Loss and gain of GroEL in the MollicutesThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 185-194 ◽  
Author(s):  
Gregory W. Clark ◽  
Elisabeth R.M. Tillier
Keyword(s):  
Phylogenetic Analysis ◽  
Protein Folding ◽  
Gene Transfer ◽  
Review Process ◽  
Peer Review Process ◽  
Host Tissue ◽  
Cellular Biology ◽  
Canadian Society ◽  
Special Issue ◽  
Selection Of

GroEL is a chaperone thought of as essential for bacterial life. However, some species of Mollicutes are missing GroEL. We use phylogenetic analysis to show that the presence of GroEL is polyphyletic among the Mollicutes, and that there is evidence for lateral gene transfer of GroEL to Mycoplasma penetrans from the Proteobacteria. Furthermore, we propose that the presence of GroEL in Mycoplasma may be required for invasion of host tissue, suggesting that GroEL may act as an adhesin–invasin.

Residue patterning in helix interiorsThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 325-337 ◽  
Author(s):  
Brent Wathen ◽  
Zongchao Jia
Keyword(s):  
Protein Folding ◽  
Review Process ◽  
Peer Review Process ◽  
Cellular Biology ◽  
Side Chain ◽  
Special Issue ◽  
Helix Formation ◽  
Apolar Residue ◽  
Α Helix ◽  
Selection Of

The α-helix remains a focus of research because of its importance to protein folding and structure. Nevertheless, despite numerous empirical, computational, and theoretical studies, the fundamental structural properties governing their formation and stability are still unclear. We have examined the statistical occurrence of polar and apolar residue patterning in helical interiors in a large, non-redundant dataset, and compared these patterns with those found in other structural environments. While the familiar amphipathic distributions for both polar and apolar residues are evident, our analysis also finds significant differences between these distributions. Non-amphipathic signals can also be discerned within both distributions. Most interestingly, among various positional patterning, an analysis of immediate (i,i + 1) helical neighbours found: (i) clear neighbouring preferences, with high (low) occurrences of hydrophobics (hydrophilics) next to Gly, Pro, and short polar residues; (ii) high negative (positive) correlation between residue helical propensities and the degree of neighbouring hydrophobicity (hydrophilicity); and (iii) a preferred ordering among neighbours, implying an inherent helix directionality. Because (i,i + 1) helical pairs have limited side chain – side chain interactions, thermodynamic considerations cannot readily explain these observations, nor can evolutionary pressures that enhance tertiary interactions via amphipathicity, as this particular spacing does not segregate residues onto either the same or opposing helical faces. We suggest that the mechanism of helix formation may be partly responsible for these observations. In particular, the high negative correlation between residue helical propensities and neighbouring hydrophobicity suggests that hydrophobicity may play a more important role in helix formation than currently recognized.

scholarly journals Structure of the H1 C-terminal domain and function in chromatin condensationThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2011 ◽  
Vol 89 (1) ◽  
pp. 35-44 ◽  
Author(s):  
Tamara L. Caterino ◽  
Jeffrey J. Hayes
Keyword(s):  
Review Process ◽  
Peer Review Process ◽  
Special Issue ◽  
Direct Role ◽  
Linker Histones ◽  
Terminal Domain ◽  
Chromatin Folding ◽  
And Function ◽  
Positively Charged ◽  
Selection Of

Linker histones are multifunctional proteins that are involved in a myriad of processes ranging from stabilizing the folding and condensation of chromatin to playing a direct role in regulating gene expression. However, how this class of enigmatic proteins binds in chromatin and accomplishes these functions remains unclear. Here we review data regarding the H1 structure and function in chromatin, with special emphasis on the C-terminal domain (CTD), which typically encompasses approximately half of the mass of the linker histone and includes a large excess of positively charged residues. Owing to its amino acid composition, the CTD was previously proposed to function in chromatin as an unstructured polycation. However, structural studies have shown that the CTD adopts detectable secondary structure when interacting with DNA and macromolecular crowding agents. We describe classic and recent experiments defining the function of this domain in chromatin folding and emerging data indicating that the function of this protein may be linked to intrinsic disorder.

Towards a unifying mechanism for ClpB/Hsp104-mediated protein disaggregation and prion propagationThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (1) ◽  
pp. 63-75 ◽  
Author(s):  
Tobias Haslberger ◽  
Bernd Bukau ◽  
Axel Mogk
Keyword(s):  
Review Process ◽  
Peer Review Process ◽  
Special Issue ◽  
Yeast Prions ◽  
Substrate Interaction ◽  
Initial Substrate ◽  
Hsp70 Chaperone ◽  
Prion Propagation ◽  
Precise Role ◽  
Selection Of

The oligomeric AAA+ chaperones ClpB/Hsp104 mediate the reactivation of aggregated proteins, an activity that is crucial for the survival of cells during severe stress. Hsp104 is also essential for the propagation of yeast prions by severing prion fibres. Protein disaggregation depends on the cooperation of ClpB/Hsp104 with a cognate Hsp70 chaperone system. While Hsp70 chaperones are also involved in prion propagation, their precise role is much less well defined compared with its function in aggregate solubilization. Therefore, it remained unclear whether both ClpB/Hsp104 activities are based on common or different mechanisms. Novel data show that ClpB/Hsp104 uses a motor threading activity to remodel both protein aggregates and prion fibrils. Moreover, transfer of both types of substrates to the ClpB/Hsp104 processing pore site requires initial substrate interaction of Hsp70. Together these data emphasize the similarity of thermotolerance and prion propagation pathways and point to a shared mechanistic principle of Hsp70–ClpB/Hsp104-mediated solubilization of amorphous and ordered aggregates.

Glycogen: an overview of possible regulatory roles of the proteins associated with the granuleThis paper is one of a selection of papers published in this Special Issue, entitled 14th International Biochemistry of Exercise Conference – Muscles as Molecular and Metabolic Machines, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 34 (3) ◽  
pp. 488-492 ◽  
Author(s):  
Terry E. Graham
Keyword(s):  
Peer Review ◽  
Muscle Glycogen ◽  
Review Process ◽  
Peer Review Process ◽  
Glycogen Granule ◽  
Special Issue ◽  
Dynamic Regulation ◽  
Considerable Evidence ◽  
The Past ◽  
Selection Of

While scientists have routinely measured muscle glycogen in many metabolic situations for over 4 decades, there is surprisingly little known regarding its regulation. In the past decade, considerable evidence has illustrated that the carbohydrate stores in muscle are not homogeneous, and it is very likely that metabolic pools exist or that each granule has independent regulation. The fundamental aspects appear to be associated with a complex set of proteins that associate with both the granule and each other in a dynamic fashion. Some of the proteins are enzymes and others play scaffolding roles. A number of the proteins can translocate, depending on the metabolic stimulus. These various processes appear to be the mechanisms that give the glycogen granule precise yet dynamic regulation. This may also allow the stores to serve as an important metabolic regulator of other metabolic events.

Saikosaponin-d attenuates the development of liver fibrosis by preventing hepatocyte injuryThis paper is one of a selection of papers in this Special Issue, entitled International Symposium on Recent Advances in Molecular, Clinical, and Social Medicine, and has undergone the Journal's usual peer-review process.

2007 ◽  
Vol 85 (2) ◽  
pp. 189-195 ◽  
Author(s):  
Jianghong Fan ◽  
Xin Li ◽  
Ping Li ◽  
Ning Li ◽  
Tailing Wang ◽  
...  
Keyword(s):  
Liver Fibrosis ◽  
Review Process ◽  
Peer Review Process ◽  
Chinese Herbs ◽  
Special Issue ◽  
Beneficial Effects ◽  
Hepatocyte Injury ◽  
Alanine Aminotransferase Level ◽  
Tgf Β1 ◽  
Selection Of

Treatment of liver fibrosis and cirrhosis remains a challenging field. Hepatocyte injury and the activation of hepatic stellate cells are the 2 major events in the development of liver fibrosis and cirrhosis. It is known that several Chinese herbs have significant beneficial effects on the liver; therefore, the purpose of the present study was to investigate the therapeutic effect of saikosaponin-d (SSd) on liver fibrosis and cirrhosis. A rat model of liver fibrosis was established using the dimethylnitrosamine method. Liver tissue and serum were used to examine the effect of SSd on liver fibrosis. A hepatocyte culture was also used to investigate how SSd can protect hepatocytes from oxidative injury induced by carbon tetrachloride. The results showed that SSd significantly reduced collagen I deposition in the liver and alanine aminotransferase level in the serum. Moreover, SSd decreased the content of TGF-β1 in the liver, which was significantly elevated after dimethylnitrosamine induced liver fibrosis. Furthermore, SSd was able to alleviate hepatocyte injury from oxidative stress. In conclusion, SSd could postpone the development of liver fibrosis by attenuating hepatocyte injury.

In vitro chromatin self-association and its relevance to genome architectureThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

2006 ◽  
Vol 84 (4) ◽  
pp. 411-417 ◽  
Author(s):  
Xu Lu ◽  
Joshua M. Klonoski ◽  
Michael G. Resch ◽  
Jeffrey C. Hansen
Keyword(s):  
Peer Review ◽  
West Coast ◽  
Review Process ◽  
Peer Review Process ◽  
Special Issue ◽  
Eukaryotic Nucleus ◽  
Self Association ◽  
Selection Of

Chromatin in a eukaryotic nucleus is condensed through 3 hierarchies: primary, secondary, and tertiary chromatin structures. In vitro, when induced with cations, chromatin can self-associate and form large oligomers. This self-association process has been proposed to mimic processes involved in the assembly and maintenance of tertiary chromatin structures in vivo. In this article, we review 30 years of studies of chromatin self-association, with an emphasis on the evidence suggesting that this in vitro process is physiologically relevant.

scholarly journals Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical frameworkThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (2) ◽  
pp. 359-369 ◽  
Author(s):  
Jeremy L. England ◽  
Vijay S. Pande
Keyword(s):  
Protein Folding ◽  
Self Assembly ◽  
Peer Review Process ◽  
Cellular Biology ◽  
Confined Water ◽  
Wide Range ◽  
Statistical Mechanical Model ◽  
Statistical Mechanical ◽  
Selection Of

Water permeates all life, and mediates forces that are essential to the process of macromolecular self-assembly. Predicting these forces in a given biological context is challenging, since water organizes itself differently next to charged and hydrophobic surfaces, both of which are typically at play on the nanoscale in vivo. In this work, we present a simple statistical mechanical model for the forces water mediates between different confining surfaces, and demonstrate that the model qualitatively unifies a wide range of phenomena known in the simulation literature, including several cases of protein folding under confinement.

scholarly journals Protection and replication of telomeres in fission yeastThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (5) ◽  
pp. 747-758 ◽  
Author(s):  
Bettina A. Moser ◽  
Toru M. Nakamura
Keyword(s):  
Cell Cycle ◽  
Fission Yeast ◽  
Review Process ◽  
Peer Review Process ◽  
Yeast Cells ◽  
Special Issue ◽  
Yeast Saccharomyces Cerevisiae ◽  
Linear Chromosomes ◽  
Selection Of ◽  
The Way

Telomeres, the natural ends of linear chromosomes, must be protected and completely replicated to guarantee genomic stability in eukaryotic cells. However, the protected state of telomeres is not compatible with recruitment of telomerase, an enzyme responsible for extending telomeric G-rich repeats during S-phase; thus, telomeres must undergo switches from a protected state to an accessible state during the cell cycle. In this minireview, we will summarize recent advances in our understanding of proteins involved in the protection and replication of telomeres, and the way these factors are dynamically recruited to telomeres during the cell cycle. We will focus mainly on recent results from fission yeast Schizosaccharomyces pombe , and compare them with results from budding yeast Saccharomyces cerevisiae and mammalian cell studies. In addition, a model for the way in which fission yeast cells replicate telomeres will be presented.

eIF4E, the mRNA cap-binding protein: from basic discovery to translational researchThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

2008 ◽  
Vol 86 (2) ◽  
pp. 178-183 ◽  
Author(s):  
Nahum Sonenberg
Keyword(s):  
Translational Control ◽  
Review Process ◽  
Peer Review Process ◽  
Initiation Factor ◽  
Special Issue ◽  
Regulate Gene Expression ◽  
Physiological Conditions ◽  
Eukaryotic Mrnas ◽  
Prime Target ◽  
Selection Of

Translational control is an important strategy by which eukaryotic cells regulate gene expression. Translation is the last step in the flow of genetic information, and regulation at this level allows an immediate and rapid response to changes under physiological conditions. Because the processes of mRNA biogenesis, including transcription, splicing, and export to the cytoplasm, are time consuming, the use of pre-existing mRNAs via the control of translation is advantageous in many circumstances. A prime target of translational control is the initiation factor eIF4E, which recognizes the m7GpppN cap structure present at the 5′ end of all nuclear transcribed eukaryotic mRNAs. In this article I describe the discovery of eIF4E, its mechanism of action in translation initiation, and its role in the control of cancer and innate immunity.

Cryo electron microscopy structures of Hsp100 proteins: crowbars in or out?This paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (1) ◽  
pp. 89-96 ◽  
Author(s):  
Petra Wendler ◽  
Helen R Saibil
Keyword(s):  
Electron Microscopy ◽  
Peer Review ◽  
Atomic Structure ◽  
Review Process ◽  
Peer Review Process ◽  
Experimental Information ◽  
Related Protein ◽  
Special Issue ◽  
Cryo Electron Microscopy ◽  
Selection Of

Independent cryo electron microscopy (cryo-EM) studies of the closely related protein disaggregases ClpB and Hsp104 have resulted in two different models of subunit arrangement in the active hexamer. We compare the EM maps and resulting atomic structure fits, discuss their differences, and relate them to published experimental information in an attempt to discriminate between models. In addition, we present some general assessment criteria for low-resolution cryo-EM maps to offer non-structural biologists tools to evaluate these structures.

Sign in / Sign up

Export Citation Format

Share Document