Protein stability in nanocages: a novel approach for influencing protein stability by molecular confinement.


Abstract

Confinement of a protein in a small inert space and microviscosity are known to increase its thermodynamic stability in a way similar to the mechanisms that stabilize protein fold in the cell. Here, to examine the influence of confinement on protein stability we choose four test cases of single domain proteins characterized by a wide range of melting temperatures, from approximately 73 degrees C of titin I27 to approximately 36 degrees C of yeast frataxin. All proteins are stabilized when confined in the gel, the most dramatic stabilization being that of yeast frataxin, whose melting temperature increased by almost 5 degrees C in the gel. In addition to being simple to use, this approach allows us to change the viscosity of the solvent without changing its composition or altering the structure of the proteins. The dimensions of the pores of the gels fall in the nanometer range, hence they are similar to those of the chaperone cavity. This method could therefore be used as a novel and powerful approach for protein folding studies. Study holds ProTherm entries: 16993, 16994, 16995, 16996, 16997, 16998, 16999, 17000, 17001, 17002, 17003, 17004, 17005, 17006, 17007, 17008, 17009, 17010, 17011, 17012, 17013, 17014 Extra Details: viscosity; confinement; nanocages; chaperones; fluorescence

Submission Details

ID: GzA7h6WT3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:49 p.m.

Version: 1

Publication Details
Bolis D;Politou AS;Kelly G;Pastore A;Temussi PA,J. Mol. Biol. (2004) Protein stability in nanocages: a novel approach for influencing protein stability by molecular confinement. PMID:14741216
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
1LY7 2002-06-26 The solution structure of the the c-terminal domain of frataxin, the protein responsible for friedreich ataxia
1TIT 1996-07-11 TITIN, IG REPEAT 27, NMR, MINIMIZED AVERAGE STRUCTURE
1TNN 1995-04-20 Tertiary structure of an immunoglobulin-like domain from the giant muscle protein titin: a new member of the I set
1TNM 1995-04-20 TERTIARY STRUCTURE OF AN IMMUNOGLOBULIN-LIKE DOMAIN FROM THE GIANT MUSCLE PROTEIN TITIN: A NEW MEMBER OF THE I SET
1NCT 1996-11-08 TITIN MODULE M5, N-TERMINALLY EXTENDED, NMR
1TIU 1996-07-11 TITIN, IG REPEAT 27, NMR, 24 STRUCTURES
2RQ8 2010-02-02 Solution NMR structure of titin I27 domain mutant
1NCU 1996-11-08 Titin Module M5, N-terminally Extended, NMR
1SOY 2004-11-23 Solution structure of the bacterial frataxin orthologue, CyaY
1BPV 1999-08-12 TITIN MODULE A71 FROM HUMAN CARDIAC MUSCLE, NMR, 50 STRUCTURES
3PUC 2011-12-21 0.96 Atomic resolution structure of titin domain M7
3T3L 2011-08-10 1.15 1.15 A structure of human frataxin variant Q153A
3T3K 2011-08-10 1.24 1.24 A Structure of Friedreich's ataxia frataxin variant Q148R
3S4M 2011-06-29 1.3 Crystal structure of wild-type human frataxin
3S5E 2011-06-29 1.31 Crystal structure of human frataxin variant W155R, one of the Friedreich's ataxia point mutations
3T3T 2011-08-10 1.38 1.38 A structure of human frataxin variant Q148G
1EW4 2000-08-09 1.4 CRYSTAL STRUCTURE OF ESCHERICHIA COLI CYAY PROTEIN REVEALS A NOVEL FOLD FOR THE FRATAXIN FAMILY
3KNB 2009-12-01 1.4 Crystal structure of the titin C-terminus in complex with obscurin-like 1
2P1X 2007-10-02 1.42 Crystal structure analysis of the complex between CyaY and Eu(III)
2WP3 2010-02-16 1.48 Crystal structure of the Titin M10-Obscurin like 1 Ig complex
3S5F 2011-06-29 1.5 Crystal structure of human frataxin variant W155F
3S5D 2011-06-29 1.5 Crystal structure of human frataxin variant W155A
5JDD 2016-09-14 1.53 Crystal structure of I9-I11 tandem from titin (P212121)
3T3X 2011-08-10 1.57 1.57 A structure of Friedreich's ataxia frataxin variant R165C
6H4L 2019-08-07 1.6 Structure of Titin M4 trigonal form
3LPW 2010-09-08 1.65 Crystal structure of the FnIII-tandem A77-A78 from the A-band of titin
2BK8 2006-08-09 1.69 M1 domain from titin
3T3J 2011-08-10 1.7 1.70 A structure of Friedreich's ataxia frataxin variant N146K
2WWK 2010-02-16 1.7 Crystal structure of the Titin M10-Obscurin like 1 Ig F17R mutant complex
5JDJ 2016-08-17 1.74 Crystal structure of domain I10 from titin in space group P212121
1WAA 2006-07-05 1.8 IG27 protein domain
2EFF 2007-10-02 1.8 Crystal structure analysis of the complex between CyaY and Co(II)
1EKG 2000-11-08 1.8 MATURE HUMAN FRATAXIN
4O00 2014-12-24 1.85 Crystal structure of the Titin A-band domain A3
5JDE 2016-09-14 1.9 Crystal structure of I9-I11 tandem from titin (P1)
2Y9R 2011-03-02 1.9 Crystal structure of the M10 domain of Titin
4C4K 2014-09-24 1.95 Crystal structure of the titin M10-Obscurin Ig domain 1 complex
2J8H 2007-08-21 1.99 Structure of the immunoglobulin tandem repeat A168-A169 of titin
5KZ5 2016-08-31 14.3 Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Complex Formed by the Iron Donor, the Sulfur Donor, and the Scaffold
2A38 2006-06-24 2.0 Crystal structure of the N-Terminus of titin
1TKI 1999-06-08 2.0 AUTOINHIBITED SERINE KINASE DOMAIN OF THE GIANT MUSCLE PROTEIN TITIN
4QEG 2015-07-22 2.0 Crystal structure of domain I10 from titin (space group P41)
3QP3 2012-02-15 2.0 Crystal structure of titin domain M4, tetragonal form
5JOE 2016-08-17 2.0 Crystal structure of I81 from titin
3Q5O 2012-02-01 2.05 Crystal structure of human titin domain M10
4JNW 2014-05-14 2.06 Bacterially expressed Titin Kinase
1G1C 2001-10-12 2.1 I1 DOMAIN FROM TITIN
2ILL 2007-02-20 2.2 Anomalous substructure of Titin-A168169
2WWM 2010-02-16 2.3 Crystal structure of the Titin M10-Obscurin like 1 Ig complex in space group P1
5BS0 2016-03-02 2.4 MAGE-A3 Reactive TCR in complex with Titin Epitope in HLA-A1
1YA5 2005-12-20 2.44 Crystal structure of the titin domains z1z2 in complex with telethonin
2J8O 2007-08-21 2.49 Structure of the immunoglobulin tandem repeat of titin A168-A169
3LCY 2011-05-25 2.5 Titin Ig tandem domains A164-A165
2F8V 2006-06-27 2.75 Structure of full length telethonin in complex with the N-terminus of titin
2NZI 2007-02-13 2.9 Crystal structure of domains A168-A170 from titin
6FWX 2019-03-27 3.0 Chimeric titin Z1Z2-Z1Z2 tandem (Z1212) functionalized with a GRGDS exogenous peptide from fibronectin
6NZU 2019-05-22 3.2 Structure of the human frataxin-bound iron-sulfur cluster assembly complex
6I0Y 2018-12-05 3.2 TnaC-stalled ribosome complex with the titin I27 domain folding close to the ribosomal exit tunnel
4UOW 2014-12-17 3.3 Crystal structure of the titin M10-Obscurin Ig domain 1 complex

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
90.6 Iron-sulfur cluster assembly protein CyaY A7MQK4 CYAY_CROS8
90.6 Iron-sulfur cluster assembly protein CyaY A4WG10 CYAY_ENT38
92.5 Iron-sulfur cluster assembly protein CyaY B5BIV3 CYAY_SALPK
92.5 Iron-sulfur cluster assembly protein CyaY Q5PKM9 CYAY_SALPA
92.5 Iron-sulfur cluster assembly protein CyaY C0Q3B5 CYAY_SALPC
92.5 Iron-sulfur cluster assembly protein CyaY Q57HR5 CYAY_SALCH
94.3 Iron-sulfur cluster assembly protein CyaY B4TNV5 CYAY_SALSV
93.4 Iron-sulfur cluster assembly protein CyaY B4SZ48 CYAY_SALNS
94.3 Iron-sulfur cluster assembly protein CyaY A9MY64 CYAY_SALPB
94.3 Iron-sulfur cluster assembly protein CyaY A9MJ08 CYAY_SALAR
94.3 Iron-sulfur cluster assembly protein CyaY P56978 CYAY_SALTY
94.3 Iron-sulfur cluster assembly protein CyaY Q8Z3A4 CYAY_SALTI
94.3 Iron-sulfur cluster assembly protein CyaY B5RFQ2 CYAY_SALG2
94.3 Iron-sulfur cluster assembly protein CyaY B5QVJ3 CYAY_SALEP
94.3 Iron-sulfur cluster assembly protein CyaY B5FNU2 CYAY_SALDC
98.1 Iron-sulfur cluster assembly protein CyaY Q0SYZ5 CYAY_SHIF8
95.3 Iron-sulfur cluster assembly protein CyaY B5EZ64 CYAY_SALA4
96.2 Iron-sulfur cluster assembly protein CyaY B4TB34 CYAY_SALHS
94.3 Iron-sulfur cluster assembly protein CyaY B5XYK9 CYAY_KLEP3
95.3 Iron-sulfur cluster assembly protein CyaY A6TGJ0 CYAY_KLEP7
96.2 Iron-sulfur cluster assembly protein CyaY A8ACV5 CYAY_CITK8
99.1 Iron-sulfur cluster assembly protein CyaY Q83IX2 CYAY_SHIFL
99.1 Iron-sulfur cluster assembly protein CyaY B5YY53 CYAY_ECO5E
99.1 Iron-sulfur cluster assembly protein CyaY Q8XAP0 CYAY_ECO57
98.1 Iron-sulfur cluster assembly protein CyaY Q8FBN9 CYAY_ECOL6
99.1 Iron-sulfur cluster assembly protein CyaY A8A6R1 CYAY_ECOHS
99.1 Iron-sulfur cluster assembly protein CyaY B7LU51 CYAY_ESCF3
99.1 Iron-sulfur cluster assembly protein CyaY Q31UI1 CYAY_SHIBS
99.1 Iron-sulfur cluster assembly protein CyaY B2TUW2 CYAY_SHIB3
99.1 Iron-sulfur cluster assembly protein CyaY Q1R4D1 CYAY_ECOUT
99.1 Iron-sulfur cluster assembly protein CyaY Q0TAR9 CYAY_ECOL5
99.1 Iron-sulfur cluster assembly protein CyaY A1AHX3 CYAY_ECOK1
99.1 Iron-sulfur cluster assembly protein CyaY B7N297 CYAY_ECO81
99.1 Iron-sulfur cluster assembly protein CyaY B7MH68 CYAY_ECO45
99.1 Iron-sulfur cluster assembly protein CyaY B7UNC2 CYAY_ECO27
99.1 Iron-sulfur cluster assembly protein CyaY B7NTD8 CYAY_ECO7I
99.1 Iron-sulfur cluster assembly protein CyaY B1LLX7 CYAY_ECOSM
100.0 Iron-sulfur cluster assembly protein CyaY Q3YVG0 CYAY_SHISS
100.0 Iron-sulfur cluster assembly protein CyaY Q329Y2 CYAY_SHIDS
100.0 Iron-sulfur cluster assembly protein CyaY B6I4E2 CYAY_ECOSE
100.0 Iron-sulfur cluster assembly protein CyaY B7NFA9 CYAY_ECOLU
100.0 Iron-sulfur cluster assembly protein CyaY P27838 CYAY_ECOLI
100.0 Iron-sulfur cluster assembly protein CyaY B1IW97 CYAY_ECOLC
100.0 Iron-sulfur cluster assembly protein CyaY B1XAH3 CYAY_ECODH
100.0 Iron-sulfur cluster assembly protein CyaY C4ZZ71 CYAY_ECOBW
100.0 Iron-sulfur cluster assembly protein CyaY B7M605 CYAY_ECO8A
100.0 Iron-sulfur cluster assembly protein CyaY B7L963 CYAY_ECO55
100.0 Iron-sulfur cluster assembly protein CyaY A7ZU09 CYAY_ECO24
100.0 60S ribosomal subunit assembly/export protein LOC1 P43586 LOC1_YEAST
100.0 60S ribosomal subunit assembly/export protein LOC1 A7A239 LOC1_YEAS7
90.9 TITIN A2ASS6 TITIN_MOUSE
100.0 Titin Q8WZ42 TITIN_HUMAN
96.8 Frataxin, mitochondrial Q8HXX9 FRDA_MACFA
100.0 Frataxin, mitochondrial Q16595 FRDA_HUMAN
95.0 Frataxin, mitochondrial O35943 FRDA_MOUSE
95.1 Frataxin, mitochondrial Q05B87 FRDA_BOVIN