Regulation of biomolecular condensates by interfacial protein clusters

Histones play important roles in chromatin functioning and gene transcription, but in the intercellular space, they are harmful since they stimulate systemic inflammatory and toxic responses. Electrophoretically homogeneous IgGs against myelin basic protein (MBP), as well as H3 and H4 histones, were isolated from sera of HIV-infected patients. In contrast to known classical proteases, these IgGs split exclusively only histones and MBP but no other control proteins. Among 13 sites of hydrolysis of H3 by IgGs against H3 and 14 sites for anti-MBP IgGs, only two sites of the hydrolysis were the same. Between seven cleavage sites of H4 with IgGs against H4 and 9 sites of this histone hydrolysis by antibodies against MBP, only three sites were the same. The sites of hydrolysis of H3 (and H4) with abzymes against these histones and against MBP were different, but several expended protein clusters containing hydrolysis sites are partially overlapped. The existence of enzymatic cross-reactivity of abzymes against H3 and H4 and MBP represents a great menace to humans since due to cell apoptosis, histones constantly occur in human blood. They can hydrolyze MBP of the myelin sheath of axons and play a negative role in the pathogenesis of HIV-infected patients.

Download Full-text

Faculty Opinions recommendation of Regulation of biomolecular condensates by interfacial protein clusters.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.740779265.793588698 ◽

2021 ◽

Author(s):

Walter Gassmann

Keyword(s):

Protein Clusters

Download Full-text

Fluorescence detection of protein clusters in individual cells and tissue sections by using toponome imaging system: sample preparation and measuring procedures

Nature Protocols ◽

10.1038/nprot.2007.320 ◽

2007 ◽

Vol 2 (9) ◽

pp. 2285-2294 ◽

Cited By ~ 58

Author(s):

Manuela Friedenberger ◽

Marcus Bode ◽

Andreas Krusche ◽

Walter Schubert

Keyword(s):

Sample Preparation ◽

Fluorescence Detection ◽

Imaging System ◽

Tissue Sections ◽

Protein Clusters

Download Full-text

Using Protein Clusters from Whole Proteomes to Construct and Augment a Dendrogram

Advances in Bioinformatics ◽

10.1155/2013/191586 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 6

Author(s):

Yunyun Zhou ◽

Douglas R. Call ◽

Shira L. Broschat

Keyword(s):

Open Source Software ◽

Protein Profile ◽

Correlation Filter ◽

New Taxon ◽

Optimal Alignment ◽

Gram Negative ◽

Protein Clusters ◽

Bacterial Plasmids ◽

Insertion Algorithm ◽

Ab Initio Approach

In this paper we present a new ab initio approach for constructing an unrooted dendrogram using protein clusters, an approach that has the potential for estimating relationships among several thousands of species based on their putative proteomes. We employ an open-source software program called pClust that was developed for use in metagenomic studies. Sequence alignment is performed by pClust using the Smith-Waterman algorithm, which is known to give optimal alignment and, hence, greater accuracy than BLAST-based methods. Protein clusters generated by pClust are used to create protein profiles for each species in the dendrogram, these profiles forming a correlation filter library for use with a new taxon. To augment the dendrogram with a new taxon, a protein profile for the taxon is created using BLASTp, and this new taxon is placed into a position within the dendrogram corresponding to the highest correlation with profiles in the correlation filter library. This work was initiated because of our interest in plasmids, and each step is illustrated using proteomes from Gram-negative bacterial plasmids. Proteomes for 527 plasmids were used to generate the dendrogram, and to demonstrate the utility of the insertion algorithm twelve recently sequenced pAKD plasmids were used to augment the dendrogram.

Download Full-text