scholarly journals Unspecific binding but specific disruption of the group I intron by the StpA chaperone

2019 ◽  
Author(s):  
Vladimir Reinharz ◽  
Tsvi Tlusty
Keyword(s):  
Amino Acids ◽  
Specific Binding ◽  
Group I Intron ◽  
Disordered Proteins ◽  
Strongly Coupled ◽  
Transient Nature ◽  
Entire Structure ◽  
Group I ◽  
Unspecific Binding ◽  
Direct Coupling Analysis

Chaperone proteins — the most disordered among all protein groups — help RNAs fold into their functional structure by destabilizing misfolded configurations or stabilizing the functional ones. But disentangling the mechanism underlying RNA chaperoning is challenging, mostly due to inherent disorder of the chaperones and the transient nature of their interactions with RNA. In particular, it is unclear how specific the interactions are and what role is played by amino acid charge and polarity patterns. Here, we address these questions in the RNA chaperone StpA. By adapting direct coupling analysis (DCA) to treat in tandem sequences written in two alphabets, nucleotides and amino acids, we could analyze StpA-RNA interactions and identify a two-pronged mechanism: StpA disrupts specific positions in the group I intron while globally and loosely binding to the entire structure. Moreover, the interaction is governed by the charge pattern: negatively charged regions in the destabilizing StpA N-terminal affect a few specific positions in the RNA, located in stems and in the pseudoknot. In contrast, positive regions in the C-terminal contain strongly coupled amino acids that promote non-specific or weakly-specific binding to the RNA. The present study opens new avenues to examine the functions of disordered proteins and to design disruptive proteins based on their charge patterns.

scholarly journals Epitope Mapping of Monoclonal Antibodies to Calreticulin Reveals That Charged Amino Acids Are Essential for Antibody Binding

Antibodies ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 31
Author(s):  
Ann Christina Bergmann ◽  
Cecilie Kyllesbech ◽  
Rimantas Slibinskas ◽  
Evaldas Ciplys ◽  
Peter Højrup ◽  
...  
Keyword(s):  
Amino Acids ◽  
Monoclonal Antibodies ◽  
Epitope Mapping ◽  
Biological Function ◽  
Specific Binding ◽  
Enzyme Linked Immunosorbent Assay ◽  
Potential Therapeutic Target ◽  
Charged Amino Acids ◽  
Chaperone Protein ◽  
Terminal Amino

Calreticulin is a chaperone protein, which is associated with myeloproliferative diseases. In this study, we used resin-bound peptides to characterize two monoclonal antibodies (mAbs) directed to calreticulin, mAb FMC 75 and mAb 16, which both have significantly contributed to understanding the biological function of calreticulin. The antigenicity of the resin-bound peptides was determined by modified enzyme-linked immunosorbent assay. Specific binding was determined to an 8-mer epitope located in the N-terminal (amino acids 34–41) and to a 12-mer peptide located in the C-terminal (amino acids 362–373). Using truncated peptides, the epitopes were identified as TSRWIESK and DEEQRLKEEED for mAb FMC 75 and mAb 16, respectively, where, especially the charged amino acids, were found to have a central role for a stable binding. Further studies indicated that the epitope of mAb FMC 75 is assessable in the oligomeric structure of calreticulin, making this epitope a potential therapeutic target.

scholarly journals Monoclonal antibody studies of creatine kinase. The ART epitope: evidence for an intermediate in protein folding

1989 ◽  
Vol 257 (2) ◽  
pp. 461-469 ◽  
Author(s):  
G E Morris
Keyword(s):  
Amino Acids ◽  
Monoclonal Antibody ◽  
Creatine Kinase ◽  
Specific Binding ◽  
Trypsin Digestion ◽  
Proteinase K ◽  
Enzyme Linked Immunosorbent Assay ◽  
Muscle Creatine Kinase ◽  
Western Blots ◽  
Methionine Residues

Chemical cleavage at cysteine residues with nitrothiocyanobenzoic acid shows that the last 98 amino acids of the 380-amino-acid sequence of chick muscle creatine kinase are sufficient for binding of the monoclonal antibody CK-ART. Removal of the last 30 amino acids by cleavage at methionine residues with CNBr results in loss of CK-ART binding. CK-ART binding is also lost when these C-terminal methionine residues are oxidized to sulphoxide, but binding is regained on reduction. Proteinase K ‘nicks’ native CK at a single site near the C-terminus and two fragments of 327 amino acides and 53 amino acids can be separated by subsequent SDS or urea treatment. CK-ART still binds normally to ‘nicked’ CK, which is enzymically inactive. After treatment with either urea (in a competition enzyme-linked immunosorbent assay) or SDS (on Western blots), however, CK-ART binds to neither of the two fragments, although these treatments do not affect binding to intact CK. This suggests that parts of both CK fragments contribute to the CK-ART epitope. CK-ART is both species- and isoenzyme-specific, binding only to chick M-CK. The only C-terminal regions containing chick-specific sequences are residues 300-312 and residues 368-371, the latter group being close to the essential methionine residues. We suggest that one, or possibly both, of these regions is involved in forming the conformational epitope on the surface of the CK molecule which CK-ART recognizes. Native CK is resistant to trypsin digestion. The C-terminal half of urea-treated and partly-refolded CK is also resistant to trypsin digestion, whereas the N-terminal half is readily digested. The results suggest a C-terminal region which can refold more rapidly than the rest of the CK molecule and provide evidence for an intermediate in CK refolding.

scholarly journals Lead cleavage sites in the core structure of group I intron-RNA

1993 ◽  
Vol 21 (2) ◽  
pp. 311-317 ◽  
Author(s):  
Barbara Striecjer ◽  
Uwe von Ahsen ◽  
Renée Schroeder
Keyword(s):  
Group I Intron ◽  
Core Structure ◽  
Cleavage Sites ◽  
The Core ◽  
Group I

An exceptional group-I intron-like insertion in the SSU rDNA of lichen mycobionts

1999 ◽  
Vol 35 (5) ◽  
pp. 536-541 ◽  
Author(s):  
M. Grube ◽  
B. Gutmann ◽  
U. Arup ◽  
A. de los Rios ◽  
J.-E. Mattsson ◽  
...  
Keyword(s):  
Group I Intron ◽  
Ssu Rdna ◽  
Exceptional Group ◽  
Group I

scholarly journals Activation of the catalytic core of a group I intron by a remote 3' splice junction.

1992 ◽  
Vol 6 (8) ◽  
pp. 1373-1385 ◽  
Author(s):  
F Michel ◽  
L Jaeger ◽  
E Westhof ◽  
R Kuras ◽  
F Tihy ◽  
...  
Keyword(s):  
Group I Intron ◽  
Splice Junction ◽  
Catalytic Core ◽  
Group I

Role of insulin and branched-chain amino acids in regulating protein metabolism during fasting

1990 ◽  
Vol 258 (6) ◽  
pp. E907-E917 ◽  
Author(s):  
M. Frexes-Steed ◽  
M. L. Warner ◽  
N. Bulus ◽  
P. Flakoll ◽  
N. N. Abumrad
Keyword(s):  
Amino Acids ◽  
Protein Metabolism ◽  
Insulin Dose ◽  
Group Iii ◽  
Group I ◽  
Tissue Sensitivity ◽  
Branched Chain ◽  
Independent Effects ◽  
Dose Dependent

This study examines the independent effects of insulin and amino acids on protein metabolism after a 12-h and 4-day fast in healthy volunteers. Leucine (Leu) kinetics were examined during sequential insulin infusions of 0 (group I) or 0.0125 (groups II and III), 1.2, and 10 mU.kg-1.min-1. Plasma Leu was maintained at 12-h fasted levels in groups I and II and at 84-h fasted levels in group III. Four-day fast (vs. 1 day, P less than 0.01) was associated with a 79% drop in plasma insulin and elevations in plasma Leu (122%), Leu rates of appearance (Ra) (21%), and Leu oxidation (56%), and no change in nonoxidative rates of disappearance (Rd). Insulin resulted in a dose-dependent suppression of endogenous Leu Ra with group III = I greater than II. Leu oxidation rose 1.7-fold in group III at the highest insulin dose but remained stable in the two other groups. In conclusion, 4-day fasting is associated with enhanced proteolysis and Leu oxidation with no change in nonoxidative Rd (protein synthesis). Elevated branched-chain (and other) amino acids were required to restore tissue sensitivity and specificity to the effects of insulin on protein metabolism after 4 days of fasting.

Effect of hyperinsulinemia and hyperaminoacidemia on muscle and liver protein synthesis in lactating goats

1994 ◽  
Vol 267 (6) ◽  
pp. E877-E885 ◽  
Author(s):  
I. Tauveron ◽  
D. Larbaud ◽  
C. Champredon ◽  
E. Debras ◽  
S. Tesseraud ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Amino Acid ◽  
Skeletal Muscles ◽  
Constant Infusion ◽  
Acid Mixture ◽  
Liver Protein ◽  
Group I ◽  
Lactating Goats ◽  
Group A

The experiment was carried out to clarify the roles of insulin and amino acids on protein synthesis in fed lactating goats (30 days postpartum). Protein synthesis in the liver and various skeletal muscles was assessed after an intravenous injection of a large dose of unlabeled valine containing a tracer dose of L-[2,3,4-3H]valine. The animals were divided into three groups. Group I was infused with insulin (1.7 mumol/min) for 2.5 h under glucose, potassium, and amino acid replacement. Group A was infused with an amino acid mixture to create stable hyperaminoacidemia for 2.5 h. Group C animals were controls. The fractional synthesis rates (FSR) were 31.5 +/- 2.2, 6.5 +/- 0.4, 4.3 +/- 0.8, 4.0 +/- 1.2, 3.9 +/- 1.2, and 3.6 +/- 0.4%/day (SD) in liver, masseter, diaphragm, anconeus, semitendinosus, and longissimus dorsi, respectively, for group C. Neither hyperinsulinemia in group I nor hyperaminoacidemia in group A had not affected by hyperinsulinemia but was stimulated by hyperaminoacidemia (+30%, P < 0.05). In contrast to previous experiments in which a labeled amino acid was constantly infused, this study revealed a stimulating effect of amino acids on protein synthesis in the liver but not in skeletal muscles. As previously observed in studies with the constant-infusion method, insulin had no effect on protein synthesis.

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