High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments.
Since the advent of large-scale genomic sequencing, and the consequent availability of large numbers of homologous protein sequences, there has been burgeoning development of methods for extracting functional information from multiple sequence alignments (MSAs). One type of analysis seeks to identify specificity determining positions (SDPs) based on the assumption that such positions are highly conserved within groups of sequences sharing functional specificity, but conserved to different amino acids in different specificity groups. This unsupervised approach to utilizing evolutionary information may elucidate mechanisms of specificity in protein-protein interactions, catalytic activity of enzymes, sensitivity to allosteric regulation, and other types of protein functionality. We present an analysis of SDPs in the LacI family of transcriptional regulators in which we 1) relax the constraint that all specificity groups must contribute to SDP signal, and 2) use a novel approach to robust treatment of sequence alignment uncertainty based on sub-sampling. We find that the vast majority of SDP signal occurs at positions with a conservation pattern that significantly complicates detection by previously described methods. This pattern, which we term "partial SDP", consists of the commonly accepted SDP conservation pattern among a subset of specificity groups and strong degeneracy among the rest. An upshot of this fact is that the SDP complement of every specificity group appears to be unique. Additionally, sub-sampling gives us the ability to assign a confidence interval to the SDP score, as well as increase fidelity, as compared to analysis of a single, comprehensive alignment-the current standard in multiple sequence alignment methodologies.
Biomedical Engineering Department, Washington University in St. Louis, St. Louis, Missouri, 63130, United States of America.|Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, United States of America.
Roman
R
Sloutsky
Biomedical Engineering Department, Washington University in St. Louis, St. Louis, Missouri, 63130, United States of America.|Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, Missouri, 63130, United States of America.
Kristen M
http://orcid.org/0000-0001-7146-9592
KM
Naegle
Nucleic Acids Res. 2016 Jan 4;44(D1):D574-80
26578574
PLoS Curr. 2010 Nov 19;2:RRN1198
21113338
Brief Bioinform. 2013 Jan;14(1):1-12
22408191
IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):1108-19
21566256
Bioinformatics. 2005 Jun 1;21(11):2629-35
15797914
J Mol Biol. 2007 Oct 26;373(3):801-10
17868687
BMC Bioinformatics. 2009 Jul 02;10:207
19573245
Mol Biol Evol. 2000 Apr;17(4):540-52
10742046
Bioinformatics. 2006 Jun 15;22(12):1440-8
16551661
J Mol Biol. 2004 Mar 5;336(5):1265-82
15037084
Nucleic Acids Res. 2016 Jul 8;44(W1):W344-50
27166375
Bioinformatics. 2008 Nov 1;24(21):2445-52
18776193
Mol Biol Evol. 2000 Dec;17(12):1842-53
11110900
Mol Biol Evol. 2010 Aug;27(8):1759-67
20207713
Bioinformatics. 2001 Jun;17(6):573-4
11395440
Bioinformatics. 2008 Jul 1;24(13):1473-80
18450811
Mol Biol Evol. 2013 Apr;30(4):772-80
23329690
J Mol Biol. 2003 Feb 28;326(4):1289-302
12589769
J Mol Biol. 2000 Oct 13;303(1):61-76
11021970
J Mol Biol. 2002 Aug 2;321(1):7-20
12139929
Protein Sci. 2004 Feb;13(2):443-56
14739328
Bioinformatics. 2008 Apr 1;24(7):908-15
18304936
Proteins. 2006 Jun 1;63(4):1018-30
16532452
Genome Res. 2004 May;14(5):942-50
15123590
Bioinformatics. 2013 Apr 15;29(8):989-95
23428640
J Mol Biol. 2016 Feb 22;428(4):671-678
26410588
J Mol Biol. 1996 Mar 29;257(2):342-58
8609628
Mol Biol Evol. 2005 Mar;22(3):792-802
15590907
Front Zool. 2010 Mar 31;7:10
20356385
Genome Biol. 2009 Feb 02;10(2):207
19226439
Genome Res. 2004 Jun;14(6):1188-90
15173120
Nat Rev Genet. 2002 Nov;3(11):827-37
12415313
Mol Biol Evol. 2006 Nov;23(11):2090-100
16891377
PLoS One. 2012;7(1):e30288
22272325
Nat Struct Biol. 1995 Feb;2(2):171-8
7749921
Science. 2008 Jan 25;319(5862):473-6
18218900
Nucleic Acids Res. 1990 Oct 25;18(20):6097-100
2172928
Mol Biol Evol. 2012 Apr;29(4):1125-39
22049066
Proteins. 2006 Aug 15;64(3):559-74
16736488
Nucleic Acids Res. 2006;34(22):6540-8
17130172
Bioinformatics. 2006 Jan 15;22(2):164-71
16278237
Nucleic Acids Res. 2012 Nov;40(21):11139-54
22965134
Mol Biol Evol. 1997 Apr;14(4):428-41
9100373
Syst Biol. 2006 Apr;55(2):314-28
16611602
Genome Biol. 2007;8(11):R232
17976239
Nucleic Acids Res. 2005 Jan 20;33(2):511-8
15661851