Site-Specific Backbone and Side-Chain Contributions to Thermodynamic Stabilizing Forces of the WW Domain

2021 ◽  
Author(s):  
Myung Keun Cho ◽  
Song-Ho Chong ◽  
Seokmin Shin ◽  
Sihyun Ham
Keyword(s):  
Side Chain ◽  
Site Specific ◽  
Ww Domain

scholarly journals Glycosylation of CD44 is implicated in CD44-mediated cell adhesion to hyaluronan.

1996 ◽  
Vol 132 (6) ◽  
pp. 1199-1208 ◽  
Author(s):  
A Bartolazzi ◽  
A Nocks ◽  
A Aruffo ◽  
F Spring ◽  
I Stamenkovic
Keyword(s):  
Cell Adhesion ◽  
Regulatory Mechanism ◽  
Cell Attachment ◽  
Glycosylation Site ◽  
Side Chain ◽  
Site Specific ◽  
Coated Substrate ◽  
Glycosylation Sites ◽  
Coated Surfaces

CD44-mediated cell adhesion to hyaluronate is controlled by mechanisms which are poorly understood. In the present work we examine the role of N-linked glycosylation and Ser-Gly motifs in regulating CD44-hyaluronate interaction. Our results show that treatment of a panel of human cell lines which constitutively express CD44 with the inhibitor of N-linked glycosylation tunicamycin results in the loss of attachment of these cells to hyaluronate-coated substrate. In contrast, treatment of the same cells with deoxymannojirimycin, which inhibits the conversion of high mannose oligosaccharides to complex N-linked carbohydrates, results in either no change or an increase in CD44-mediated adhesion to hyaluronate, suggesting that complex N-linked oligosaccharides may not be required for and may even inhibit CD44-HA interaction. Using human melanoma cells stably transfected with CD44 N-linked glycosylation site-specific mutants, we show that integrity of five potential N-linked glycosylation sites within the hyaluronate recognition domain of CD44 is critical for hyaluronate binding. Mutation of any one of these potential N-linked glycosylation sites abrogates CD44-mediated melanoma cell attachment to hyaluronate-coated surfaces, suggesting that all five sites are necessary to maintain the HA-recognition domain in the appropriate conformation. We also demonstrate that mutation of serine residues which constitute the four Ser-Gly motifs in the membrane proximal domain, and provide potential sites for glycosaminoglycan side chain attachment, impairs hyaluronate binding. Taken together, these observations indicate that changes in glycosylation of CD44 can have profound effects on its interaction with hyaluronic acid and suggest that glycosylation may provide an important regulatory mechanism of CD44 function.

Impact of Site-Specific PEGylation on the Conformational Stability and Folding Rate of the Pin WW Domain Depends Strongly on PEG Oligomer Length

2013 ◽  
Vol 24 (5) ◽  
pp. 796-802 ◽  
Author(s):  
Brijesh K. Pandey ◽  
Mason S. Smith ◽  
Chad Torgerson ◽  
Paul B. Lawrence ◽  
Sam S. Matthews ◽  
...  
Keyword(s):  
Conformational Stability ◽  
Folding Rate ◽  
Site Specific ◽  
Ww Domain

scholarly journals Infrared spectrum of the cold ortho-fluorinated protonated neurotransmitter 2-phenylethylamine: competition between NH+⋯π and NH+⋯F interactions

2016 ◽  
Vol 18 (38) ◽  
pp. 26980-26989 ◽  
Author(s):  
Markus Schütz ◽  
Aude Bouchet ◽  
Otto Dopfer
Keyword(s):  
Infrared Spectrum ◽  
Ir Spectra ◽  
Side Chain ◽  
Rare Gas ◽  
Site Specific

IR spectra of cold rare-gas tagged ions reveal the switch of the preferred conformation of the highly flexible side chain of a prototypical protonated neurotransmitter induced by site-specific aromatic fluorination.

scholarly journals Site-specific 19 F NMR chemical shift and side chain relaxation analysis of a membrane protein labeled with an unnatural amino acid

2010 ◽  
Vol 20 (1) ◽  
pp. 224-228 ◽  
Author(s):  
Pan Shi ◽  
Hu Wang ◽  
Zhaoyong Xi ◽  
Chaowei Shi ◽  
Ying Xiong ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chemical Shift ◽  
Membrane Protein ◽  
Unnatural Amino Acid ◽  
Side Chain ◽  
Nmr Chemical Shift ◽  
Site Specific ◽  
Relaxation Analysis ◽  
19 F Nmr

scholarly journals Too packed to change: site-specific substitution rates and side-chain packing in protein evolution

2014 ◽  
Author(s):  
María Laura Marcos ◽  
Julian Echave
Keyword(s):  
Protein Evolution ◽  
Packing Density ◽  
Main Chain ◽  
Side Chain ◽  
Side Chains ◽  
Contact Density ◽  
Chain Packing ◽  
Site Specific ◽  
Stress Theory ◽  
Side Chain Packing

In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates is packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN), the sum of inverse square distances between the site’s Cαand the other Cαs . According to a mechanistic stress model proposed recently, rates are determined by packing because mutating packed sites stresses and destabilizes the protein’s active conformation. While WCN is a measure of Cαpacking, mutations replace side chains, which prompted us to consider whether a site’s evolutionary divergence is constrained by main-chain packing or side-chain packing. To address this issue, we extended the stress theory to model side chains explicitly. The theory predicts that rates should depend solely on side-chain packing. We tested these predictions on a data set of structurally and functionally diverse monomeric enzymes. We found that, on average, side-chain contact density (WCNρ) explains 39.1% of among-sites rate variation, larger than main-chain contact density (WCNα) which explains 32.1%. More importantly, the independent contribution of WCNαis only 0.7%. Thus, as predicted by the stress theory, site-specific evolutionary rates are determined by side-chain packing.

scholarly journals Crystal structure of phytochromobilin synthase in complex with biliverdin IXα, a key enzyme in the biosynthesis of phytochrome

2019 ◽  
Vol 295 (3) ◽  
pp. 771-782
Author(s):  
Masakazu Sugishima ◽  
Kei Wada ◽  
Keiichi Fukuyama ◽  
Ken Yamamoto
Keyword(s):  
Crystal Structure ◽  
Red Light ◽  
Binding Pocket ◽  
Side Chain ◽  
Release Mechanism ◽  
Salt Bridges ◽  
Enzymatic Assays ◽  
Site Specific ◽  
Terminal Loop ◽  
Key Enzyme

Phytochromobilin (PΦB) is a red/far-red light sensory pigment in plant phytochrome. PΦB synthase is a ferredoxin-dependent bilin reductase (FDBR) that catalyzes the site-specific reduction of bilins, which are sensory and photosynthesis pigments, and produces PΦB from biliverdin, a heme-derived linear tetrapyrrole pigment. Here, we determined the crystal structure of tomato PΦB synthase in complex with biliverdin at 1.95 Å resolution. The overall structure of tomato PΦB synthase was similar to those of other FDBRs, except for the addition of a long C-terminal loop and short helices. The structure further revealed that the C-terminal loop is part of the biliverdin-binding pocket and that two basic residues in the C-terminal loop form salt bridges with the propionate groups of biliverdin. This suggested that the C-terminal loop is involved in the interaction with ferredoxin and biliverdin. The configuration of biliverdin bound to tomato PΦB synthase differed from that of biliverdin bound to other FDBRs, and its orientation in PΦB synthase was inverted relative to its orientation in the other FDBRs. Structural and enzymatic analyses disclosed that two aspartic acid residues, Asp-123 and Asp-263, form hydrogen bonds with water molecules and are essential for the site-specific A-ring reduction of biliverdin. On the basis of these observations and enzymatic assays with a V121A PΦB synthase variant, we propose the following mechanistic product release mechanism: PΦB synthase-catalyzed stereospecific reduction produces 2(R)-PΦB, which when bound to PΦB synthase collides with the side chain of Val-121, releasing 2(R)-PΦB from the synthase.

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