Comparative analysis of the Epstein-Barr virus encoded nuclear proteins of EBNA-3 family

Surya Pavan Yenamandra; Ramakrishna Sompallae; George Klein; Elena Kashuba

doi:10.1016/j.compbiomed.2009.08.006

Comparative analysis of the Epstein-Barr virus encoded nuclear proteins of EBNA-3 family

Surya Pavan Yenamandra
, Ramakrishna Sompallae
, George Klein
, Elena Kashuba

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Abstract

It is known that the EBNA-3 family proteins (EBNA-3, -4 and -6, alternative nomenclature EBNA-3A, B and C correspondingly) show a limited sequence similarity. We have analyzed EBNA-3 proteins both at the primary sequence and secondary structure levels. EBNA-3 and EBNA-4 were structurally more similar compared to other combinations with EBNA-6. We found "Stonin Homology Domain" profile in EBNA-4 and "Proline Rich Domain" in all EBNA-3 family of proteins. We have also found positive and negative charge clusters in all three proteins and mixed charge clusters in EBNA-3. Charged clusters are believed to play an important role in interactions with DNA or signaling proteins. Additionally, unique primary sequence repeats were found in all three proteins.

Original language	English
Pages (from-to)	1036-1042
Number of pages	7
Journal	Computers in Biology and Medicine
Volume	39
Issue number	11
DOIs	https://doi.org/10.1016/j.compbiomed.2009.08.006
State	Published - Nov 2009
Externally published	Yes

Keywords

Charge clusters
EBNA3 family proteins
Praline rich domain
Secondary structure analysis
Stonin homology domain

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10.1016/j.compbiomed.2009.08.006

Cite this

@article{8d3d9c0db4104fb492a924f0b8fb39f3,

title = "Comparative analysis of the Epstein-Barr virus encoded nuclear proteins of EBNA-3 family",

abstract = "It is known that the EBNA-3 family proteins (EBNA-3, -4 and -6, alternative nomenclature EBNA-3A, B and C correspondingly) show a limited sequence similarity. We have analyzed EBNA-3 proteins both at the primary sequence and secondary structure levels. EBNA-3 and EBNA-4 were structurally more similar compared to other combinations with EBNA-6. We found {"}Stonin Homology Domain{"} profile in EBNA-4 and {"}Proline Rich Domain{"} in all EBNA-3 family of proteins. We have also found positive and negative charge clusters in all three proteins and mixed charge clusters in EBNA-3. Charged clusters are believed to play an important role in interactions with DNA or signaling proteins. Additionally, unique primary sequence repeats were found in all three proteins.",

keywords = "Charge clusters, EBNA3 family proteins, Praline rich domain, Secondary structure analysis, Stonin homology domain",

author = "Yenamandra, \{Surya Pavan\} and Ramakrishna Sompallae and George Klein and Elena Kashuba",

note = "Funding Information: We thank professor Chanchal K Mitra and Dr. Tatyana Sandalova for a fruitful discussion of this work. Swedish Institute, Cancer Foundation, a matching grant from the Concern Foundation, Los Angeles, and the Cancer Research Institute, New York supported this work.",

year = "2009",

month = nov,

doi = "10.1016/j.compbiomed.2009.08.006",

language = "English",

volume = "39",

pages = "1036--1042",

journal = "Computers in Biology and Medicine",

issn = "0010-4825",

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T1 - Comparative analysis of the Epstein-Barr virus encoded nuclear proteins of EBNA-3 family

AU - Yenamandra, Surya Pavan

AU - Sompallae, Ramakrishna

AU - Klein, George

AU - Kashuba, Elena

N1 - Funding Information: We thank professor Chanchal K Mitra and Dr. Tatyana Sandalova for a fruitful discussion of this work. Swedish Institute, Cancer Foundation, a matching grant from the Concern Foundation, Los Angeles, and the Cancer Research Institute, New York supported this work.

PY - 2009/11

Y1 - 2009/11

N2 - It is known that the EBNA-3 family proteins (EBNA-3, -4 and -6, alternative nomenclature EBNA-3A, B and C correspondingly) show a limited sequence similarity. We have analyzed EBNA-3 proteins both at the primary sequence and secondary structure levels. EBNA-3 and EBNA-4 were structurally more similar compared to other combinations with EBNA-6. We found "Stonin Homology Domain" profile in EBNA-4 and "Proline Rich Domain" in all EBNA-3 family of proteins. We have also found positive and negative charge clusters in all three proteins and mixed charge clusters in EBNA-3. Charged clusters are believed to play an important role in interactions with DNA or signaling proteins. Additionally, unique primary sequence repeats were found in all three proteins.

AB - It is known that the EBNA-3 family proteins (EBNA-3, -4 and -6, alternative nomenclature EBNA-3A, B and C correspondingly) show a limited sequence similarity. We have analyzed EBNA-3 proteins both at the primary sequence and secondary structure levels. EBNA-3 and EBNA-4 were structurally more similar compared to other combinations with EBNA-6. We found "Stonin Homology Domain" profile in EBNA-4 and "Proline Rich Domain" in all EBNA-3 family of proteins. We have also found positive and negative charge clusters in all three proteins and mixed charge clusters in EBNA-3. Charged clusters are believed to play an important role in interactions with DNA or signaling proteins. Additionally, unique primary sequence repeats were found in all three proteins.

KW - Charge clusters

KW - EBNA3 family proteins

KW - Praline rich domain

KW - Secondary structure analysis

KW - Stonin homology domain

UR - https://www.scopus.com/pages/publications/70349787153

U2 - 10.1016/j.compbiomed.2009.08.006

DO - 10.1016/j.compbiomed.2009.08.006

M3 - Article

C2 - 19762010

AN - SCOPUS:70349787153

SN - 0010-4825

VL - 39

SP - 1036

EP - 1042

JO - Computers in Biology and Medicine

JF - Computers in Biology and Medicine

IS - 11

ER -

Comparative analysis of the Epstein-Barr virus encoded nuclear proteins of EBNA-3 family

Abstract

Keywords

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