scholarly journals Dynamics-function relationship of N-terminal acetyltransferases: the β6β7 loop modulates substrate accessibility to the catalytic site

2018 ◽  
Author(s):  
Angèle Abboud ◽  
Pierre Bédoucha ◽  
Jan Byška ◽  
Thomas Arnesen ◽  
Nathalie Reuter
Keyword(s):  
Normal Mode Analysis ◽  
Network Models ◽  
Catalytic Site ◽  
Mode Analysis ◽  
Ligand Specificity ◽  
Hairpin Loop ◽  
Domains Of Life ◽  
Function Relationship ◽  
Relationship Of

N-terminal acetyltransferases (NATs) are enzymes catalysing the transfer of the acetyl from Ac-CoA to the N-terminus of proteins, one of the most common protein modifications. Unlike NATs, lysine acetyltransferases (KATs) transfer an acetyl onto the amine group of internal lysines. To date, not much is known on the exclusive substrate specificity of NATs towards protein N-termini. All the NATs and some KATs share a common fold called GNAT. The main difference between NATs and KATs is an extra hairpin loop found only in NATs called β6β7 loop. It covers the active site as a lid. The hypothesized role of the loop is that of a barrier restricting the access to the catalytic site and preventing acetylation of internal lysines. We investigated the dynamics-function relationships of all available structures of NATs covering the three domains of life. Using elastic network models and normal mode analysis, we found a common dynamics pattern conserved through the GNAT fold; a rigid V-shaped groove, formed by the β4 and β5 strands and three relatively more dynamic loops α1α2, β3β4 and β6β7. We identified two independent dynamical domains in the GNAT fold, which is split at the β5 strand. We characterized the β6β7 hairpin loop slow dynamics and show that its movements are able to significantly widen the mouth of the ligand binding site thereby influencing its size and shape. Taken together our results show that NATs may have access to a broader ligand specificity range than anticipated.

Role of aromatic residues in the structure-function relationship of .alpha.-bungarotoxin

Biochemistry ◽  
1982 ◽  
Vol 21 (11) ◽  
pp. 2592-2600 ◽  
Author(s):  
Yee Hsiung Chen ◽  
Jang Chyi Tai ◽  
Wan Jen Huang ◽  
Ming Zong Lai ◽  
Mien Chie Hung ◽  
...  
Keyword(s):  
Structure Function ◽  
Aromatic Residues ◽  
Structure Function Relationship ◽  
Function Relationship ◽  
Alpha Bungarotoxin ◽  
Relationship Of

Uncovering the ultrastructure of ramiform pits in the parenchyma cells of bamboo [Phyllostachys edulis (Carr.) J. Houz.]

Holzforschung ◽  
2020 ◽  
Vol 74 (3) ◽  
pp. 321-331 ◽  
Author(s):  
Caiping Lian ◽  
Shuqin Zhang ◽  
Xianmiao Liu ◽  
Junji Luo ◽  
Feng Yang ◽  
...  
Keyword(s):  
Environmental Scanning Electron Microscopy ◽  
Environmental Scanning ◽  
Type I ◽  
Aperture Diameter ◽  
Parenchyma Cells ◽  
Vascular Parenchyma ◽  
Function Relationship ◽  
Relationship Of ◽  
Important Evidence

AbstractPits are the main transverse channels of intercellular liquid transport in bamboo. Ramiform pits are a special type of simple pit with two or more branches. However, little is known about the morphology and physiological functions of ramiform pits. The anatomy of plants can provide important evidence for the role of cells. To better understand the ultrastructure and the structure-function relationship of ramiform pits, their characteristics need to be investigated. In this study, both qualitative and quantitative features of ramiform pits were studied using field-emission environmental scanning electron microscopy (FE-ESEM). The samples included the native structures and the replica structures obtained by resin castings. The results show that the ramiform pits have a diverse morphology that can be divided into main categories: type I (the primary branches) and type II (the secondary branches). The distribution of ramiform pits is different in ground parenchyma cells (GPCs) and vascular parenchyma cells (VPCs). The number, the pit aperture diameter and the pit canal length of ramiform pits in the VPCs were, respectively, greater (3-fold), larger (2–3-fold) and shorter (1.3-fold) than those in the GPCs.

scholarly journals The Role of the Fibronectin IGD Motif in Stimulating Fibroblast Migration

2007 ◽  
Vol 282 (49) ◽  
pp. 35530-35535 ◽  
Author(s):  
Christopher J. Millard ◽  
Ian R. Ellis ◽  
Andrew R. Pickford ◽  
Ana M. Schor ◽  
Seth L. Schor ◽  
...  
Keyword(s):  
Fibroblast Migration ◽  
Wide Range ◽  
Migration Stimulating Factor ◽  
Function Relationship ◽  
Relationship Of ◽  
Stimulating Factor ◽  
Insight Into ◽  
Stimulation Of

The motogenic activity of migration-stimulating factor, a truncated isoform of fibronectin (FN), has been attributed to the IGD motifs present in its FN type 1 modules. The structure-function relationship of various recombinant IGD-containing FN fragments is now investigated. Their structure is assessed by solution state NMR and their motogenic ability tested on fibroblasts. Even conservative mutations in the IGD motif are inactive or have severely reduced potency, while the structure remains essentially the same. A fragment with two IGD motifs is 100 times more active than a fragment with one and up to 106 times more than synthetic tetrapeptides. The wide range of potency in different contexts is discussed in terms of cryptic FN sites and cooperativity. These results give new insight into the stimulation of fibroblast migration by IGD motifs in FN.

Structure network analysis to gain insights into GPCR function

2016 ◽  
Vol 44 (2) ◽  
pp. 613-618 ◽  
Author(s):  
Francesca Fanelli ◽  
Angelo Felline ◽  
Francesco Raimondi ◽  
Michele Seeber
Keyword(s):  
G Protein ◽  
Normal Mode Analysis ◽  
Network Models ◽  
Md Simulations ◽  
G Protein Coupled Receptors ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Biomolecular Systems ◽  
Retinal Chromophore ◽  
G Protein Coupled

G protein coupled receptors (GPCRs) are allosteric proteins whose functioning fundamentals are the communication between the two poles of the helix bundle. Protein structure network (PSN) analysis is one of the graph theory-based approaches currently used to investigate the structural communication in biomolecular systems. Information on system's dynamics can be provided by atomistic molecular dynamics (MD) simulations or coarse grained elastic network models paired with normal mode analysis (ENM–NMA). The present review article describes the application of PSN analysis to uncover the structural communication in G protein coupled receptors (GPCRs). Strategies to highlight changes in structural communication upon misfolding, dimerization and activation are described. Focus is put on the ENM–NMA-based strategy applied to the crystallographic structures of rhodopsin in its inactive (dark) and signalling active (meta II (MII)) states, highlighting changes in structure network and centrality of the retinal chromophore in differentiating the inactive and active states of the receptor.

scholarly journals CriTER-A: A Novel Temperature-Dependent Noncoding RNA Switch in the Telomeric Transcriptome of Chironomus riparius

2021 ◽  
Vol 22 (19) ◽  
pp. 10310
Author(s):  
Cristina Romero-López ◽  
Alfredo Berzal-Herranz ◽  
José Luis Martínez-Guitarte ◽  
Mercedes de la Fuente
Keyword(s):  
Thermal Stress ◽  
Noncoding Rna ◽  
Relative Proportion ◽  
Chironomus Riparius ◽  
Temperature Dependent ◽  
Differential Behaviour ◽  
High Sequence Homology ◽  
Function Relationship ◽  
Relationship Of

The telomeric transcriptome of Chironomus riparius has been involved in thermal stress response. One of the telomeric transcripts, the so-called CriTER-A variant, is highly overexpressed upon heat shock. On the other hand, its homologous variant CriTER-B, which is the most frequently encoded noncoding RNA in the telomeres of C. riparius, is only slightly affected by thermal stress. Interestingly, both transcripts show high sequence homology, but less is known about their folding and how this could influence their differential behaviour. Our study suggests that CriTER-A folds as two different conformers, whose relative proportion is influenced by temperature conditions. Meanwhile, the CriTER-B variant shows only one dominant conformer. Thus, a temperature-dependent conformational equilibrium can be established for CriTER-A, suggesting a putative functional role of the telomeric transcriptome in relation to thermal stress that could rely on the structure–function relationship of the CriTER-A transcripts.

Predicting Phonon Transport in Two-Dimensional Boron Nitride-Graphene Superlattices

2014 ◽  
Author(s):  
Carlos da Silva ◽  
Julia Sborz ◽  
David A. Romero ◽  
Cristina H. Amon
Keyword(s):  
Boron Nitride ◽  
Normal Mode Analysis ◽  
Phonon Transport ◽  
Mode Analysis ◽  
Spectral Energy ◽  
Phonon Modes ◽  
Support Engineering ◽  
Group Velocities ◽  
Phonon Properties

The synthesis of boron nitride (BN) - graphene hybrid materials is now a reality that has opened opportunities for creation of new nanostructures with enhanced mechanical, electronic and thermal properties, of particular interest for nanoelectronics applications. Properties of these materials are still not well understood, and modelling approaches are needed to support engineering design of these novel nanostructures. In this work, we study thermal transport in BN-graphene superlattices from a phonon transport perspective. We predict phonon properties (phonon group velocities and phonon lifetimes) using normal mode analysis based on phonon spectral energy density (SED) in these superlattices, with especial emphasis on the role of the orientation of the atoms at the BN - graphene interfaces. We consider various superlattices compositions with two highly symmetric orientation, i.e., zig-zag and armchair. Our results show that phonon group velocities are higher for the zig-zag interface orientation. We also found that phonon modes at small frequencies are more sensitive to the superlattice configurations.

scholarly journals An Algorithm to Predict the Possible SARS-CoV-2 Mutations

2021 ◽  
Vol 3 (1) ◽  
pp. 1-7
Author(s):  
Raúl Isea
Keyword(s):  
Free Energy ◽  
Protein Data Bank ◽  
Gibbs Free Energy ◽  
Human Population ◽  
Normal Mode Analysis ◽  
Network Models ◽  
Data Bank ◽  
Mode Analysis ◽  
Vibration Modes ◽  
Anisotropic Network

An algorithm to determine the possible mutations that can occur in the S protein responsible of the Covid-19 in humans is designed. To do that, nine tridimensional sequences available in the Protein Data Bank similar to the initial strain sequenced in Wuhan (December 2019) are identified. The conditions driving this potential mutation are: (1) an accumulated number of mutations greater than (or equal to) 5 in each position; (2), a cumulative value of the different variations of Gibbs free energy less than -2.0 Kcal/mol; and (3), a squared fluctuation greater than 1.6 Å obtained according to calculations for normal mode analysis based on anisotropic network models (ANM) after averaging the first 20 vibration modes. The result is that 491 positions can mutate, while 424 positions did not provide any mutation. Finally, the results reveal that there are mutations that cannot be predicted, so more studies are needed to determine why they are present in the human population.

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