scholarly journals Comparative analysis of 13C chemical shifts of β-sheet amyloid proteins and outer membrane proteins

2021 ◽  
Author(s):  
Noah H. Somberg ◽  
Martin D. Gelenter ◽  
Mei Hong
Keyword(s):  
Comparative Analysis ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Chemical Shifts ◽  
Outer Membrane Proteins ◽  
Amyloid Proteins ◽  
13C Chemical Shifts ◽  
Β Sheet

Analysis of the Membrane proteins of an Antarctic Bacterium Pseudomonas Syringae

2011 ◽  
Vol 4 ◽  
pp. PRI.S5383 ◽  
Author(s):  
M.V. Jagannadham ◽  
S. Saranya
Keyword(s):  
Comparative Analysis ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Pseudomonas Syringae ◽  
Cold Adaptation ◽  
Outer Membrane Proteins ◽  
Protein Preparation ◽  
Preparation Methods ◽  
Outer Membranes ◽  
Antarctic Bacterium

The proteins of an Antarctic bacterium Pseudomonas syringae Lz4W, identified earlier by different membrane protein preparation methods, were combined together and the redundant identities removed. In total, 1479 proteins including 148 outer membrane proteins from this bacterium were predicted by the algorithm PSORTb3.0. A detailed analysis on their subcellular localization was undertaken which was determined using TMHMM, TMB-hunt and BOMP. A comparison of PSORTb predicted outer membrane proteins with BOMP, revealed that most of the proteins predicted by the former, contained β–barrels in the outer membranes. A comparative analysis of PSORTb, TMHMM and TMB-hunt reveals that most of the outer membranes proteins of this bacterium could be identified using this approach. Thus, by using a combination of biochemical and different bioinformatics algorithms, the membrane proteins of P. syringae are analyzed. In particular, PSORTb results are compared and supported by other algorithms, to improve the strength of OM proteins prediction. Several proteins, having an important role in cold adaptation of the organism, could also be identified.

Comparative analysis of the main outer membrane proteins of Brucella in the diagnosis of brucellosis

2021 ◽  
Vol 560 ◽  
pp. 126-131
Author(s):  
Qiongqiong Bai ◽  
Han Li ◽  
Xiling Wu ◽  
Jihong Shao ◽  
Mingjun Sun ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Outer Membrane Proteins

scholarly journals Omp85Tt from Thermus thermophilus HB27: an Ancestral Type of the Omp85 Protein Family

2008 ◽  
Vol 190 (13) ◽  
pp. 4568-4575 ◽  
Author(s):  
Jutta Nesper ◽  
Alexander Brosig ◽  
Philippe Ringler ◽  
Geetika J. Patel ◽  
Shirley A. Müller ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Single Channel ◽  
Cell Envelope ◽  
Thermus Thermophilus ◽  
Outer Membrane Proteins ◽  
Thermophilic Bacterium ◽  
Outer Membranes ◽  
Β Sheet ◽  
Ancestral Type

ABSTRACT Proteins belonging to the Omp85 family are involved in the assembly of β-barrel outer membrane proteins or in the translocation of proteins across the outer membrane in bacteria, mitochondria, and chloroplasts. The cell envelope of the thermophilic bacterium Thermus thermophilus HB27 is multilayered, including an outer membrane that is not well characterized. Neither the precise lipid composition nor much about integral membrane proteins is known. The genome of HB27 encodes one Omp85-like protein, Omp85Tt, representing an ancestral type of this family. We overexpressed Omp85Tt in T. thermophilus and purified it from the native outer membranes. In the presence of detergent, purified Omp85Tt existed mainly as a monomer, composed of two stable protease-resistant modules. Circular dichroism spectroscopy indicated predominantly β-sheet secondary structure. Electron microscopy of negatively stained lipid-embedded Omp85Tt revealed ring-like structures with a central cavity of ∼1.5 nm in diameter. Single-channel conductance recordings indicated that Omp85Tt forms ion channels with two different conducting states, characterized by conductances of ∼0.4 nS and ∼0.65 nS, respectively.

scholarly journals The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 451
Author(s):  
Pablo Mier ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Bacterial Species ◽  
Outer Membrane Proteins ◽  
Subcellular Location ◽  
Low Complexity ◽  
Extracellular Proteins ◽  
Bacterial Strains ◽  
Bacterial Proteins ◽  
Protein Subcellular Location

Low complexity regions (LCRs) in proteins are characterized by amino acid frequencies that differ from the average. These regions evolve faster and tend to be less conserved between homologs than globular domains. They are not common in bacteria, as compared to their prevalence in eukaryotes. Studying their conservation could help provide hypotheses about their function. To obtain the appropriate evolutionary focus for this rapidly evolving feature, here we study the conservation of LCRs in bacterial strains and compare their high variability to the closeness of the strains. For this, we selected 20 taxonomically diverse bacterial species and obtained the completely sequenced proteomes of two strains per species. We calculated all orthologous pairs for each of the 20 strain pairs. Per orthologous pair, we computed the conservation of two types of LCRs: compositionally biased regions (CBRs) and homorepeats (polyX). Our results show that, in bacteria, Q-rich CBRs are the most conserved, while A-rich CBRs and polyA are the most variable. LCRs have generally higher conservation when comparing pathogenic strains. However, this result depends on protein subcellular location: LCRs accumulate in extracellular and outer membrane proteins, with conservation increased in the extracellular proteins of pathogens, and decreased for polyX in the outer membrane proteins of pathogens. We conclude that these dependencies support the functional importance of LCRs in host–pathogen interactions.

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