A journey through the evolutionary diversification of archaeal Lsm and Hfq proteins*

2018 ◽  
Vol 2 (4) ◽  
pp. 647-657 ◽  
Author(s):  
Robert Reichelt ◽  
Dina Grohmann ◽  
Sarah Willkomm
Keyword(s):  
Secondary Structure ◽  
Biological Function ◽  
Binding Pocket ◽  
Rna Metabolism ◽  
Structural Features ◽  
Evolutionary Development ◽  
Evolutionary Diversification ◽  
Strong Focus ◽  
Domains Of Life ◽  
Structural Diversification

Sm-like (Lsm) proteins are found in all three domains of life. They are crucially involved in the RNA metabolism of prokaryotic organisms. To exert their function, they assemble into hexa- or heptameric rings and bind RNA via a conserved binding pocket for uridine stretches in the inner pore of the ring. Despite the conserved secondary structure of Lsm proteins, there are several features that lead to a structural diversification of this protein family that mediates their participation in a variety of processes related to RNA metabolism. Until recently, the cellular function of archaeal Sm-like proteins was not well understood. In this review, we discuss structural features of Lsm proteins with a strong focus on archaeal variants, reflect on the evolutionary development of archaeal Lsm proteins and present recent insights into their biological function.

A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools

2019 ◽  
Vol 16 (2) ◽  
pp. 159-172 ◽  
Author(s):  
Elaheh Kashani-Amin ◽  
Ozra Tabatabaei-Malazy ◽  
Amirhossein Sakhteman ◽  
Bagher Larijani ◽  
Azadeh Ebrahim-Habibi
Keyword(s):  
Systematic Review ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Web Of Science ◽  
Secondary Structure Prediction ◽  
Structural Information ◽  
Protein Secondary Structure ◽  
Structural Features ◽  
Prediction Tools ◽  
Insight Into

Background: Prediction of proteins’ secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. Objective: A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Methods: Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. Results: Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. Conclusion: This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.

scholarly journals Mapping the glycosyltransferase fold landscape using interpretable deep learning

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rahil Taujale ◽  
Zhongliang Zhou ◽  
Wayland Yeung ◽  
Kelley W. Moremen ◽  
Sheng Li ◽  
...  
Keyword(s):  
Deep Learning ◽  
Secondary Structure ◽  
Structural Features ◽  
Functional Diversification ◽  
Sequence Structure ◽  
Cellular Processes ◽  
And Function ◽  
Deep Learning Model ◽  
Fold Prediction ◽  
Primary Sequence Alignment

AbstractGlycosyltransferases (GTs) play fundamental roles in nearly all cellular processes through the biosynthesis of complex carbohydrates and glycosylation of diverse protein and small molecule substrates. The extensive structural and functional diversification of GTs presents a major challenge in mapping the relationships connecting sequence, structure, fold and function using traditional bioinformatics approaches. Here, we present a convolutional neural network with attention (CNN-attention) based deep learning model that leverages simple secondary structure representations generated from primary sequences to provide GT fold prediction with high accuracy. The model learns distinguishing secondary structure features free of primary sequence alignment constraints and is highly interpretable. It delineates sequence and structural features characteristic of individual fold types, while classifying them into distinct clusters that group evolutionarily divergent families based on shared secondary structural features. We further extend our model to classify GT families of unknown folds and variants of known folds. By identifying families that are likely to adopt novel folds such as GT91, GT96 and GT97, our studies expand the GT fold landscape and prioritize targets for future structural studies.

scholarly journals Cryo-EM Structures of Prestin and the Molecular Basis of Outer Hair Cell Electromotility

2021 ◽  
Author(s):  
Navid Bavi ◽  
Michael D Clark ◽  
Gustavo F Contreras ◽  
Rong Shen ◽  
Bharat Reddy ◽  
...  
Keyword(s):  
Outer Hair Cell ◽  
Binding Pocket ◽  
Structural Features ◽  
Outer Hair Cells ◽  
Anion Binding ◽  
Structural Basis ◽  
Inhibition Mechanism ◽  
Core Domain ◽  
The Core ◽  
Voltage Dependent

The voltage-dependent motor protein, Prestin (SLC26A5) is responsible for the electromotive behavior of outer hair cells (OHCs). Here, we determined the structure of dolphin Prestin in complex with Cl- and the inhibitor Salicylate using single particle cryo-electron microscopy. These structures establish the specific structural features of mammalian Prestin and reveal small but significant differences with the transporter members of the SLC26 family of membrane proteins. Comparison with SLC26A9 point to conformational differences in the special relationship between the core and gate domains. Importantly, we highlight substantial alterations to the hydrophobic footprint of Prestin as it relates to the membrane, which point to a potential influence of Prestin on its surrounding lipid. The structure of Prestin bound to the inhibitor Salicylate confirms the nature of the anion binding pocket, formed by TM3 and TM10 in the Core domain and a set of anion coordinating residues which include Q97, F101, F137, S398 and R399. The presence of a well-defined density for Salycilate points to an inhibition mechanism based on competition for the anion-binding pocket of Prestin. These observations illuminate the structural basis of Prestin electromotility, a key component in the mammalian cochlear amplifier.

scholarly journals Investigation of the Relationship between the S1 Domain and Its Molecular Functions Derived from Studies of the Tertiary Structure

Molecules ◽  
2019 ◽  
Vol 24 (20) ◽  
pp. 3681 ◽  
Author(s):  
Evgenia I. Deryusheva ◽  
Andrey V. Machulin ◽  
Maxim A. Matyunin ◽  
Oxana V. Galzitskaya
Keyword(s):  
Protein Binding ◽  
Tertiary Structure ◽  
Relative Number ◽  
Structural Features ◽  
Statistical Tools ◽  
Binding Partners ◽  
Protein Functions ◽  
Domains Of Life ◽  
Molecular Functions ◽  
The Relationship

S1 domain, a structural variant of one of the “oldest” OB-folds (oligonucleotide/oligosaccharide-binding fold), is widespread in various proteins in three domains of life: Bacteria, Eukaryotes, and Archaea. In this study, it was shown that S1 domains of bacterial, eukaryotic, and archaeal proteins have a low percentage of identity, which indicates the uniqueness of the scaffold and is associated with protein functions. Assessment of the predisposition of tertiary flexibility of S1 domains using computational and statistical tools showed similar structural features and revealed functional flexible regions that are potentially involved in the interaction of natural binding partners. In addition, we analyzed the relative number and distribution of S1 domains in all domains of life and established specific features based on sequences and structures associated with molecular functions. The results correlate with the presence of repeats of the S1 domain in proteins containing the S1 domain in the range from one (bacterial and archaeal) to 15 (eukaryotic) and, apparently, are associated with the need for individual proteins to increase the affinity and specificity of protein binding to ligands.

scholarly journals Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life

Open Biology ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 190020 ◽  
Author(s):  
Daniel Gebert ◽  
Julia Jehn ◽  
David Rosenkranz
Keyword(s):  
Secondary Structure ◽  
Gc Content ◽  
Secondary Structures ◽  
Coding Sequences ◽  
Rna Secondary Structures ◽  
Synonymous Mutations ◽  
Codon Composition ◽  
Domains Of Life ◽  
Low Levels ◽  
Selection For

Codon composition, GC content and local RNA secondary structures can have a profound effect on gene expression, and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that, in some cases, selection favours more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and whether this is a universal phenomenon in nature. We searched for signs of structural selection in a global manner, analysing a set of 1 million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed software PACKEIS. We show that codon composition and amino acid identity are main determinants of RNA secondary structure. In addition, we show that the arrangement of synonymous codons within coding sequences is non-random, yielding extremely high, but also extremely low, RNA structuredness significantly more often than expected by chance. Taken together, we demonstrate that selection for high and low levels of secondary structure is a widespread phenomenon. Our results provide another line of evidence that synonymous mutations are less neutral than commonly thought, which is of importance for many evolutionary models.

scholarly journals Structural and Functional Analysis of the RNA Transport Element, a Member of an Extensive Family Present in the Mouse Genome

2005 ◽  
Vol 79 (4) ◽  
pp. 2356-2365 ◽  
Author(s):  
Sergey Smulevitch ◽  
Daniel Michalowski ◽  
Andrei S. Zolotukhin ◽  
Ralf Schneider ◽  
Jenifer Bear ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Nuclear Export ◽  
Mammalian Cells ◽  
Minimal Element ◽  
Structural Features ◽  
Rna Transport ◽  
Immunodeficiency Virus ◽  
Responsive Element ◽  
Nuclear Export Receptor ◽  
Intracisternal A Particle

ABSTRACT We previously identified an RNA transport element (RTE), present in a subclass of rodent intracisternal A particle retroelements (F. Nappi, R. Schneider, A. Zolotukhin, S. Smulevitch, D. Michalowski, J. Bear, B. Felber, and G. Pavlakis, J. Virol. 75:4558-4569, 2001), that is able to replace Rev-responsive element regulation in human immunodeficiency virus type 1. RTE-directed mRNA export is mediated by a still-unknown cellular factor(s), is independent of the CRM1 nuclear export receptor, and is conserved among vertebrates. Here we show that this RTE folds into an extended RNA secondary structure and thus does not resemble any known RTEs. Computer searches revealed the presence of 105 identical elements and more than 3,000 related elements which share at least 70% sequence identity with the RTE and which are found on all mouse chromosomes. These related elements are predicted to fold into RTE-like structures. Comparison of the sequences and structures revealed that the RTE and related elements can be divided into four groups. Mutagenesis of the RTE revealed that the minimal element contains four internal stem-loops, which are indispensable for function in mammalian cells. In contrast, only part of the element is essential to mediate RNA transport in microinjected Xenopus laevis oocyte nuclei. Importantly, the minimal RTE able to promote RNA transport has key structural features which are preserved in all the RTE-related elements, further supporting their functional importance. Therefore, RTE function depends on a complex secondary structure that is important for the interaction with the cellular export factor(s).

Bioinformatics Analysis and Characteristics of Ser/Thr Protein Kinase Encoded by UL13 Gene of Duck Plague Virus

2011 ◽  
Vol 393-395 ◽  
pp. 617-627
Author(s):  
Xi Xia Hu ◽  
An Chun Cheng ◽  
Ming Shu Wang
Keyword(s):  
Protein Kinase ◽  
Secondary Structure ◽  
Physicochemical Properties ◽  
Evolutionary Relationship ◽  
Alpha Helix ◽  
Structural Features ◽  
Functional Study ◽  
Online Tools ◽  
Multiple Sequences ◽  
Sequences Alignment

This report showed some physicochemical properties and structural features about DPV-UL13 protein predicted by some software and online tools. The online analysis of the physicochemical properties demonstrates that the protein has thirty-four potential phosphorylation sites when the threshold of prediction score is above 0.5 and both the signal peptide and the transmembrance region are not found. In addition, the protein has hydrophilic amine acid districts more than hydrophobic districts and subcellular localization largely locates at mitochondrial with 43.5%. The secondary structure results revealed that random coils dominated among secondary structure elements followed by alpha helix and extended strand. The phylogenetic tree shows that DPV-UL13 protein has close evolutionary relationship with the genus Mardivirus. And the multiple sequences alignment of UL13 protein in 156-436 sequence among DPV, HSV-1 and Mardivirus genus suggests highly conserved characteristic. These analysis surpports the guess that DPV-UL13 product may be a Ser/Thr protein kinase. All the data will be a basis for the further functional study of the DPV-UL13 protein.

scholarly journals Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants

2017 ◽  
Author(s):  
Rajesh K. Gazara ◽  
Kanhu C. Moharana ◽  
Daniel Bellieny-Rabelo ◽  
Thiago M. Venancio
Keyword(s):  
Gene Expression ◽  
Evolutionary Relationship ◽  
Strong Support ◽  
Binding Pocket ◽  
Structural Features ◽  
Land Plants ◽  
Legume Seeds ◽  
Wide Range ◽  
Systematic Identification

ABSTRACTGibberellic acid (gibberellins, GA) controls key developmental processes in the life-cycle of land plants. By interacting with the GIBBERELLIN INSENSITIVE DWARF1 (GID1) receptor, GA regulates the expression of a wide range of genes through different pathways. Here we report the systematic identification and classification of GID1s in 52 plants genomes, encompassing from bryophytes and lycophytes, to several monocots and eudicots. We investigated the evolutionary relationship of GID1s using a comparative genomics framework and found strong support a previously proposed phylogenetic classification of this family in land plants. We identified lineage-specific expansions of particular subfamilies (i.e. GID1ac and GID1b) in different eudicot lineages (e.g. GID1b in legumes). Further, we found both, shared and divergent structural features between GID1ac and GID1b subgroups in eudicots, which provide mechanistic insights on their functions. Gene expression data from several species show that at least one GID1 gene is expressed in every sampled tissue, with a strong bias of GID1b expression towards underground tissues and dry legume seeds (typically with low GA levels). Taken together, our results support that GID1ac retained canonical GA signaling roles, whereas GID1b specialized in conditions of low GA concentrations. We propose that this functional specialization occurred initially at the gene expression level and was later fine-tuned by specific mutations that conferred greater GA affinity to GID1b, including a Phe residue in the GA-binding pocket. Finally, we discuss the importance of our findings to understand the diversification of GA perception mechanisms in land plants.

scholarly journals Partial deglycosylation of alpha subunit modifies sturgeon gonadotropin function.

2000 ◽  
Vol 47 (3) ◽  
pp. 815-819 ◽  
Author(s):  
H Zenkevics ◽  
V Vose ◽  
I Vosekalne ◽  
A Bũcena
Keyword(s):  
Secondary Structure ◽  
Biological Function ◽  
Cd Spectroscopy ◽  
Carbohydrate Content ◽  
Alpha Subunit ◽  
Sugar Moiety ◽  
Hormonal Function ◽  
Alpha Beta ◽  
Chemical Deglycosylation ◽  
Acipenser Gueldenstaedti

Chemical deglycosylation (dg) of sturgeon Acipenser gueldenstaedti Br. (alphaGTH) resulted in the loss of 83% of its initial carbohydrate content. It altered also recombinant dg alphaGTH + betaGTH dimer molecule, reducing its immunoreactivity by 30%, and fully blocking the hormonal function. CD spectroscopy showed that deglycosylation led to changes in the secondary structure of dg alphaGTH and in the alpha-beta recombinant. The sugar moiety of sturgeon alphaGTH is suggested to play an important role in maintaining the biological function of the hormone dimer molecule.

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