PMID- 25156076
OWN - NLM
STAT- MEDLINE
DCOM- 20150616
LR  - 20141010
IS  - 1476-928X (Electronic)
IS  - 1476-9271 (Linking)
VI  - 52
DP  - 2014 Oct
TI  - Molecular dynamics simulations of lectin domain of FimH and immunoinformatics for 
      the design of potential vaccine candidates.
PG  - 18-24
LID - S1476-9271(14)00081-4 [pii]
LID - 10.1016/j.compbiolchem.2014.08.002 [doi]
AB  - Adhesion of uropathogenic E. coli (UPEC) to uroepithelial cell receptors is 
      facilitated through the lectin domain of FimH adhesin. In the current study, 
      Molecular Dynamics (MD) simulations were performed for the lectin domain of FimH 
      from UPEC J96. The high affinity state lectin domain was found to be stable and 
      rigid during the simulations. Further, based on conserved subsequences around one 
      of the disulfide forming cysteines, two sequence motifs were designed. An 
      immunoinformatics approach was utilized to identify linear and discontinuous 
      epitopes for the lectin domain of FimH. We propose that the accessibility of 
      predicted epitopes should also be assessed in a dynamic aqueous environment to 
      evaluate the potential of vaccine candidates. Since MD simulation data enables 
      assessing the accessibility in a dynamic environment, we evaluated the 
      accessibility of the top ranked discontinuous and linear epitopes using 
      structures obtained at every nanosecond (ns) in the 1-20 ns MD simulation 
      timeframe. Knowledge gained in this study has a potential utility in the design 
      of vaccine candidates for Urinary Tract Infection (UTI).
CI  - Copyright (c) 2014 Elsevier Ltd. All rights reserved.
FAU - Singaravelu, Muthukumar
AU  - Singaravelu M
AD  - Centre for Biotechnology, Anna University, Chennai 600 025, India; National 
      Institute of Ocean Technology, Chennai 600 100, India.
FAU - Selvan, Anitha
AU  - Selvan A
AD  - Centre for Biotechnology, Anna University, Chennai 600 025, India.
FAU - Anishetty, Sharmila
AU  - Anishetty S
AD  - Centre for Biotechnology, Anna University, Chennai 600 025, India. Electronic 
      address: s_anishetty@yahoo.co.uk.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140815
PL  - England
TA  - Comput Biol Chem
JT  - Computational biology and chemistry
JID - 101157394
RN  - 0 (Adhesins, Escherichia coli)
RN  - 0 (Epitopes)
RN  - 0 (Lectins)
RN  - 0 (Vaccines)
RN  - 0 (fimH protein, E coli)
RN  - 147680-16-8 (Fimbriae Proteins)
SB  - IM
MH  - Adhesins, Escherichia coli/*chemistry
MH  - Computational Biology
MH  - *Epitopes
MH  - Fimbriae Proteins/*chemistry
MH  - Lectins/*chemistry
MH  - Molecular Dynamics Simulation
MH  - Protein Structure, Tertiary
MH  - Vaccines
OTO - NOTNLM
OT  - FimH adhesin
OT  - Immunoinformatics
OT  - Molecular dynamics simulation
OT  - Motif
OT  - Rigidity
OT  - Vaccine
EDAT- 2014/08/27 06:00
MHDA- 2015/06/17 06:00
CRDT- 2014/08/27 06:00
PHST- 2014/04/02 00:00 [received]
PHST- 2014/08/11 00:00 [revised]
PHST- 2014/08/11 00:00 [accepted]
PHST- 2014/08/27 06:00 [entrez]
PHST- 2014/08/27 06:00 [pubmed]
PHST- 2015/06/17 06:00 [medline]
AID - S1476-9271(14)00081-4 [pii]
AID - 10.1016/j.compbiolchem.2014.08.002 [doi]
PST - ppublish
SO  - Comput Biol Chem. 2014 Oct;52:18-24. doi: 10.1016/j.compbiolchem.2014.08.002. 
      Epub 2014 Aug 15.