Searching for methyllysine-binding aromatic cages

2021 ◽  
Vol 478 (19) ◽  
pp. 3613-3619
Author(s):  
Kendra R. Vann ◽  
Yashavantha L. Vishweshwaraiah ◽  
Nikolay V. Dokholyan ◽  
Tatiana G. Kutateladze
Keyword(s):  
Cell Signaling ◽  
Cell Nucleus ◽  
Structural Motif ◽  
Histone Proteins ◽  
Mining Algorithm ◽  
Biological Importance ◽  
Lysine Residues ◽  
Binding Mechanisms

Methylation of lysine residues plays crucial roles in a wide variety of cell signaling processes. While the biological importance of recognition of methylated histones by reader domains in the cell nucleus is well established, the processes associated with methylation of non-histone proteins, particularly in the cytoplasm of the cell, are not well understood. Here, we describe a search for potential methyllysine readers using a rapid structural motif-mining algorithm Erebus, the PDB database, and knowledge of the methyllysine binding mechanisms.

Thiazolidinone: A Structural Motif of Great Synthetic and Biological Importance

2021 ◽  
pp. 131771
Author(s):  
Faisal M. Aqlan ◽  
Abdullah S. Al-Bogami ◽  
Norah F. Alqahtani ◽  
Mohmmad Younus Wani ◽  
Salman A. Khan
Keyword(s):  
Structural Motif ◽  
Biological Importance

scholarly journals Role of HSV-1 Capsid Vertex-Specific Component (CVSC) and Viral Terminal DNA in Capsid Docking at the Nuclear Pore

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2515
Author(s):  
José Ramon Villanueva-Valencia ◽  
Efthymios Tsimtsirakis ◽  
Alex Evilevitch
Keyword(s):  
Cell Nucleus ◽  
Experimental System ◽  
Structural Motif ◽  
Nuclear Pore ◽  
Structural Element ◽  
Viral Dna ◽  
Specific Component ◽  
Correct Orientation ◽  
Hsv 1

Penetration of the viral genome into a host cell nucleus is critical for initiation of viral replication for most DNA viruses and a few RNA viruses. For herpesviruses, viral DNA ejection into a nucleus occurs when the capsid docks at the nuclear pore complex (NPC) basket with the correct orientation of the unique capsid portal vertex. It has been shown that capsid vertex-specific component (CVSC) proteins, which are located at the twelve vertices of the human herpes simplex virus type 1 (HSV-1) capsid, interact with nucleoporins (Nups) of NPCs. However, it remained unclear whether CVSC proteins determine capsid-to-NPC binding. Furthermore, it has been speculated that terminal DNA adjacent to the portal complex of DNA-filled C-capsids forms a structural motif with the portal cap (which retains DNA in the capsid), which mediates capsid-NPC binding. We demonstrate that terminal viral DNA adjacent to the portal proteins does not present a structural element required for capsid-NPC binding. Our data also show that level of CVSC proteins on the HSV-1 capsid affects level of NPC binding. To elucidate the capsid-binding process, we use an isolated, reconstituted cell nucleus system that recapitulates capsid-nucleus binding in vivo without interference from trafficking kinetics of capsids moving toward the nucleus. This allows binding of non-infectious capsid maturation intermediates with varying levels of vertex-specific components. This experimental system provides a platform for investigating virus–host interaction at the nuclear membrane.

Histone modifications and their role in epigenetics of cancer

2021 ◽  
Vol 28 ◽  
Author(s):  
Sumera Zaib ◽  
Nehal Rana ◽  
Imtiaz Khan
Keyword(s):  
Histone Modifications ◽  
Cell Function ◽  
Contributing Factors ◽  
Histone Proteins ◽  
Dna Repair Mechanisms ◽  
Current Review ◽  
Lysine Residues ◽  
Repair Mechanisms ◽  
Enhanced Expression

: Epigenetic regulations play a crucial role in the expression of various genes that are important in the normal cell function. Any alteration in these epigenetic mechanisms can lead to the modification of histone and DNA resulting in the silencing or enhanced expression of some genes causing various diseases. Acetylation, methylation, ribosylation or phosphorylation of histone proteins modifies its interaction with the DNA, consequently changing the ratio of heterochromatin and euchromatin. Terminal lysine residues of histone proteins serve as potential targets of such epigenetic modifications. The current review focuses on the histone modifications, their contributing factors, role of these modifications on metabolism leading to cancer and methylation of histone in cancer affects the DNA repair mechanisms.

scholarly journals Consciousness and Cell Memory: A Dynamic Epigenetic Interrelationship

2011 ◽  
Vol 38 (5) ◽  
pp. 681-688 ◽  
Author(s):  
Arthur J. Hudson
Keyword(s):  
Amino Acids ◽  
Cell Nucleus ◽  
Memory Consolidation ◽  
Human Studies ◽  
Methyl Groups ◽  
Cell Memory ◽  
Histone Proteins ◽  
Non Coding Rnas ◽  
The Brain

ABSTRACT:There have been great advances in the neurological sciences in recent years including some in the higher functions of the brain such as memory but one of the more critical of these with close ties to memory is consciousness which remains an enigma. Revolutionary developments in genetics during the last two decades, referred to as epigenetics, have provided opportunity for discovery. The chromatin in the cell nucleus consists mainly of DNA nucleotides and histone proteins and the DNA is dynamically and epigenetically altered by the local actions of enzymes and trans-acting factors on the adjacent histone amino acids. DNA is also directly activated or inhibited by methyl groups and by non-coding RNAs. Epigenetics is a determinant in long-term cell memory consolidation and, as recently demonstrated in animal and human studies and described here, these effects enable a rapid and extraordinarily complex cognitive matching of cell memory to experience during consciousness.

Organization of transcription and pre-mRNA splicing within the mammalian cell nucleus

1995 ◽  
Vol 53 ◽  
pp. 768-769
Author(s):  
D.L. Spector ◽  
S. Huang ◽  
S. Kaurin
Keyword(s):  
Rna Polymerase Ii ◽  
Cell Nucleus ◽  
Functional Organization ◽  
Mrna Splicing ◽  
Splicing Factors ◽  
Interchromatin Granule Clusters ◽  
Interchromatin Granule ◽  
Nuclear Regions ◽  
Relationship Of ◽  
Perichromatin Fibrils

We have been interested in the organization of RNA polymerase II transcription and pre-mRNA splicing within the cell nucleus. Several models have been proposed for the functional organization of RNA within the eukaryotic nucleus and for the relationship of this organization to the distribution of pre-mRNA splicing factors. One model suggests that RNAs which must be spliced are capable of recruiting splicing factors to the sites of transcription from storage and/or reassembly sites. When one examines the organization of splicing factors in the nucleus in comparison to the sites of chromatin it is clear that splicing factors are not localized in coincidence with heterochromatin (Fig. 1). Instead, they are distributed in a speckled pattern which is composed of both perichromatin fibrils and interchromatin granule clusters. The perichromatin fibrils are distributed on the periphery of heterochromatin and on the periphery of interchromatin granule clusters as well as being diffusely distributed throughout the nucleoplasm. These nuclear regions have been previously shown to represent initial sites of incorporation of 3H-uridine.

Immunolocalization of nuclear antigens in cryofixed cells which have been prepared by molecular distillation drying or freeze-substitution

1990 ◽  
Vol 48 (3) ◽  
pp. 898-899
Author(s):  
David L. Spector ◽  
Robert J. Derby
Keyword(s):  
Cell Nucleus ◽  
Molecular Distillation ◽  
Functional Organization ◽  
Freeze Substitution ◽  
3 Dimensional ◽  
Small Nuclear Ribonucleoprotein ◽  
Nuclear Antigens ◽  
Dimensional Reconstruction ◽  
Nuclear Regions ◽  
Immunoperoxidase Labeling

Studies in our laboratory are involved in evaluating the structural and functional organization of the mammalian cell nucleus. Since several major classes (U1, U2, U4/U6, U5) of small nuclear ribonucleoprotein particles (snRNPs) play a crucial role in the processing of pre-mRNA molecules, we have been interested in the localization of these particles within the cell nucleus. Using pre-embedding immunoperoxidase labeling combined with 3-dimensional reconstruction, we have recently shown that nuclear regions enriched in snRNPs form a reticular network within the nucleoplasm which extends between the nucleolar surface and the nuclear envelope. In the present study we were inte rested in extending these nuclear localizations using cell preparation techniques which avoid slow penetration of fixatives, chemical crosslinking of potential antigens and solvent extraction. CHOC 400 cells were cryofixed using a CF 100 ultra rapid cooling device (LifeCell Corp.). After cryofixation cells were molecular distillation dried, vapor osmicated, in filtra ted in 100% Spurr resin in vacuo and polymerized in molds a t 60°C. Using this procedure we were able to evaluate the distribution of snRNPs in resin embedded cells which had not been chemically fixed, incubated in cryoprotectants or extracted with solvents.

The Biological Importance of Bile Salts

1979 ◽  
Vol 7 (6) ◽  
pp. 1323-1323
Author(s):  
H. DANIELSSON
Keyword(s):  
Bile Salts ◽  
Biological Importance
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