scholarly journals Topological analysis of TMEM180, a newly identified membrane protein that is highly expressed in colorectal cancer cells

2019 ◽  
Author(s):  
Takahiro Anzai ◽  
Yasuhiro Matsumura
Keyword(s):  
Colorectal Cancer ◽  
Membrane Protein ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Transmembrane Protein ◽  
Topological Analysis ◽  
Homology Model ◽  
Cation Binding ◽  
List Type ◽  
Cation Binding Site

AbstractNew target molecules for diagnosis of and drug development for colorectal cancer (CRC) are always in great demand. Previously, we identified a new colorectal cancer–specific protein, TMEM180, and successfully developed an anti-TMEM180 monoclonal antibody (mAb) for the diagnosis and treatment of CRC. Although TMEM180 is categorized as a member of the cation symporter family and multi-pass membrane protein, little is known about its function. In this study, we examined topology of this membrane protein and analyzed its function. Using a homology model of human TMEM180, we experimentally determined that the protein has 12 transmembrane domains, and that its N-terminal and C-termini are exposed extracellularly. Moreover, we found that the putative cation-binding site of TMEM180 is conserved among orthologs, and that its position is similar to that of melibiose transporter MelB. These results suggest that TMEM180 acts as a cation symporter. Our topological analysis based on the homology model provides insight into functional and structural roles of TMEM180 that may help to elucidate the pathology of CRC.HighlightsA homology model of human TMEM180 was generated by secondary structure prediction.Putative cation-binding residues are conserved in TMEM180 orthologs.Both the N-terminus and C-terminus of TMEM180 are extracellularly exposed.TMEM180 is a 12-transmembrane protein.TMEM180 could act as a cation symporter.

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 Can computationally designed protein sequences improve secondary structure prediction?

2011 ◽  
Vol 24 (5) ◽  
pp. 455-461 ◽  
Author(s):  
R. Bondugula ◽  
A. Wallqvist ◽  
M. S. Lee
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Protein Sequences

scholarly journals Predicting the Structure and Dynamics of Membrane Protein GerAB from Bacillus subtilis

2021 ◽  
Vol 22 (7) ◽  
pp. 3793
Author(s):  
Sophie Blinker ◽  
Jocelyne Vreede ◽  
Peter Setlow ◽  
Stanley Brul
Keyword(s):  
Bacillus Subtilis ◽  
Membrane Protein ◽  
Spore Germination ◽  
Structural Information ◽  
Transmembrane Protein ◽  
Homology Modelling ◽  
Water Channel ◽  
Md Simulations ◽  
Integral Membrane Protein ◽  
Starting Point

Bacillus subtilis forms dormant spores upon nutrient depletion. Germinant receptors (GRs) in spore’s inner membrane respond to ligands such as L-alanine, and trigger spore germination. In B. subtilis spores, GerA is the major GR, and has three subunits, GerAA, GerAB, and GerAC. L-Alanine activation of GerA requires all three subunits, but which binds L-alanine is unknown. To date, how GRs trigger germination is unknown, in particular due to lack of detailed structural information about B subunits. Using homology modelling with molecular dynamics (MD) simulations, we present structural predictions for the integral membrane protein GerAB. These predictions indicate that GerAB is an α-helical transmembrane protein containing a water channel. The MD simulations with free L-alanine show that alanine binds transiently to specific sites on GerAB. These results provide a starting point for unraveling the mechanism of L-alanine mediated signaling by GerAB, which may facilitate early events in spore germination.

scholarly journals Effect of Urea on the Divalent Cation Binding Site of Pyruvate Kinase

1971 ◽  
Vol 246 (13) ◽  
pp. 4363-4365 ◽  
Author(s):  
Gene L. Cottam ◽  
Albert S. Mildvan
Keyword(s):  
Binding Site ◽  
Pyruvate Kinase ◽  
Divalent Cation ◽  
Cation Binding ◽  
Cation Binding Site
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