Using Small Peptide Segments of Amyloid-β and Humanin to Examine their Physical Interactions

2019 ◽  
Vol 26 (7) ◽  
pp. 502-511 ◽  
Author(s):  
Deborah L. Heyl ◽  
Brandon Iwaniec ◽  
Daniel Esckilsen ◽  
Deanna Price ◽  
Prathyusha Guttikonda ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amyloid Fibrils ◽  
Amyloid Β ◽  
Full Length ◽  
Binding Kinetics ◽  
Amino Acid Residues ◽  
Aβ Peptides ◽  
Physical Interactions ◽  
Peptide Segments ◽  
Kinetics Of

Background: Amyloid fibrils in Alzheimer’s disease are composed of amyloid-β (Aβ) peptides of variant lengths. Humanin (HN), a 24 amino acid residue neuroprotective peptide, is known to interact with the predominant Aβ isoform in the brain, Aβ (1-40). Methods: Here, we constructed smaller segments of Aβ and HN and identified residues in HN important for both HN-HN and HN-Aβ interactions. Peptides corresponding to amino acid residues 5- 15 of HN, HN (5-15), HN (5-15, L11S), where Leu11 was replaced with Ser, and residues 17-28 of Aβ, Aβ (17-28), were synthesized and tested for their ability to block formation of the complex between HN and Aβ (1-40). Results: Co-immunoprecipitation and binding kinetics showed that HN (5-15) was more efficient at blocking the complex between HN and Aβ (1-40) than either HN (5-15, L11S) or Aβ (17-28). Binding kinetics of these smaller peptides with either full-length HN or Aβ (1-40) showed that HN (5- 15) was able to bind either Aβ (1-40) or HN more efficiently than HN (5-15, L11S) or Aβ (17-28). Compared to full-length HN, however, HN (5-15) bound Aβ (1-40) with a weaker affinity suggesting that while HN (5-15) binds Aβ, other residues in the full length HN peptide are necessary for maximum interactions. Conclusion: L11 was more important for interactions with Aβ (1-40) than with HN. Aβ (17-28) was relatively ineffective at binding to either Aβ (1-40) or HN. Moreover, HN, and the smaller HN (5-15), HN (5-15 L11S), and Aβ (17-28) peptides, had different effects on regulating Aβ (1-40) aggregation kinetics.

scholarly journals Analysis of the Secondary Structure of β-Amyloid (Aβ42) Fibrils by Systematic Proline Replacement

2004 ◽  
Vol 279 (50) ◽  
pp. 52781-52788 ◽  
Author(s):  
Akira Morimoto ◽  
Kazuhiro Irie ◽  
Kazuma Murakami ◽  
Yuichi Masuda ◽  
Hajime Ohigashi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Amyloid Fibrils ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Aβ Peptides ◽  
Amyloid Peptides ◽  
Aggregation Inhibitors ◽  
Β Amyloid ◽  
Β Sheet

Amyloid fibrils in Alzheimer's disease mainly consist of 40- and 42-mer β-amyloid peptides (Aβ40 and Aβ42) that exhibit aggregative ability and neurotoxicity. Although the aggregates of Aβ peptides are rich in intermolecular β-sheet, the precise secondary structure of Aβ in the aggregates remains unclear. To identify the amino acid residues involved in the β-sheet formation, 34 proline-substituted mutants of Aβ42 were synthesized and their aggregative ability and neurotoxicity on PC12 cells were examined. Prolines are rarely present in β-sheet, whereas they are easily accommodated in β-turn as a Pro-Xcorner. Among the mutants at positions 15-32, only E22P-Aβ42 extensively aggregated with stronger neurotoxicity than wild-type Aβ42, suggesting that the residues at positions 15-21 and 24-32 are involved in the β-sheet and that the turn at positions 22 and 23 plays a crucial role in the aggregation and neurotoxicity of Aβ42. The C-terminal proline mutants (A42P-, I41P-, and V40P-Aβ42) hardly aggregated with extremely weak cytotoxicity, whereas the C-terminal threonine mutants (A42T- and I41T-Aβ42) aggregated potently with significant cytotoxicity. These results indicate that the hydrophobicity of the C-terminal two residues of Aβ42 is not related to its aggregative ability and neurotoxicity, rather the C-terminal three residues adopt the β-sheet. These results demonstrate well the large difference in aggregative ability and neurotoxicity between Aβ42 and Aβ40. In contrast, the proline mutants at the N-terminal 13 residues showed potent aggregative ability and neurotoxicity similar to those of wild-type Aβ42. The identification of the β-sheet region of Aβ42 is a basis for designing new aggregation inhibitors of Aβ peptides.

scholarly journals Purification and characterization of human H-ras proteins expressed in Escherichia coli.

1985 ◽  
Vol 5 (5) ◽  
pp. 1015-1024 ◽  
Author(s):  
M Gross ◽  
R W Sweet ◽  
G Sathe ◽  
S Yokoyama ◽  
O Fasano ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Binding Activity ◽  
Full Length ◽  
Binding Kinetics ◽  
Amino Acid Residues ◽  
Ras Proteins ◽  
Truncated Protein ◽  
Amino Terminal ◽  
Carboxyl Terminal

The full-length normal and T24 mutant human H-ras proteins and two truncated derivatives of the T24 mutant were expressed efficiently in Escherichia coli. The proteins accumulated to 1 to 5% of total cellular protein, and each was specifically recognized by anti-ras monoclonal antibodies. The two full-length proteins as well as a carboxyl-terminal truncated derivative (deleted for 23 amino acid residues) were soluble upon cell lysis and were purified to 90% homogeneity without the use of denaturants. In contrast, an amino-terminal truncated ras derivative (deleted for 22 amino acid residues) required treatment with urea for its solubilization. The guanine nucleotide binding activity of these four proteins was assessed by a combination of ligand binding on proteins blots, immunoprecipitation, and standard filter binding procedures. The full-length proteins showed similar binding kinetics and a stoichiometry approaching 1 mol of GTP bound per mol of protein. The showed similar binding kinetics and a stoichiometry approaching 1 mol of GTP bound per mol of protein. The carboxyl-terminal truncated protein also bound GTP, but to a reduced extent, whereas the amino-terminal truncated protein did not have binding activity. Apparently, the carboxyl-terminal domain of ras, although important for transforming function, does not play a critical role in GTP binding.

scholarly journals Purification and characterization of human H-ras proteins expressed in Escherichia coli

1985 ◽  
Vol 5 (5) ◽  
pp. 1015-1024
Author(s):  
M Gross ◽  
R W Sweet ◽  
G Sathe ◽  
S Yokoyama ◽  
O Fasano ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Binding Activity ◽  
Full Length ◽  
Binding Kinetics ◽  
Amino Acid Residues ◽  
Ras Proteins ◽  
Truncated Protein ◽  
Amino Terminal ◽  
Carboxyl Terminal

The full-length normal and T24 mutant human H-ras proteins and two truncated derivatives of the T24 mutant were expressed efficiently in Escherichia coli. The proteins accumulated to 1 to 5% of total cellular protein, and each was specifically recognized by anti-ras monoclonal antibodies. The two full-length proteins as well as a carboxyl-terminal truncated derivative (deleted for 23 amino acid residues) were soluble upon cell lysis and were purified to 90% homogeneity without the use of denaturants. In contrast, an amino-terminal truncated ras derivative (deleted for 22 amino acid residues) required treatment with urea for its solubilization. The guanine nucleotide binding activity of these four proteins was assessed by a combination of ligand binding on proteins blots, immunoprecipitation, and standard filter binding procedures. The full-length proteins showed similar binding kinetics and a stoichiometry approaching 1 mol of GTP bound per mol of protein. The showed similar binding kinetics and a stoichiometry approaching 1 mol of GTP bound per mol of protein. The carboxyl-terminal truncated protein also bound GTP, but to a reduced extent, whereas the amino-terminal truncated protein did not have binding activity. Apparently, the carboxyl-terminal domain of ras, although important for transforming function, does not play a critical role in GTP binding.

scholarly journals Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies

2021 ◽  
Vol 22 (4) ◽  
pp. 1859
Author(s):  
Satoru Itoh ◽  
Hisashi Okumura
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Membrane Surface ◽  
Amyloid Β ◽  
Inhibition Mechanism ◽  
Amyloid Β Peptide ◽  
Amino Acid Residues ◽  
High Concentration ◽  
Aβ Peptides ◽  
A Cell

Aggregates of amyloid-β (Aβ) peptides are known to be related to Alzheimer’s disease. Their aggregation is enhanced at hydrophilic–hydrophobic interfaces, such as a cell membrane surface and air-water interface, and is inhibited by polyphenols, such as myricetin and rosmarinic acid. We review molecular dynamics (MD) simulation approaches of a full-length Aβ peptide, Aβ40, and Aβ(16–22) fragments in these environments. Since these peptides have both hydrophilic and hydrophobic amino acid residues, they tend to exist at the interfaces. The high concentration of the peptides accelerates the aggregation there. In addition, Aβ40 forms a β-hairpin structure, and this structure accelerates the aggregation. We also describe the inhibition mechanism of the Aβ(16–22) aggregation by polyphenols. The aggregation of Aβ(16–22) fragments is caused mainly by the electrostatic attraction between charged amino acid residues known as Lys16 and Glu22. Since polyphenols form hydrogen bonds between their hydroxy and carboxyl groups and these charged amino acid residues, they inhibit the aggregation.

Computational analysis of the effect of [Tea][Ms] and [Tea][H2PO4] ionic liquids on the structure and stability of Aβ(17–42) amyloid fibrils

2021 ◽  
Vol 23 (11) ◽  
pp. 6695-6709
Author(s):  
D. Gobbo ◽  
A. Cavalli ◽  
P. Ballone ◽  
A. Benedetto
Keyword(s):  
Ionic Liquid ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Liquid Water ◽  
Computational Analysis ◽  
Amyloid Fibrils ◽  
Aβ Peptides ◽  
Structure And Stability ◽  
Water Solutions ◽  
Kinetics Of

Tight coordination of peptides by organic anions driven by hydrogen bonding affects the fibrillation kinetics of Aβ peptides in ionic liquid/water solutions.

scholarly journals Probing the Influence of Single-Site Mutations in the Central Cross-β Region of Amyloid β (1–40) Peptides

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1848
Author(s):  
Jacob Fritzsch ◽  
Alexander Korn ◽  
Dayana Surendran ◽  
Martin Krueger ◽  
Holger A. Scheidt ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Β ◽  
Neuronal Cell ◽  
Cell Toxicity ◽  
X Ray Diffraction ◽  
Hydrophobic Contact ◽  
Aβ Peptides ◽  
Tht Fluorescence ◽  
Modified Peptides ◽  
Aβ Fibrils

Amyloid β (Aβ) is a peptide known to form amyloid fibrils in the brain of patients suffering from Alzheimer’s disease. A complete mechanistic understanding how Aβ peptides form neurotoxic assemblies and how they kill neurons has not yet been achieved. Previous analysis of various Aβ40 mutants could reveal the significant importance of the hydrophobic contact between the residues Phe19 and Leu34 for cell toxicity. For some mutations at Phe19, toxicity was completely abolished. In the current study, we assessed if perturbations introduced by mutations in the direct proximity of the Phe19/Leu34 contact would have similar relevance for the fibrillation kinetics, structure, dynamics and toxicity of the Aβ assemblies. To this end, we rationally modified positions Phe20 or Gly33. A small library of Aβ40 peptides with Phe20 mutated to Lys, Tyr or the non-proteinogenic cyclohexylalanine (Cha) or Gly33 mutated to Ala was synthesized. We used electron microscopy, circular dichroism, X-ray diffraction, solid-state NMR spectroscopy, ThT fluorescence and MTT cell toxicity assays to comprehensively investigate the physicochemical properties of the Aβ fibrils formed by the modified peptides as well as toxicity to a neuronal cell line. Single mutations of either Phe20 or Gly33 led to relatively drastic alterations in the Aβ fibrillation kinetics but left the global, as well as the local structure, of the fibrils largely unchanged. Furthermore, the introduced perturbations caused a severe decrease or loss of cell toxicity compared to wildtype Aβ40. We suggest that perturbations at position Phe20 and Gly33 affect the fibrillation pathway of Aβ40 and, thereby, influence the especially toxic oligomeric species manifesting so that the region around the Phe19/Leu34 hydrophobic contact provides a promising site for the design of small molecules interfering with the Aβ fibrillation pathway.

scholarly journals Identification and in silico characterization of hemocyanin γ-type subunit protein in Vibrio harveyi infected freshwater prawn, Macrobrachium rosenbergii

2021 ◽  
Vol 42 (1) ◽  
pp. 14-23
Author(s):  
B.B. Patnaik ◽  
◽  
S. Baliarsingh ◽  
S. Sahoo ◽  
J.M. Chung ◽  
...  
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Vibrio Harveyi ◽  
Macrobrachium Rosenbergii ◽  
Full Length ◽  
Freshwater Prawn ◽  
Amino Acid Residues ◽  
Subunit Protein ◽  
In Silico Tools

Aim: Identification of full-length ORF of hemocyanin subunit-1 (Mr_HC_1) from the hepatopancreas transcriptome of freshwater prawn, Macrobrachium rosenbergii infected with Vibrio harveyi and characterization of its sequence and structure by in silico tools and softwares. Methodology: Illumina HiSeq and de novo assembled unigenes were scanned against PANM-DB to screen Mr_HC_1. FGENESH gene prediction and SMART programs were used to predict the ORF region. Subsequently, Clustal X2 and MEGA in-silico tools were used to understand the sequence relatedness and evolutionary status of Mr_HC_1. Structural prediction was performed by SWISS-MODEL and Ramachandran plot modeling programs Results: The full-length ORF was 1983 bp in length encoding a polypeptide of 661 amino acid residues. Mr_HC_1 showed a putative signal peptide of 21 amino acid residues at the N-terminus and three hemocyanin domains. Homology analysis of Mr_HC_1 amino acid sequence confirms maximum identity to M. nipponense hemocyanin subunit-1 (Mn_HC_1). Phylogenetic analysis showed that Mr_HC_1 is more closely related to the hemocyanin γ-type subunit of freshwater shrimps. Homology modeling of Mr_HC_1 showed homo-hexameric protein containing 12 copper ions. With a QMEAN score of -3.33 and model-template sequence identity of 59.15%, the predicted model of Mr_HC_1 is convincing Interpretation: This study characterizes the hemocyanin γ-type subunit protein of freshwater prawn, M. rosenbergii for future studies on host defense mechanisms.

Protein truncation is required for the activation of the c-myb proto-oncogene

1991 ◽  
Vol 11 (8) ◽  
pp. 3987-3996
Author(s):  
F A Grässer ◽  
T Graf ◽  
J S Lipsick
Keyword(s):  
Amino Acid ◽  
Bone Marrow Cells ◽  
Protein Product ◽  
Full Length ◽  
Carboxyl Terminus ◽  
Amino Acid Substitutions ◽  
Amino Acid Residues ◽  
Avian Myeloblastosis Virus ◽  
Virally Encoded ◽  
Myb Proteins

The protein product of the v-myb oncogene of avian myeloblastosis virus, v-Myb, differs from its normal cellular counterpart, c-Myb, by (i) expression under the control of a strong viral long terminal repeat, (ii) truncation of both its amino and carboxyl termini, (iii) replacement of these termini by virally encoded residues, and (iv) substitution of 11 amino acid residues. We had previously shown that neither the virally encoded termini nor the amino acid substitutions are required for transformation by v-Myb. We have now constructed avian retroviruses that express full-length or singly truncated forms of c-Myb and have tested them for the transformation of chicken bone marrow cells. We conclude that truncation of either the amino or carboxyl terminus of c-Myb is sufficient for transformation. In contrast, the overexpression of full-length c-Myb does not result in transformation. We have also shown that the amino acid substitutions of v-Myb by themselves are not sufficient for the activation of c-Myb. Rather, the presence of either the normal amino or carboxyl terminus of c-Myb can suppress transformation when fused to v-Myb. Cells transformed by c-Myb proteins truncated at either their amino or carboxyl terminus appear to be granulated promyelocytes that express the Mim-1 protein. Cells transformed by a doubly truncated c-Myb protein are not granulated but do express the Mim-1 protein, in contrast to monoblasts transformed by v-Myb that neither contain granules nor express Mim-1. These results suggest that various alterations of c-Myb itself may determine the lineage of differentiating hematopoietic cells.

scholarly journals A cellular complex of BACE1 and γ-secretase sequentially generates Aβ from its full-length precursor

2019 ◽  
Vol 218 (2) ◽  
pp. 644-663 ◽  
Author(s):  
Lei Liu ◽  
Li Ding ◽  
Matteo Rovere ◽  
Michael S. Wolfe ◽  
Dennis J. Selkoe
Keyword(s):  
Molecular Weight ◽  
Cultured Cells ◽  
Amyloid Β ◽  
Full Length ◽  
Aβ Peptides ◽  
Whole Cells ◽  
Sequential Processing ◽  
Catalytically Active ◽  
Cellular Complex

Intramembrane proteolysis of transmembrane substrates by the presenilin–γ-secretase complex is preceded and regulated by shedding of the substrate’s ectodomain by α- or β-secretase. We asked whether β- and γ-secretases interact to mediate efficient sequential processing of APP, generating the amyloid β (Aβ) peptides that initiate Alzheimer’s disease. We describe a hitherto unrecognized multiprotease complex containing active β- and γ-secretases. BACE1 coimmunoprecipitated and cofractionated with γ-secretase in cultured cells and in mouse and human brain. An endogenous high molecular weight (HMW) complex (∼5 MD) containing β- and γ-secretases and holo-APP was catalytically active in vitro and generated a full array of Aβ peptides, with physiological Aβ42/40 ratios. The isolated complex responded properly to γ-secretase modulators. Alzheimer’s-causing mutations in presenilin altered the Aβ42/40 peptide ratio generated by the HMW β/γ-secretase complex indistinguishably from that observed in whole cells. Thus, Aβ is generated from holo-APP by a BACE1–γ-secretase complex that provides sequential, efficient RIP processing of full-length substrates to final products.

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