Cavities of alpha(1)-antitrypsin that play structural and functional roles.


Abstract

The native form of inhibitory serine protease inhibitors (serpins) is strained, which is critical for their inhibitory activity. Previous studies on stabilizing mutations of alpha(1)-antitrypsin, a prototype of serpins, indicated that cavities provide a structural basis for the native strain of the molecule. We have systematically mapped the cavities of alpha(1)-antitrypsin that play such structural and functional roles by designing cavity-filling mutations at residues that line the walls of the cavities. Results show that energetically unfavorable cavities are distributed throughout the alpha(1)-antitrypsin molecule, and the cavity-filling mutations stabilized the native conformation at 8 out of 10 target sites. The stabilization effect of the individual cavity-filling mutations of alpha(1)-antitrypsin varied (0.2-1.9 kcal/mol for each additional methylene group) and appeared to depend largely on the structural flexibility of the cavity environment. Cavity-filling mutations that decreased inhibitory activity of alpha(1)-antitrypsin were localized in the loop regions that interact with beta-sheet A distal from the reactive center loop. The results are consistent with the notion that beta-sheet A and the structure around it mobilize when alpha(1)-antitrypsin forms a complex with a target protease. Study holds ProTherm entries: 11578, 11579, 11580, 11581, 11582, 11583, 11584, 11585, 11586, 11587, 11588, 11589, 11590, 11591, 11592, 11593, 11594, 11595, 11596, 11597, 11598, 11599, 11600, 11601, 11602, 11603, 11604, 11605 Extra Details: additive : EDTA(1 mM), alpha1-antitrypsin; cavity-filling mutations; conformational stability;,native strain; molecular packing

Submission Details

ID: bGQQcUSY3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:42 p.m.

Version: 1

Publication Details
Lee C;Maeng JS;Kocher JP;Lee B;Yu MH,Protein Sci. (2001) Cavities of alpha(1)-antitrypsin that play structural and functional roles. PMID:11420446
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1ATU 1997-05-11T00:00:00+0000 2.7 UNCLEAVED ALPHA-1-ANTITRYPSIN
1D5S 1999-10-11T00:00:00+0000 3.0 CRYSTAL STRUCTURE OF CLEAVED ANTITRYPSIN POLYMER
1D5S 1999-10-11T00:00:00+0000 3.0 CRYSTAL STRUCTURE OF CLEAVED ANTITRYPSIN POLYMER
1EZX 2000-05-12T00:00:00+0000 2.6 CRYSTAL STRUCTURE OF A SERPIN:PROTEASE COMPLEX
1EZX 2000-05-12T00:00:00+0000 2.6 CRYSTAL STRUCTURE OF A SERPIN:PROTEASE COMPLEX
1HP7 2000-12-12T00:00:00+0000 2.1 A 2.1 ANGSTROM STRUCTURE OF AN UNCLEAVED ALPHA-1-ANTITRYPSIN SHOWS VARIABILITY OF THE REACTIVE CENTER AND OTHER LOOPS
1IZ2 2002-09-19T00:00:00+0000 2.2 Interactions causing the kinetic trap in serpin protein folding
1KCT 1996-08-06T00:00:00+0000 3.46 ALPHA1-ANTITRYPSIN
1OO8 2003-03-03T00:00:00+0000 2.65 CRYSTAL STRUCTURE OF A1PI-PITTSBURGH IN THE NATIVE CONFORMATION
1OPH 2003-03-05T00:00:00+0000 2.3 NON-COVALENT COMPLEX BETWEEN ALPHA-1-PI-PITTSBURGH AND S195A TRYPSIN

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
93.1 Alpha-1-antitrypsin O00394 A1AT_CHLAE
92.4 Alpha-1-antitrypsin P01010 A1AT_PAPAN
96.4 Alpha-1-antitrypsin Q5RCW5 A1AT_PONAB
100.0 Alpha-1-antitrypsin P01009 A1AT_HUMAN