FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2035952020> ?p ?o ?g. }

• W2035952020 endingPage "2012" @default.
• W2035952020 startingPage "2011" @default.
• W2035952020 abstract "In their comment, Ainavarapu et al. argue the discrepancy in ligand-free dihydrofolate reductase (DHFR) stability between their and our study could be due to a low force cutoff of 30 pN used in our study for unfolding force histograms. The simplicity of this argument may be tempting at first sight, but does not withstand closer examination. In almost all our curves, both in the absence and in the presence of ligands, we observe unfolding of DHFR after one or two Ddfilamin domains have unfolded. Such a curve for ligand-free DHFR is shown in Fig. 1 a. Since this class of curves constitutes the vast majority of events we observe, a cutoff of 30 pN introduced to ensure reliable force and distance measurements will not influence the measured distribution. This cutoff must not be confused with the minimum force detectable in our experiments, which is determined by thermal noise. Our experimental assay allows detection of DHFR events reliably at forces above 20 pN (see the 20 pN line in Fig. 1). We can therefore readily check the potential presence of a dominant population of low-force DHFR unfolding events postulated by Ainavarapu et al. The fraction of such events where ligand-free DHFR unfolds before the filamin domains at forces <30 pN is almost negligible (<5%). One of the rare examples we find in our data is shown in Fig. 1 b, where we observe DHFR unfolding at a force of 23 pN followed by unfolding of the DHFR intermediate at 17 pN. This sample curve shows that we do have the resolution to detect such low-force events. Extremely rare observation of low-force events preceding filamin unfolding is hence in perfect agreement with a mechanically stable conformation of DHFR but not with the force distribution reported by Ainavarapu et al. Moreover, the design of our modular protein is such that in all events where at least three Ddfilamin domains, including ddFLN4, unfold we can be sure that also DHFR must have unfolded (see inset in Fig. 1). In contrast to Ainavarapu et al., we do not observe a significant fraction of events with featureless spacers preceding Ddfilamin unfolding. Taken this evidence together, we can exclude a low-force population of ligand-free mouse DHFR in our experiments. Our data hence show that in the absence of ligands, mouse DHFR can exist in a conformation mechanically equally stable than the ligand-bound forms. Interestingly, in a recent study, Wilcox et al. investigated mechanical stability of DHFR from Escherichia coli and also reported high unfolding forces for the wild-type protein in the absence of ligands (1.Wilcox A.J. Choy J. Bustamante C. Matouschek A. Effect of protein structure on mitochondrial import.Proc. Natl. Acad. Sci. USA. 2005; 102: 15435-15440Crossref PubMed Scopus (74) Google Scholar) and no change in unfolding force upon methotrexate (MTX) addition (A. Matouschek, Northwestern University, personal communication, 2006). This is in perfect agreement with our results. Even though the sequences of DHFR from E. coli and mouse differ, this comparison is relevant since in mitochondrial import experiments, addition of MTX blocks import for both DHFR variants (1.Wilcox A.J. Choy J. Bustamante C. Matouschek A. Effect of protein structure on mitochondrial import.Proc. Natl. Acad. Sci. USA. 2005; 102: 15435-15440Crossref PubMed Scopus (74) Google Scholar, 2.Eilers M. Schatz G. Binding of a specific ligand inhibits import of a purified precursor protein into mitochondria.Nature. 1986; 322: 228-232Crossref PubMed Scopus (466) Google Scholar). What could be a possible explanation for the apparent discrepancy between the two studies? It is important to note that the DHFR variants (mouse and Chinese hamster ovary) used in the two studies are homologous but not identical (sequence identity of 96%). We propose that differences in the proteins as well as in the experimental conditions (e.g., temperature) are likely explanations for the apparently different stabilities. It has been reported that DHFR, in the absence of ligands, can exist in at least two different conformations that are populated to varying degrees at different temperatures (3.Clark A.C. Frieden C. Native Escherichia coli and murine dihydrofolate reductases contain late-folding non-native structures.J. Mol. Biol. 1999; 285: 1765-1776Crossref PubMed Scopus (26) Google Scholar). We hence propose that the different results reflect a complex conformational behavior of DHFR enzymes rather than potential shortcomings of the experimental design. Further support for this interpretation comes from the consistent observation of an unfolding intermediate in mouse DHFR, which Ainavarapu et al. did not report. Exploring these differences will be an important task for the future. Mechanical stability measurements are an important contribution to understanding protein import. However, relating unfolding force measurements to import efficiencies is not simple and will require a bigger picture. Otherwise, it will be difficult to explain that the mechanically very stable domain I27 from titin (200 pN unfolding force) is readily imported into mitochondria, whereas DHFR complexed with MTX (60 pN unfolding force) blocks import (4.Okamoto K. Brinker A. Paschen S.A. Moarefi I. Hayer-Hartl M. Neupert W. Brunner M. The protein import motor of mitochondria: a targeted molecular ratchet driving unfolding and translocation.EMBO J. 2002; 21: 3659-3671Crossref PubMed Scopus (88) Google Scholar)." @default.
• W2035952020 created "2016-06-24" @default.
• W2035952020 creator A5015801201 @default.
• W2035952020 creator A5018266345 @default.
• W2035952020 creator A5046289240 @default.
• W2035952020 creator A5077832966 @default.
• W2035952020 creator A5079678964 @default.
• W2035952020 date "2006-09-01" @default.
• W2035952020 modified "2023-09-23" @default.
• W2035952020 title "Response to the Comment by Ainavarapu et al." @default.
• W2035952020 cites W1982108616 @default.
• W2035952020 cites W1994077306 @default.
• W2035952020 cites W2069074279 @default.
• W2035952020 cites W2084520521 @default.
• W2035952020 doi "https://doi.org/10.1529/biophysj.106.087486" @default.
• W2035952020 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/1544299" @default.
• W2035952020 hasPublicationYear "2006" @default.
• W2035952020 type Work @default.
• W2035952020 sameAs 2035952020 @default.
• W2035952020 citedByCount "7" @default.
• W2035952020 countsByYear W20359520202013 @default.
• W2035952020 crossrefType "journal-article" @default.
• W2035952020 hasAuthorship W2035952020A5015801201 @default.
• W2035952020 hasAuthorship W2035952020A5018266345 @default.
• W2035952020 hasAuthorship W2035952020A5046289240 @default.
• W2035952020 hasAuthorship W2035952020A5077832966 @default.
• W2035952020 hasAuthorship W2035952020A5079678964 @default.
• W2035952020 hasBestOaLocation W20359520201 @default.
• W2035952020 hasConcept C116569031 @default.
• W2035952020 hasConcept C121332964 @default.
• W2035952020 hasConcept C144024400 @default.
• W2035952020 hasConcept C149923435 @default.
• W2035952020 hasConcept C170493617 @default.
• W2035952020 hasConcept C181199279 @default.
• W2035952020 hasConcept C185592680 @default.
• W2035952020 hasConcept C2778217198 @default.
• W2035952020 hasConcept C2781320022 @default.
• W2035952020 hasConcept C2908647359 @default.
• W2035952020 hasConcept C46141821 @default.
• W2035952020 hasConcept C55493867 @default.
• W2035952020 hasConcept C62520636 @default.
• W2035952020 hasConceptScore W2035952020C116569031 @default.
• W2035952020 hasConceptScore W2035952020C121332964 @default.
• W2035952020 hasConceptScore W2035952020C144024400 @default.
• W2035952020 hasConceptScore W2035952020C149923435 @default.
• W2035952020 hasConceptScore W2035952020C170493617 @default.
• W2035952020 hasConceptScore W2035952020C181199279 @default.
• W2035952020 hasConceptScore W2035952020C185592680 @default.
• W2035952020 hasConceptScore W2035952020C2778217198 @default.
• W2035952020 hasConceptScore W2035952020C2781320022 @default.
• W2035952020 hasConceptScore W2035952020C2908647359 @default.
• W2035952020 hasConceptScore W2035952020C46141821 @default.
• W2035952020 hasConceptScore W2035952020C55493867 @default.
• W2035952020 hasConceptScore W2035952020C62520636 @default.
• W2035952020 hasIssue "5" @default.
• W2035952020 hasLocation W20359520201 @default.
• W2035952020 hasLocation W20359520202 @default.
• W2035952020 hasLocation W20359520203 @default.
• W2035952020 hasOpenAccess W2035952020 @default.
• W2035952020 hasPrimaryLocation W20359520201 @default.
• W2035952020 hasRelatedWork W1970776535 @default.
• W2035952020 hasRelatedWork W1974972246 @default.
• W2035952020 hasRelatedWork W1980377213 @default.
• W2035952020 hasRelatedWork W2028255422 @default.
• W2035952020 hasRelatedWork W2028906117 @default.
• W2035952020 hasRelatedWork W2035952020 @default.
• W2035952020 hasRelatedWork W2077632209 @default.
• W2035952020 hasRelatedWork W2091400298 @default.
• W2035952020 hasRelatedWork W2739417245 @default.
• W2035952020 hasRelatedWork W2952244581 @default.
• W2035952020 hasVolume "91" @default.
• W2035952020 isParatext "false" @default.
• W2035952020 isRetracted "false" @default.
• W2035952020 magId "2035952020" @default.
• W2035952020 workType "article" @default.