Effects of a disulfide bridge prior to amyloid formation of the ABRI peptide

RSC Advances ◽  
2014 ◽  
Vol 4 (70) ◽  
pp. 36923-36928 ◽  
Author(s):  
Jorge A. Ceballos ◽  
Marco A. Giraldo ◽  
Pilar Cossio

Computational studies characterize remarkable differences between the most probable structures of the monomeric amyloidogenic peptide, ABRI, with and without a single disulfide bond; the peptide is compact and alpha-helical with the bond, otherwise it is partially extended with slight β-bridges and an exposed hydrophobic surface area.

2012 ◽  
Vol 12 (6) ◽  
pp. 4919-4927 ◽  
Author(s):  
Nithi Atthi ◽  
Jakrapong Supadech ◽  
Gaetan Dupuy ◽  
On-uma Nimittrakoolchai ◽  
Apirak Pankiew ◽  
...  

2011 ◽  
Vol 11 (9) ◽  
pp. 4191-4207 ◽  
Author(s):  
B. J. Murray ◽  
S. L. Broadley ◽  
T. W. Wilson ◽  
J. D. Atkinson ◽  
R. H. Wills

Abstract. Clouds composed of both ice particles and supercooled liquid water droplets exist at temperatures above ~236 K. These mixed phase clouds, which strongly impact climate, are very sensitive to the presence of solid particles that can catalyse freezing. In this paper we describe experiments to determine the conditions at which the clay mineral kaolinite nucleates ice when immersed within water droplets. These are the first immersion mode experiments in which the ice nucleating ability of kaolinite has been determined as a function of clay surface area, cooling rate and also at constant temperatures. Water droplets containing a known amount of clay mineral were supported on a hydrophobic surface and cooled at rates of between 0.8 and 10 K min−1 or held at constant sub-zero temperatures. The time and temperature at which individual 10–50 μm diameter droplets froze were determined by optical microscopy. For a cooling rate of 10 K min−1, the median nucleation temperature of 10–40 μm diameter droplets increased from close to the homogeneous nucleation limit (236 K) to 240.8 ± 0.6 K as the concentration of kaolinite in the droplets was increased from 0.005 wt% to 1 wt%. This data shows that the probability of freezing scales with surface area of the kaolinite inclusions. We also show that at a constant temperature the number of liquid droplets decreases exponentially as they freeze over time. The constant cooling rate experiments are consistent with the stochastic, singular and modified singular descriptions of heterogeneous nucleation; however, freezing during cooling and at constant temperature can be reconciled best with the stochastic approach. We report temperature dependent nucleation rate coefficients (nucleation events per unit time per unit area) for kaolinite and present a general parameterisation for immersion nucleation which may be suitable for cloud modelling once nucleation by other important ice nucleating species is quantified in the future.


2014 ◽  
Vol 70 (4) ◽  
pp. 1005-1014 ◽  
Author(s):  
Beatriz G. Guimarães ◽  
Djemel Hamdane ◽  
Christophe Lechauve ◽  
Michael C. Marden ◽  
Béatrice Golinelli-Pimpaneau

Neuroglobin plays an important function in the supply of oxygen in nervous tissues. In human neuroglobin, a cysteine at position 46 in the loop connecting the C and D helices of the globin fold is presumed to form an intramolecular disulfide bond with Cys55. Rupture of this disulfide bridge stabilizes bi-histidyl haem hexacoordination, causing an overall decrease in the affinity for oxygen. Here, the first X-ray structure of wild-type human neuroglobin is reported at 1.74 Å resolution. This structure provides a direct observation of two distinct conformations of the CD region containing the intramolecular disulfide link and highlights internal cavities that could be involved in ligand migration and/or are necessary to enable the conformational transition between the low and high oxygen-affinity states following S—S bond formation.


2019 ◽  
Vol 10 (4) ◽  
pp. 666-670 ◽  
Author(s):  
Massimiliano Meli ◽  
Hamutal Engel ◽  
Dana Laor ◽  
Ehud Gazit ◽  
Giorgio Colombo

1979 ◽  
Vol 57 (3) ◽  
pp. 279-285 ◽  
Author(s):  
Maire E. Percy ◽  
Lebe Chang ◽  
Catherine Demoliou ◽  
Reuben Baumal

After 5 years of subcutaneous transfer in Balb/C mice, our MOPC 173 myeloma tumour line (originally an IgG2a,κ H2L2-producer) exclusively synthesized an unusual IgG2b,κ protein lacking inter-heavy (H) chain disulfide bonds. This protein was designated MOPC 173B. On sodium dodecyl sulfate – polyacrylamide gel electrophoresis, it migrated with an apparent molecular weight of 77 000; following complete reduction and alkylation, the mobilities of its constituent H and light (L) chains were found to differ slightly from those of MOPC 173 H2L2. MOPC 173B was serologically identical to another typical IgG2b,κ myeloma protein, MOPC 195, and peptide mapping studies showed that it possessed only the inter H–L disulfide bond characteristic of typical IgG2b,κ proteins. In a nondissociating solvent, the sedimentation coefficient of the protein was 6.3S even at concentrations as low as 0.2 mg/ml, indicating that noncovalent interactions existed between two half-molecule subunits. Since this unusual IgG myeloma protein contained only a single category of interchain disulfide bridge, the inter H–L bond, it was an ideal model system for characterization of the kinetics of formation and reduction of interchain disulfide bonds. The kinetics of the glutathione-catalyzed reoxidation of the inter H–L disulfide bridge in MOPC 173B followed an apparent second-order rate equation. In contrast, reduction of its inter H–L bridge under anaerobic conditions with dithioerythritol in excess, was strictly a first-order process and not a simple reversal of the reoxidation. These studies provide the basis for the more complex mathematical models that describe the reoxidation and reduction of typical immunoglobulin molecules.


2019 ◽  
Vol 32 (2) ◽  
pp. 77-85
Author(s):  
Mohammad Ashhar I Khan ◽  
Ulrich Weininger ◽  
Sven Kjellström ◽  
Shashank Deep ◽  
Mikael Akke

Abstract Intracellular aggregates of superoxide dismutase 1 (SOD1) are associated with amyotrophic lateral sclerosis. In vivo, aggregation occurs in a complex and dense molecular environment with chemically heterogeneous surfaces. To investigate how SOD1 fibril formation is affected by surfaces, we used an in vitro model system enabling us to vary the molecular features of both SOD1 and the surfaces, as well as the surface area. We compared fibril formation in hydrophilic and hydrophobic sample wells, as a function of denaturant concentration and extraneous hydrophobic surface area. In the presence of hydrophobic surfaces, SOD1 unfolding promotes fibril nucleation. By contrast, in the presence of hydrophilic surfaces, increasing denaturant concentration retards the onset of fibril formation. We conclude that the mechanism of fibril formation depends on the surrounding surfaces and that the nucleating species might correspond to different conformational states of SOD1 depending on the nature of these surfaces.


2020 ◽  
Vol 73 (4) ◽  
pp. 312
Author(s):  
Balasubramanyam Chittoor ◽  
Bankala Krishnarjuna ◽  
Rodrigo A. V. Morales ◽  
Raymond S. Norton

Disulfide bonds play a key role in the oxidative folding, conformational stability, and functional activity of many peptides. A few disulfide-rich peptides with privileged architecture such as the inhibitor cystine knot motif have garnered attention as templates in drug design. The single disulfide-directed β-hairpin (SDH), a novel fold identified more recently in contryphan-Vc1, has been shown to possess remarkable thermal, conformational, and chemical stability and can accept a short bioactive epitope without compromising the core structure of the peptide. In this study, we demonstrated that the single disulfide bond is critical in maintaining the native fold by replacing both cysteine residues with serine. We also designed an analogue with an additional, non-native disulfide bridge by replacing Gln1 and Tyr9 with Cys. Contryphan-Vc11–22[Q1C, Y9C] was synthesised utilising orthogonal cysteine protection and its solution structure determined using solution NMR spectroscopy. This analogue maintained the overall fold of native contryphan-Vc1. Previous studies had shown that the β-hairpin core of contryphan-Vc1 was resistant to proteolysis by trypsin and α-chymotrypsin but susceptible to cleavage by pepsin. Contryphan-Vc11–22[Q1C, Y9C] proved to be completely resistant to pepsin, thus confirming our design strategy. These results highlight the role of the disulfide bond in maintaining the SDH fold and provide a basis for the design of more stable analogues for peptide epitope grafting.


2005 ◽  
Vol 386 (11) ◽  
Author(s):  
Takeo Yoshinaga ◽  
Keisuke Nakatome ◽  
Jun-ichi Nozaki ◽  
Motoko Naitoh ◽  
Jun Hoseki ◽  
...  

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1043-1043
Author(s):  
Jacques Rochette ◽  
Gerald Le Gac ◽  
Isabelle Gourlaouen ◽  
Kaiss Lassoued ◽  
Claude Ferec ◽  
...  

Abstract Abstract 1043 Introduction: Mutations in the HFE gene may result in iron overload and can produce hereditary hemochromatosis. Most patients with hereditary hemochromatosis are homozygous for a single mutation of the HFE gene (p.Cys282Tyr). The molecular defect lies in the loss of the unique disulfide bridge present in the α3 domain of the protein, which is required for proper folding of HFE, trafficking to the cell surface and binding to β2-microglobulin. We have studied the impact of a new missense mutation (p.Arg226Gly) on the structure of the α3-domain of HFE by means of Molecular Dynamics (MD) calculations in explicit solvent. Materials and Methods: A computer model structure of the α3 domain (i.e. 93 residues, Gln205-Trp297) was generated based on the X-Ray crystal structure. All MD simulations were performed with the SANDER module of the AMBER10 program suite using the Hornak et al. all-atom model force field (FF99SB parameters). Structural properties were analyzed with the PTRAJ module present within AmberTools1.2. The relative stability of the HFEWT and HFER226G proteins was evaluated in terms of free energy of the relevant systems by post-processing the molecular dynamics trajectories with the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) technique. Results: The patient was a 45-year-old male from Brittany presenting with abdominal pain and asthenia. He had serum ferritin (SF) of 2325 microg.l−1 (N: 10–300 microg.l−1), and transferrin saturation (TSat) level of 49 % (N < 45 %). Molecular genetics analysis revealed a new C282Y/R226G compound heterozygote genotype. A 33 years old brother in the same compound heterozygous state had an elevated SF of 552 microg.l−1 and a TSat level of 47%. No other known iron gene was mutated in those described as being responsible for hemochromatosis. The Arg226Gly substitution is located in the vicinity of the Cys225S-S282Cys disulfide bond. Our results show: i) that the p.Arg226Gly mutation S-S prevents the formation of the Cys225S-S282Cys disulfide bridge in increasing the distance between the 225–282 sulfur groups [d= 3.57 Å ± 0.21 for HFEWT and 4.25 Å ± 0.52 for HFE226G]; ii) consequently, many others local features of the protein, such as the solvation free energy and hydrophobicity are modified, although the global secondary structure of the α3 domain is conserved. This is confirmed altogether by the rmsd/rmsf plots and the superimposition of three-dimensional structures. This lack of global conformational modifications points out the structural adaptability and flexibility of proteins to adapt to missense mutations with minor local rearrangements. Analyses to control formation or deformation of salt-bridges were undergone as well. Surprisingly, Arg226 is not involved in any of new salt bridges on the contrary of its Arg224 neighbor. Instead of causing conformational disruption, losing the 225S-S282 disulfide bridge destabilizes the native state and modifies the stability of the protein. Instability is caused by the absence of internal water molecules in the vicinity of the mutation as evidenced on the rdfs curves. Compared to HFEWT, the mutant presents two additional hydrophobic pockets, one positioned around residue 226, whereas the second one is located slightly above the two cysteine residues (225 and 282) conferring the mutant with additional properties. Conclusion: The p.Arg226G substitution in HFE is one of the very rare natural examples of a loss of a disulfide bond without a cysteine substitution. As it is not possible to study extensively all naturally occurring mutations in proteins by using biochemical tests and physiological experiments including animal models, computer approaches represent a very useful alternative when the X ray structure is known for the wild type protein. Disclosures: No relevant conflicts of interest to declare.


2002 ◽  
Vol 277 (43) ◽  
pp. 41140-41146 ◽  
Author(s):  
Wei Feng ◽  
Jing-Song Fan ◽  
Ming Jiang ◽  
Ya-Wei Shi ◽  
Mingjie Zhang

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