Role of the Propionic Side Chains for the Photoconversion of Bacterial Phytochromes

Biochemistry ◽  
2019 ◽  
Vol 58 (33) ◽  
pp. 3504-3519 ◽  
Author(s):  
Maria Fernandez Lopez ◽  
Anh Duc Nguyen ◽  
Francisco Velazquez Escobar ◽  
Ronald González ◽  
Norbert Michael ◽  
...  
Keyword(s):  
Side Chains ◽  
Bacterial Phytochromes

Heparan sulfate side chains have a critical role in the inhibitory effects of perlecan on vascular smooth muscle cell response to arterial injury

2014 ◽  
Vol 307 (3) ◽  
pp. H337-H345 ◽  
Author(s):  
Lara Gotha ◽  
Sang Yup Lim ◽  
Azriel B. Osherov ◽  
Rafael Wolff ◽  
Beiping Qiang ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Critical Role ◽  
Arterial Injury ◽  
Side Chains ◽  
Wild Type ◽  
Injury Response ◽  
Migratory Response

Perlecan is a proteoglycan composed of a 470-kDa core protein linked to three heparan sulfate (HS) glycosaminoglycan chains. The intact proteoglycan inhibits the smooth muscle cell (SMC) response to vascular injury. Hspg2Δ3/Δ3 (MΔ3/Δ3) mice produce a mutant perlecan lacking the HS side chains. The objective of this study was to determine differences between these two types of perlecan in modifying SMC activities to the arterial injury response, in order to define the specific role of the HS side chains. In vitro proliferative and migratory activities were compared in SMC isolated from MΔ3/Δ3 and wild-type mice. Proliferation of MΔ3/Δ3 SMC was 1.5× greater than in wild type ( P < 0.001), increased by addition of growth factors, and showed a 42% greater migratory response than wild-type cells to PDGF-BB ( P < 0.001). In MΔ3/Δ3 SMC adhesion to fibronectin, and collagen types I and IV was significantly greater than wild type. Addition of DRL-12582, an inducer of perlecan expression, decreased proliferation and migratory response to PDGF-BB stimulation in wild-type SMC compared with MΔ3/Δ3. In an in vivo carotid artery wire injury model, the medial thickness, medial area/lumen ratio, and macrophage infiltration were significantly increased in the MΔ3/Δ3 mice, indicating a prominent role of the HS side chain in limiting vascular injury response. Mutant perlecan that lacks HS side chains had a marked reduction in the inhibition of in vitro SMC function and the in vivo arterial response to injury, indicating the critical role of HS side chains in perlecan function in the vessel wall.

Electronic Transport via Homopeptides: The Role of Side Chains and Secondary Structure

2015 ◽  
Vol 137 (30) ◽  
pp. 9617-9626 ◽  
Author(s):  
Lior Sepunaru ◽  
Sivan Refaely-Abramson ◽  
Robert Lovrinčić ◽  
Yulian Gavrilov ◽  
Piyush Agrawal ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Electronic Transport ◽  
Side Chains

scholarly journals Uncovering the Role of Key Active Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalysed by Wild-Type and Variants of Triosephosphate Isomerase

2019 ◽  
Author(s):  
Yashraj S. Kulkarni ◽  
Tina L. Amyes ◽  
John Richard ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Active Site ◽  
Triosephosphate Isomerase ◽  
Valence Bond ◽  
Side Chains ◽  
Wild Type ◽  
Empirical Valence Bond

Manuscript and supporting information outlining an analysis of an extended Brønsted relationship obtained from empirical valence bond simulations of substrate deprotonation catalyzed by wild-type and mutant variants of triosephosphate isomerase.

scholarly journals Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics

2021 ◽  
Author(s):  
Pär Söderhjelm ◽  
Mandar Kulkarni
Keyword(s):  
Free Energy ◽  
Trypsin Inhibitor ◽  
Side Chain ◽  
Side Chains ◽  
Aromatic Residues ◽  
Basic Pancreatic Trypsin Inhibitor ◽  
Pancreatic Trypsin Inhibitor ◽  
Energy Surfaces ◽  
Aromatic Side Chains

Aromatic side-chains (phenylalanine and tyrosine) of a protein flip by 180° around the Cβ-Cγ axis (χ2 dihedral of side-chain) producing two symmetry-equivalent states. The ring-flip dynamics act as an NMR probe to understand local conformational fluctuations. Ring-flips are categorized as slow (ms onwards) or fast (ns to near ms) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to discriminate between slow and fast ring-flips for eight individual aromatic side-chains (F4, Y10, Y21, F22, Y23, F33, Y35, F45) of basic pancreatic trypsin inhibitor (BPTI). Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues. The results indicate that χ2 as a standalone collective variable (CV) is not sufficient to classify fast and slow ring-flips. Most of the residues needed χ1 (N−Cχα) as a complementary CV, indicating the importance of librational motions in ring-flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events are observed for residues F22 and F33, indicating a possible role of friction effects in the ring-flipping. The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.

Copper(II) coordination properties of GxG peptides: Key role of side chains of central residues on coordination of formed systems; combined potentiometric and ITC studies

2019 ◽  
Vol 128 ◽  
pp. 336-343
Author(s):  
Joanna Makowska ◽  
Dariusz Wyrzykowski ◽  
Bogusław Pilarski ◽  
Damian Neubauer ◽  
Elżbieta Kamysz ◽  
...  
Keyword(s):  
Side Chains ◽  
Coordination Properties

scholarly journals Poly(phenylene methylene)-Based Coatings for Corrosion Protection: Replacement of Additives by Use of Copolymers

2019 ◽  
Vol 9 (17) ◽  
pp. 3551 ◽  
Author(s):  
D’Elia ◽  
Magni ◽  
Trasatti ◽  
Schweizer ◽  
Niederberger ◽  
...  
Keyword(s):  
Corrosion Protection ◽  
Electrochemical Corrosion ◽  
Side Chains ◽  
Hydrophobic Coating ◽  
Corrosion Studies ◽  
Proper Design ◽  
Common Problems ◽  
Hydrocarbon Polymer ◽  
Protection Of The Metal

Poly(phenylene methylene) (PPM) is a thermally stable, hydrophobic, fluorescent hydrocarbon polymer. Recently, blended PPM has been proposed as a valuable anti-corrosion coating material, and, in particular, rheological additives such as external plasticizers resulted crucial to prevent crack formation. Accordingly, to avoid common problems related to the use of external plasticizers, the development of PPM-related copolymer-based coatings containing n-octyloxy side chains and their anti-corrosion behavior were explored in this study. The aluminum alloy AA2024, widely employed for corrosion studies, was selected as a substrate, covered with a thin layer of a polybenzylsiloxane in order to improve adhesion between the underlying hydrophilic substrate and the top hydrophobic coating. Gratifyingly, coatings with those copolymers were free of bubbles and cracks. The n-octyloxy side-chains may be regarded to adopt the role of a bound plasticizer, as the glass transition temperature of the copolymers decreases with increasing content of alkoxy side-chains. Electrochemical corrosion tests on PPM-substituted coatings exhibited good corrosion protection of the metal surface towards a naturally aerated near-neutrally 3.5% wt.% NaCl neutral solution, providing comparable results to blended PPM formulations, previously reported. Hence, the application of rheological additives can be avoided by use of proper design copolymers.

Structure-activity studies of dermorphin. The role of side chains of amino acid residues on the biological activity of dermorphin

Peptides ◽  
1984 ◽  
Vol 5 (4) ◽  
pp. 687-689 ◽  
Author(s):  
Krzysztof Darłak ◽  
Zbigniew Grzonka ◽  
Pawel Krzaścik ◽  
Piotr Janicki ◽  
S.Witold Gumułka
Keyword(s):  
Biological Activity ◽  
Amino Acid ◽  
Side Chains ◽  
Amino Acid Residues ◽  
Structure Activity

Self-assembled structures formed by a wedge-shaped molecule in 2D and 3D: the role of flexible side chains and polar head groups

2010 ◽  
Vol 12 (7) ◽  
pp. 1444-1452 ◽  
Author(s):  
Xiaomin Zhu ◽  
Ahmed Mourran ◽  
Uwe Beginn ◽  
Martin Möller ◽  
Denis V. Anokhin ◽  
...  
Keyword(s):  
Side Chains ◽  
Polar Head ◽  
Head Groups ◽  
Self Assembled ◽  
2D And 3D

A study of the role of histidine side-chains at the active centre of amylolytic enzymes

1980 ◽  
Vol 81 (1) ◽  
pp. 145-156 ◽  
Author(s):  
Ágoston Hoschke ◽  
Elemér László ◽  
János Holló
Keyword(s):  
Side Chains ◽  
Active Centre ◽  
Amylolytic Enzymes
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