Four second-sphere residues of Thermus thermophilus SG0.5JP17-16 laccase tune the catalysis by hydrogen-bonding networks

2018 ◽  
Vol 102 (9) ◽  
pp. 4049-4061 ◽  
Author(s):  
Huiping Liu ◽  
Yanyun Zhu ◽  
Xiaorong Yang ◽  
Ying Lin
Keyword(s):  
Hydrogen Bonding ◽  
Thermus Thermophilus ◽  
Hydrogen Bonding Networks

scholarly journals Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michela Quadrini
Keyword(s):  
Hydrogen Bonding ◽  
Secondary Structure ◽  
Nucleotide Sequence ◽  
Thermus Thermophilus ◽  
Three Dimensional ◽  
Secondary Structures ◽  
Structural Effect ◽  
Biological Processes ◽  
Structural Pattern ◽  
Rna Molecules

Abstract RNA molecules play crucial roles in various biological processes. Their three-dimensional configurations determine the functions and, in turn, influences the interaction with other molecules. RNAs and their interaction structures, the so-called RNA–RNA interactions, can be abstracted in terms of secondary structures, i.e., a list of the nucleotide bases paired by hydrogen bonding within its nucleotide sequence. Each secondary structure, in turn, can be abstracted into cores and shadows. Both are determined by collapsing nucleotides and arcs properly. We formalize all of these abstractions as arc diagrams, whose arcs determine loops. A secondary structure, represented by an arc diagram, is pseudoknot-free if its arc diagram does not present any crossing among arcs otherwise, it is said pseudoknotted. In this study, we face the problem of identifying a given structural pattern into secondary structures or the associated cores or shadow of both RNAs and RNA–RNA interactions, characterized by arbitrary pseudoknots. These abstractions are mapped into a matrix, whose elements represent the relations among loops. Therefore, we face the problem of taking advantage of matrices and submatrices. The algorithms, implemented in Python, work in polynomial time. We test our approach on a set of 16S ribosomal RNAs with inhibitors of Thermus thermophilus, and we quantify the structural effect of the inhibitors.

scholarly journals The Multiple Hydrogen-Bonding Networks of Polyol Ribitol

2018 ◽  
Vol 24 (51) ◽  
pp. 13408-13412 ◽  
Author(s):  
Isabel Peña ◽  
Maria Eugenia Sanz ◽  
Elena R. Alonso ◽  
José L. Alonso
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonding Networks ◽  
Multiple Hydrogen Bonding

Small Molecule-Based Fluorescent Organic Nanoassemblies with Strong Hydrogen Bonding Networks for Fine Tuning and Monitoring Drug Delivery in Cancer Cells

Small ◽  
2018 ◽  
Vol 14 (38) ◽  
pp. 1802307 ◽  
Author(s):  
Joanna Boucard ◽  
Camille Linot ◽  
Thibaut Blondy ◽  
Steven Nedellec ◽  
Philippe Hulin ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Hydrogen Bonding ◽  
Cancer Cells ◽  
Small Molecule ◽  
Fine Tuning ◽  
Monitoring Drug ◽  
Hydrogen Bonding Networks

Hydrogen-bonding networks of purine derivatives and their bilayers for guest intercalation

CrystEngComm ◽  
2016 ◽  
Vol 18 (1) ◽  
pp. 62-67
Author(s):  
Yoona Jang ◽  
Seo Yeon Yoo ◽  
Hye Rin Gu ◽  
Yu Jin Lee ◽  
Young Shin Cha ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Two Dimensional ◽  
Purine Derivatives ◽  
Guest Molecules ◽  
Π Interactions ◽  
Hydrogen Bonding Networks ◽  
Hydrogen Bonded

6-Chloro-9-propyl-purin-2-amine (pr-GCl) forms two-dimensional hydrogen-bonded networks which in turn stack via π–π interactions, leading to the formation of bilayers that can accommodate organic guest molecules.

scholarly journals Improving the Substrate Affinity and Catalytic Efficiency of β-Glucosidase Bgl3A from Talaromyces leycettanus JCM12802 by Rational Design

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1882
Author(s):  
Wei Xia ◽  
Yingguo Bai ◽  
Pengjun Shi
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Substrate Binding ◽  
Enzymatic Saccharification ◽  
Catalytic Efficiency ◽  
Binding Pocket ◽  
Glycoside Hydrolases ◽  
Cellulosic Biomass ◽  
Substrate Affinity ◽  
Hydrogen Bonding Networks

Improving the substrate affinity and catalytic efficiency of β-glucosidase is necessary for better performance in the enzymatic saccharification of cellulosic biomass because of its ability to prevent cellobiose inhibition on cellulases. Bgl3A from Talaromyces leycettanus JCM12802, identified in our previous work, was considered a suitable candidate enzyme for efficient cellulose saccharification with higher catalytic efficiency on the natural substrate cellobiose compared with other β-glucosidase but showed insufficient substrate affinity. In this work, hydrophobic stacking interaction and hydrogen-bonding networks in the active center of Bgl3A were analyzed and rationally designed to strengthen substrate binding. Three vital residues, Met36, Phe66, and Glu168, which were supposed to influence substrate binding by stabilizing adjacent binding site, were chosen for mutagenesis. The results indicated that strengthening the hydrophobic interaction between stacking aromatic residue and the substrate, and stabilizing the hydrogen-bonding networks in the binding pocket could contribute to the stabilized substrate combination. Four dominant mutants, M36E, M36N, F66Y, and E168Q with significantly lower Km values and 1.4–2.3-fold catalytic efficiencies, were obtained. These findings may provide a valuable reference for the design of other β-glucosidases and even glycoside hydrolases.

Trans Doubly N-Confused Porphyrins:  Cu(III) Complexation and Formation of Rodlike Hydrogen-Bonding Networks

2003 ◽  
Vol 125 (51) ◽  
pp. 15690-15691 ◽  
Author(s):  
Hiromitsu Maeda ◽  
Atsuhiro Osuka ◽  
Hiroyuki Furuta
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonding Networks
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