, and probably occur as surface loops. Most of the positions corresponding to exon boundaries are located between regions predicted to have secondary-structural elements consistent with a compact structure. The predominantly alternating alpha/beta structure predicted is consistent with the alpha/beta-barrel structure indicated by preliminary high-resolution X-ray diffraction studies on rabbit muscle aldolase [Sygusch, Beaudry & Allaire (1986) Biophys. J. 49, 287a].

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