scholarly journals Mechanics and dynamics of B1 domain of protein G: Role of packing and surface hydrophobic residues

2008 ◽  
Vol 8 (1) ◽  
pp. 147-160 ◽  
Author(s):  
Marc A. Ceruso ◽  
Andrea Amadei ◽  
Alfredo Di Nola
Keyword(s):  
Protein G ◽  
Hydrophobic Residues ◽  
B1 Domain

scholarly journals The Role of E27-K31 and E56-K10 Salt-Bridge Pairs in the Unfolding Mechanism of the B1 Domain of Protein G

2018 ◽  
Vol 18 (1) ◽  
pp. 186
Author(s):  
Tony Ibnu Sumaryada ◽  
Kania Nur Sawitri ◽  
Setyanto Tri Wahyudi
Keyword(s):  
Tertiary Structure ◽  
Salt Bridge ◽  
Protein G ◽  
Core Collapse ◽  
Hydrophobic Core ◽  
B1 Domain ◽  
Collapse Model ◽  
Α Helix ◽  
Dynamics Simulations

Molecular dynamics simulations of the B1 fragment of protein G (56 residues) have been performed at 325, 350, 375, 400, 450 and 500 K for 10 ns. An analysis of its structural and energetic parameters has indicated that the unfolding process of the GB1 protein begins at 900 ps of a 500-K simulation. The unfolding process is initiated when hydrogen bonds in the hydrophobic core region are broken; it continues with the α-helix transformation into coils and turns and ends with the destruction of the β-hairpins. These unfolding events are consistent with the hybrid model of the protein folding/unfolding mechanism, which is a compromise between the hydrophobic core collapse model and the zipper model. Salt-bridge pairs were found to play an important role in the unfolding process by maintaining the integrity of the tertiary structure of the protein. The breaking (or disappearance) of the salt-bridge pairs E27–K31 (in the α-helix) and E56–K10 (connecting β4 and β1) has resulted in the destruction of secondary structures and indicates the beginning of the unfolding process. Our results also suggest that the unfolding process in this simulation was not a complete denaturation of the protein because some β-hairpins remained

Role of the amino acid sequence in domain swapping of the B1 domain of protein G

2008 ◽  
Vol 72 (1) ◽  
pp. 88-104 ◽  
Author(s):  
Fernanda L. Sirota ◽  
Stephanie Héry-Huynh ◽  
Sebastian Maurer-Stroh ◽  
Shoshana J. Wodak
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Domain Swapping ◽  
Protein G ◽  
B1 Domain

scholarly journals Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes

2006 ◽  
Vol 103 (32) ◽  
pp. 11904-11909 ◽  
Author(s):  
P. Selenko ◽  
Z. Serber ◽  
B. Gadea ◽  
J. Ruderman ◽  
G. Wagner
Keyword(s):  
Xenopus Laevis ◽  
Protein G ◽  
Nmr Analysis ◽  
Quantitative Nmr ◽  
B1 Domain ◽  
Egg Extracts

scholarly journals Complement assembly of two fragments of the streptococcal protein G B1 domain in aqueous solution

FEBS Letters ◽  
1995 ◽  
Vol 366 (2-3) ◽  
pp. 99-103 ◽  
Author(s):  
Naohiro Kobayashi ◽  
Shinya Honda ◽  
Hirofumi Yoshii ◽  
Hatsuho Uedaira ◽  
Eisuke Munekata
Keyword(s):  
Aqueous Solution ◽  
Protein G ◽  
B1 Domain ◽  
Streptococcal Protein G

Role of Cationic Groove and Hydrophobic Residues in Phosphatidylinositol-Dependent Membrane-Binding Properties of Tks5-Phox Homology Domain

2018 ◽  
Vol 3 (4) ◽  
pp. 1205-1214 ◽  
Author(s):  
Sukhamoy Gorai ◽  
Debasish Paul ◽  
Rituparna Borah ◽  
Nandan Haloi ◽  
Manas Kumar Santra ◽  
...  
Keyword(s):  
Membrane Binding ◽  
Binding Properties ◽  
Hydrophobic Residues ◽  
Phox Homology

scholarly journals Role of a DEF/Y motif in histone H2A-H2B recognition and nucleosome editing

2020 ◽  
Vol 117 (7) ◽  
pp. 3543-3550 ◽  
Author(s):  
Yan Huang ◽  
Lu Sun ◽  
Leonidas Pierrakeas ◽  
Linchang Dai ◽  
Lu Pan ◽  
...  
Keyword(s):  
Dna Interaction ◽  
General Strategy ◽  
Histone H2a ◽  
Hydrophobic Residues ◽  
Intrinsically Disordered ◽  
Chromatin Regulators ◽  
A Subunit

The SWR complex edits the histone composition of nucleosomes at promoters to facilitate transcription by replacing the two nucleosomal H2A-H2B (A-B) dimers with H2A.Z-H2B (Z-B) dimers. Swc5, a subunit of SWR, binds to A-B dimers, but its role in the histone replacement reaction was unclear. In this study, we showed that Swc5 uses a tandem DEF/Y motif within an intrinsically disordered region to engage the A-B dimer. A 2.37-Å X-ray crystal structure of the histone binding domain of Swc5 in complex with an A-B dimer showed that consecutive acidic residues and flanking hydrophobic residues of Swc5 form a cap over the histones, excluding histone–DNA interaction. Mutations in Swc5 DEF/Y inhibited the nucleosome editing function of SWR in vitro. Swc5 DEF/Y interacts with histones in vivo, and the extent of this interaction is dependent on the remodeling ATPase of SWR, supporting a model in which Swc5 acts as a wedge to promote A-B dimer eviction. Given that DEF/Y motifs are found in other evolutionary unrelated chromatin regulators, this work provides the molecular basis for a general strategy used repeatedly during eukaryotic evolution to mobilize histones in various genomic functions.

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