The rod-shaped conformation of Starmaker

Kapłon, Tomasz; Michnik, Anna; Drzazga, Z.; Richter, Klaus; Kochman, Marian; Ożyhar, Andrzej

doi:10.1016/j.bbapap.2009.07.010

Cited by 19 publications

(27 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…There have been numerous reports of disordered proteins undergoing a conformational transition upon binding of a metal ligand [37, 55, 107, 108]. Due to the numerous charged residues in the sequence of PGR, as well as the well-defined role of Zn 2+ in the function of the Aap B-repeat superdomain [15, 18], we were interested in testing biologically relevant, divalent metal ions as potential ligands.…”

Section: Resultsmentioning

confidence: 99%

The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction

Yarawsky

English

Whitten

et al. 2017

Journal of Molecular Biology

View full text Add to dashboard Cite

Staphylococcus epidermidis is one of the primary bacterial species responsible for healthcare-associated infections. The most significant virulence factor for S. epidermidis is its ability to form a biofilm, which renders the bacteria highly resistant to host immune responses and antibiotic action. Intercellular adhesion within the biofilm is mediated by the accumulation-associated protein (Aap), a cell wall-anchored protein that self-assembles in a zinc-dependent manner. The C-terminal portion of Aap contains a proline/glycine-rich, 135 amino acid-long region that has not yet been characterized. The region contains a set of 18 nearly identical AEPGKP repeats. Analysis of the proline/glycine-rich region (PGR) using biophysical techniques demonstrated the region is a highly extended, intrinsically disordered polypeptide (IDP) with unusually high polyproline type II helix (PPII) propensity. In contrast to many IDPs, there was a minimal temperature dependence of the global conformational state of PGR in solution as measured by analytical ultracentrifugation and dynamic light scattering. Furthermore, PGR was resistant to conformational collapse or α-helix formation upon addition of the osmolyte TMAO or the cosolvent TFE. Collectively, these results suggest PGR functions as a resilient, extended stalk that projects the rest of Aap outward from the bacterial cell wall, promoting intercellular adhesion between cells in the biofilm. This work sheds light on regions of low complexity often found near the attachment point of bacterial cell wall-anchored proteins.

show abstract

Section: Resultsmentioning

confidence: 99%

The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction

Yarawsky

English

Whitten

et al. 2017

Journal of Molecular Biology

View full text Add to dashboard Cite

show abstract

“…For larger proteins, collapse upon denaturant dilution has been observed in time-resolved SAXS experiments, but in those cases the presence of stable folding intermediates modulating the observed R g cannot be excluded 26–28 . In contrast, FRET 11,29–35 and PET 34,36 data show an increase in the average distance between labeled sites with denaturant, and NMR 20 , DLS 15,37 , 1- and 2f-FCS 38–40 , as well as analytical size exclusion chromatography studies 41 provide evidence for an increase in hydrodynamic radius ( R h ) with increasing denaturant concentration. Such an expansion would be consistent with improved solvation by the denaturant solution 33,42,43 , currently understood to be the mechanism by which denaturant destabilizes folded proteins 33 .…”

Section: Introductionmentioning

confidence: 89%

Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods

et al. 2016

View full text Add to dashboard Cite

There has been a long-standing controversy regarding the effect of chemical denaturants on the dimensions of unfolded and intrinsically disordered proteins: A wide range of experimental techniques suggest that polypeptide chains expand with increasing denaturant concentration, but several studies using small-angle X-ray scattering (SAXS) reported no such increase of the radius of gyration (Rg). This inconsistency challenges our current understanding of the mechanism of chemical denaturants, which are widely employed to investigate protein folding and stability. Here, we use a combination of single-molecule Förster resonance energy transfer (FRET), SAXS, dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) to characterize the denaturant dependence of the unfolded state of the spectrin domain R17 and the intrinsically disordered protein ACTR in two different denaturants. Standard analysis of the primary data clearly indicates an expansion of the unfolded state with increasing denaturant concentration irrespective of the protein, denaturant, or experimental method used. This is the first case in which SAXS and FRET have yielded even qualitatively consistent results regarding expansion in denaturant when applied to the same proteins. To more directly illustrate this self-consistency, we have used both SAXS and FRET data in a Bayesian procedure to refine structural ensembles representative of the observed unfolded state. This analysis demonstrates that both of these experimental probes are compatible with a common ensemble of protein configurations for each denaturant concentration. Furthermore, the resulting ensembles reproduce the trend of increasing hydrodynamic radius with denaturant concentration obtained by 2f-FCS and DLS. We were thus able to reconcile the results from all four experimental techniques quantitatively, to obtain a comprehensive structural picture of denaturant-induced unfolded state expansion, and to identify the most likely sources of earlier discrepancies.

show abstract

“…Mammals DMP1 4.0 CD, DLS, FTIR, SAXS (Gericke et al, 2010;He et al, 2003aHe et al, , 2003b DPP 2.8 CD, NMR, SAXS (Cross et al, 2005;Evans et al, 1994;Fujisawa & Kuboki, 1998;George & Hao, 2005;He et al, 2005b;Lee et al, 1977) BSP 4.1 CD, NMR, SAXS (Fisher et al, 2001;Tye et al, 2003Tye et al, , 2005Wuttke et al, 2001) OPN 4.4 CD, NMR, FTIR (Fisher et al, 2001;Gorski et al, 1995) amelogenin 6.6 CD, NMR (Buchko et al, 2010;Delak et al, 2009b;Ndao et al, 2011;Shaw et al, 2008) statherin 8.0 CD, NMR (Long et al, 2001;Naganagowda et al, 1998;Raj et al, 1992) lithostathine 5.7 CD (Gerbaud et al, 2000) Haliotis rufescens AP7 5.2 CD, NMR (Kim et al, 2004(Kim et al, , 2006aMichenfelder et al, 2003;Wustman et al, 2004) Atrina rigita Asprich 2.7-3.5 CD, NMR (Collino et al, 2006;Delak et al, 2009aDelak et al, , 2008Kim et al, 2008;Ndao et al, 2010) Procambrus clarkii CAP-1 3.9 CD (Inoue et al, 2007) Strongylocentrotus purpuratus SM50 10.8 CD, NMR (Xu & Evans, 1999;Zhang et al, 2000) PM27 8.1 CD, NMR Danio rerio Stm 4.1 CD, gel filtration (Kaplon et al, 2008(Kaplon et al, , 2009 Table 1. IDPs involved in biomineralization of calcium carbonate and phosphate for which a disordered structure has been confirmed...…”

Section: Protein Pi Methods Referencementioning

confidence: 99%

“…Interestingly, calcium ions led to a lower hydrodynamic radius, probably by decreasing electrostatic repulsion. Also, solvent-induced denaturation of Stm indicated the lack of an ordered structure in the molecule (Kaplon et al, 2008(Kaplon et al, , 2009. Recently, another homolog of Starmaker has been identified: Starmaker-like from Oryzias latipes.…”

Section: Otolith Related Idpmentioning

confidence: 99%