Side-chain contributions to membrane protein structure and stability.


Abstract

The molecular forces that stabilize membrane protein structure are poorly understood. To investigate these forces we introduced alanine substitutions at 24 positions in the B helix of bacteriorhodopsin and examined their effects on structure and stability. Although most of the results can be rationalized in terms of the folded structure, there are a number of surprises. (1) We find a remarkably high frequency of stabilizing mutations (17%), indicating that membrane proteins are not highly optimized for stability. (2) Helix B is kinked, with the kink centered around Pro50. The P50A mutation has no effect on stability, however, and a crystal structure reveals that the helix remains bent, indicating that tertiary contacts dominate in the distortion of this helix. (3) We find that the protein is stabilized by about 1kcal/mol for every 38A(2) of surface area buried, which is quite similar to soluble proteins in spite of their dramatically different environments. (4) We find little energetic difference, on average, in the burial of apolar surface or polar surface area, implying that van der Waals packing is the dominant force that drives membrane protein folding. Study holds ProTherm entries: 17314, 17315, 17316, 17317, 17318, 17319, 17320, 17321, 17322, 17323, 17324, 17325, 17326, 17327, 17328, 17329, 17330, 17331, 17332, 17333, 17334, 17335, 17336, 17337 Extra Details: 15 mM DMPC and 16 mM CHAPSO were added in the experiment. bacteriorhodopsin; hydrogen bond; van der Waals; protein folding; helix kink

Submission Details

ID: SfZyHtsR3

Submitter: Connie Wang

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

Version: 1

Publication Details
Faham S;Yang D;Bare E;Yohannan S;Whitelegge JP;Bowie JU,J. Mol. Biol. (2004) Side-chain contributions to membrane protein structure and stability. PMID:14659758
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
1BHA 1994-01-31 THREE-DIMENSIONAL STRUCTURE OF (1-71) BACTERIOOPSIN SOLUBILIZED IN METHANOL-CHLOROFORM AND SDS MICELLES DETERMINED BY 15N-1H HETERONUCLEAR NMR SPECTROSCOPY
1L0M 2002-03-27 Solution structure of Bacteriorhodopsin
1R84 2003-11-11 NMR structure of the 13-cis-15-syn retinal in dark_adapted bacteriorhodopsin
1R2N 2003-10-28 NMR structure of the all-trans retinal in dark-adapted Bacteriorhodopsin
1BCT 1994-04-30 THREE-DIMENSIONAL STRUCTURE OF PROTEOLYTIC FRAGMENT 163-231 OF BACTERIOOPSIN DETERMINED FROM NUCLEAR MAGNETIC RESONANCE DATA IN SOLUTION
1BHB 1994-01-31 Three-dimensional structure of (1-71) bacterioopsin solubilized in methanol-chloroform and SDS micelles determined by 15N-1H heteronuclear NMR spectroscopy
5ZIM 2018-10-10 1.25 Crystal structure of bacteriorhodopsin at 1.25 A resolution
5ZIN 2018-10-10 1.27 Crystal structure of bacteriorhodopsin at 1.27 A resolution
5ZIL 2018-10-10 1.29 Crystal structure of bacteriorhodopsin at 1.29 A resolution
1M0M 2002-09-11 1.43 BACTERIORHODOPSIN M1 INTERMEDIATE AT 1.43 A RESOLUTION
1M0K 2002-09-11 1.43 BACTERIORHODOPSIN K INTERMEDIATE AT 1.43 A RESOLUTION
1M0L 2002-09-11 1.47 BACTERIORHODOPSIN/LIPID COMPLEX AT 1.47 A RESOLUTION
6G7H 2018-06-27 1.5 Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: resting state structure
1P8H 2003-07-07 1.52 BACTERIORHODOPSIN M1 INTERMEDIATE PRODUCED AT ROOM TEMPERATURE
2NTU 2006-12-26 1.53 Bacteriorhodopsin, wild type, before illumination
2NTW 2006-12-26 1.53 Bacteriorhodopsin, wild type, after illumination to produce the L intermediate
1C3W 1999-09-15 1.55 BACTERIORHODOPSIN/LIPID COMPLEX AT 1.55 A RESOLUTION
3HAP 2009-09-22 1.6 Crystal structure of bacteriorhodopsin mutant L111A crystallized from bicelles
1P8U 2003-07-08 1.62 BACTERIORHODOPSIN N' INTERMEDIATE AT 1.62 A RESOLUTION
1O0A 2003-04-22 1.62 BACTERIORHODOPSIN L INTERMEDIATE AT 1.62 A RESOLUTION
1KGB 2001-12-05 1.65 structure of ground-state bacteriorhodopsin
1PXR 2003-12-16 1.7 Structure of Pro50Ala mutant of Bacteriorhodopsin
3HAR 2009-09-22 1.7 Crystal structure of bacteriorhodopsin mutant I148V crystallized from bicelles
6GA1 2019-04-24 1.7 Bacteriorhodopsin, dark state, cell 1
1F50 2000-08-09 1.7 BACTERIORHODOPSIN-BR STATE OF THE E204Q MUTANT AT 1.7 ANGSTROM RESOLUTION
4MD2 2014-10-08 1.73 Ground state of bacteriorhodopsin from Halobacterium salinarum
4MD1 2014-10-08 1.73 Orange species of bacteriorhodopsin from Halobacterium salinarum
3NSB 2011-05-11 1.78 Structure of bacteriorhodopsin ground state before and after X-ray modification
3NS0 2011-05-11 1.78 X-ray structure of bacteriorhodopsin
5BR2 2016-09-14 1.8 Structure of bacteriorhodopsin crystallized from ND-MSP1
1PY6 2003-12-16 1.8 Bacteriorhodopsin crystallized from bicells
6GA2 2019-04-24 1.8 Bacteriorhodopsin, dark state, cell 2
6RQP 2019-07-17 1.8 Steady-state-SMX dark state structure of bacteriorhodopsin
6GA4 2019-04-24 1.8 Bacteriorhodopsin, 1 ps state, real-space refined against 15% extrapolated map
6GA6 2019-04-24 1.8 Bacteriorhodopsin, 10 ps state, real-space refined against 10% extrapolated map
1C8R 1999-10-20 1.8 BACTERIORHODOPSIN D96N BR STATE AT 2.0 A RESOLUTION
6GA7 2019-04-24 1.8 BACTERIORHODOPSIN, 240FS STATE, REAL-SPACE REFINED AGAINST 10% EXTRAPOLATED MAP
6GAD 2019-04-24 1.8 BACTERIORHODOPSIN, 530 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
6GAA 2019-04-24 1.8 BACTERIORHODOPSIN, 430 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
6RMK 2019-06-05 1.8 Bacteriorhodopsin, dark state, cell 2, refined using the same protocol as sub-ps time delays
6GA9 2019-04-24 1.8 BACTERIORHODOPSIN, 390 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
6GAF 2019-04-24 1.8 BACTERIORHODOPSIN, 590 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
6GAH 2019-04-24 1.8 BACTERIORHODOPSIN, 680 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
6GAI 2019-04-24 1.8 BACTERIORHODOPSIN, 740 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
6GAB 2019-04-24 1.8 BACTERIORHODOPSIN, 460 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
6GAE 2019-04-24 1.8 BACTERIORHODOPSIN, 560 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
6GAC 2019-04-24 1.8 BACTERIORHODOPSIN, 490 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
6GA8 2019-04-24 1.8 BACTERIORHODOPSIN, 330 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
1F4Z 2000-08-09 1.8 BACTERIORHODOPSIN-M PHOTOINTERMEDIATE STATE OF THE E204Q MUTANT AT 1.8 ANGSTROM RESOLUTION
6GAG 2019-04-24 1.8 BACTERIORHODOPSIN, 630 FS STATE, REAL-SPACE REFINED AGAINST 15% EXTRAPOLATED STRUCTURE FACTORS
1KG9 2001-12-05 1.81 Structure of a 'mock-trapped' early-M intermediate of bacteriorhosopsin
2I21 2006-10-10 1.84 Bacteriorhodopsin/lipid complex, T46V mutant
1P8I 2003-07-08 1.86 F219L BACTERIORHODOPSIN MUTANT
6GA5 2019-04-24 1.9 Bacteriorhodopsin, 3 ps state, REAL-SPACE REFINEMED AGAINST 10% EXTRAPOLATED MAP
6G7K 2018-06-27 1.9 Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: 10 ps state structure
4X32 2015-02-18 1.9 Bacteriorhodopsin ground state structure collected in cryo conditions from crystals obtained in LCP with PEG as a precipitant.
1QHJ 1999-07-21 1.9 X-RAY STRUCTURE OF BACTERIORHODOPSIN GROWN IN LIPIDIC CUBIC PHASES
6G7I 2018-06-27 1.9 Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: 49-406 fs state structure
6G7J 2018-06-27 1.9 Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: 457-646 fs state structure
3HAS 2009-09-22 1.9 Crystal structure of bacteriorhodopsin mutant L152A crystallized from bicelles
4XXJ 2015-07-01 1.9 Crystal Structure of Escherichia coli-Expressed Halobacterium salinarum Bacteriorhodopsin in the Trimeric Form
6G7L 2018-06-27 1.9 Retinal isomerization in bacteriorhodopsin revealed by a femtosecond X-ray laser: 8.3 ms state structure
4HYX 2013-03-20 1.99 Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-4 DMPC Bicelle
1KME 2002-02-13 2.0 CRYSTAL STRUCTURE OF BACTERIORHODOPSIN CRYSTALLIZED FROM BICELLES
1KG8 2001-12-05 2.0 X-ray structure of an early-M intermediate of bacteriorhodopsin
2I1X 2006-10-10 2.0 Bacteriorhodopsin/lipid complex, D96A mutant
1S53 2004-03-02 2.0 Thr46Ser Bacteriorhodopsin
3MBV 2010-11-03 2.0 Structure of bacterirhodopsin crystallized in betta-XylOC(16+4) meso phase
4HWL 2013-03-20 2.0 Crystal Structure Analysis of the Bacteriorhodopsin in Facial Amphiphile-7 DMPC Bicelle
1C8S 1999-10-20 2.0 BACTERIORHODOPSIN D96N LATE M STATE INTERMEDIATE
5BR5 2016-09-14 2.0 Structure of bacteriorhodopsin crystallized from ND-MSP1E3D1
1S51 2004-03-02 2.0 Thr24Ser Bacteriorhodopsin
1JV6 2001-10-31 2.0 BACTERIORHODOPSIN D85S/F219L DOUBLE MUTANT AT 2.00 ANGSTROM RESOLUTION
6RQO 2019-07-17 2.0 Steady-state-SMX activated state structure of bacteriorhodopsin
1MGY 2003-07-07 2.0 Structure of the D85S mutant of bacteriorhodopsin with bromide bound
5B6V 2016-12-21 2.0 A three dimensional movie of structural changes in bacteriorhodopsin: resting state structure
4OV0 2014-10-01 2.0 Structure of Bacteriorhdopsin Transferred from Amphipol A8-35 to a Lipidic Mesophase
2ZZL 2009-10-06 2.03 Structure of bacteriorhodopsin's M intermediate at pH 7
3UTV 2012-05-09 2.06 Crystal structure of bacteriorhodopsin mutant Y57F
2I20 2006-10-10 2.08 Bacteriorhodopsin/lipid complex, M state of D96A mutant
5H2L 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 5.25 us after photoexcitation
5B6Z 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 1.725 ms us after photoexcitation
5B6W 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 16 ns after photoexcitation
5H2O 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 250 us after photoexcitation
5H2I 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 110 ns after photoexcitation
5H2N 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 95.2 us after photoexcitation
6GA3 2019-04-24 2.1 Bacteriorhodopsin, 33 ms state, ensemble refinement
5B6X 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 760 ns after photoexcitation
1Q5J 2004-01-06 2.1 Crystal structure of bacteriorhodopsin mutant P91A crystallized from bicelles
5B34 2016-11-09 2.1 Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA
5H2J 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 290 ns after photoexcitation
5H2K 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 2 us after photoexcitation
1QKO 1999-10-24 2.1 HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE
1QKP 1999-10-24 2.1 HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE
5B6Y 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 36.2 us after photoexcitation
5H2P 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 657 us after photoexcitation
5H2M 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 13.8 us after photoexcitation
1E0P 2000-08-19 2.1 L intermediate of bacteriorhodopsin
5H2H 2016-12-21 2.1 A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 40 ns after photoexcitation
2WJL 2010-08-25 2.15 Bacteriorhodopsin mutant E194D
1PXS 2003-12-16 2.2 Structure of Met56Ala mutant of Bacteriorhodopsin
1TN5 2004-10-19 2.2 Structure of bacterorhodopsin mutant K41P
1XJI 2005-04-19 2.2 Bacteriorhodopsin crystallized in bicelles at room temperature
1S54 2004-03-02 2.2 Thr24Ala Bacteriorhodopsin
1CWQ 1999-10-20 2.25 M INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN COMBINATION WITH THE GROUND STATE STRUCTURE
1JV7 2001-10-31 2.25 BACTERIORHODOPSIN O-LIKE INTERMEDIATE STATE OF THE D85S MUTANT AT 2.25 ANGSTROM RESOLUTION
5A44 2015-11-11 2.29 Structure of Bacteriorhodopsin obtained from 20um crystals by multi crystal data collection
3HAQ 2009-09-22 2.3 Crystal structure of bacteriorhodopsin mutant I148A crystallized from bicelles
1X0I 2005-08-02 2.3 Crystal Structure of the Acid Blue Form of Bacteriorhodopsin
1VJM 2004-04-06 2.3 Deformation of helix C in the low-temperature L-intermediate of bacteriorhodopsin
1Q5I 2004-01-06 2.3 Crystal structure of bacteriorhodopsin mutant P186A crystallized from bicelles
3VHZ 2012-06-13 2.3 Crystal structure of the trans isomer of the L93A mutant of bacteriorhodopsin
5J7A 2016-08-31 2.3 Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography
1S8J 2004-06-08 2.3 Nitrate-bound D85S mutant of bacteriorhodopsin
3VI0 2012-06-13 2.3 Crystal structure of the O intermediate of the L93A mutant of bacteriorhodopsin
1S8L 2004-06-08 2.3 Anion-free form of the D85S mutant of bacteriorhodopsin from crystals grown in the presence of halide
1IW6 2002-12-11 2.3 Crystal Structure of the Ground State of Bacteriorhodopsin
1BRX 1999-01-27 2.3 BACTERIORHODOPSIN/LIPID COMPLEX
2WJK 2010-08-25 2.3 Bacteriorhodopsin mutant E204D
1S52 2004-03-02 2.3 Thr24Val Bacteriorhodopsin
3COC 2008-04-08 2.31 Crystal Structure of D115A mutant of Bacteriorhodopsin
1AP9 1998-09-16 2.35 X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES
3UTY 2012-05-09 2.37 Crystal structure of bacteriorhodopsin mutant P50A/T46A
4X31 2015-02-18 2.4 Room temperature structure of bacteriorhodopsin from lipidic cubic phase obtained with serial millisecond crystallography using synchrotron radiation
3UTW 2012-05-09 2.4 Crystal structure of bacteriorhodopsin mutant P50A/Y57F
1UCQ 2003-12-30 2.4 Crystal structure of the L intermediate of bacteriorhodopsin
3UTX 2012-05-09 2.47 Crystal structure of bacteriorhodopsin mutant T46A
3HAO 2009-09-22 2.49 Crystal structure of bacteriorhodopsin mutant L94A crystallized from bicelles
2ZFE 2008-11-11 2.5 Crystal structure of bacteriorhodopsin-xenon complex
1DZE 2000-08-16 2.5 Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K
1X0S 2005-08-30 2.5 Crystal structure of the 13-cis isomer of bacteriorhodopsin
1TN0 2004-10-12 2.5 Structure of bacterorhodopsin mutant A51P
1IW9 2003-12-23 2.5 Crystal Structure of the M Intermediate of Bacteriorhodopsin
1QM8 2000-08-16 2.5 Structure of Bacteriorhodopsin at 100 K
5A45 2015-11-11 2.57 Structure of Bacteriorhodopsin obtained from 5um crystals by multi crystal data collection
5VN9 2017-07-12 2.59 Structure of bacteriorhodopsin from crystals grown at 4 deg C using GlyNCOC15+4 as an LCP host lipid
6RPH 2019-07-17 2.6 TR-SMX open state structure (10-15ms) of bacteriorhodopsin
6RNJ 2019-07-17 2.6 TR-SMX closed state structure (0-5ms) of bacteriorhodopsin
1IXF 2002-12-18 2.6 Crystal Structure of the K intermediate of bacteriorhodopsin
1X0K 2005-08-02 2.6 Crystal Structure of Bacteriorhodopsin at pH 10
4FPD 2013-02-27 2.65 Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway
5VN7 2017-07-12 2.7 Structure of bacteriorhodopsin from crystals grown at 20 deg Celcius using GlyNCOC15+4 as an LCP host lipid
3COD 2008-04-08 2.7 Crystal Structure of T90A/D115A mutant of Bacteriorhodopsin
3HAN 2009-09-22 2.75 Crystal structure of bacteriorhodopsin mutant V49A crystallized from bicelles
1BRR 1998-09-30 2.9 X-RAY STRUCTURE OF THE BACTERIORHODOPSIN TRIMER/LIPID COMPLEX
2AT9 1999-04-27 3.0 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM BY ELECTRON CRYSTALLOGRAPHY
1AT9 1998-09-16 3.0 STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY
3T45 2011-12-21 3.01 Crystal structure of bacteriorhodopsin mutant A215T, a phototaxis signaling mutant at 3.0 A resolution
1FBK 2000-08-09 3.2 CRYSTAL STRUCTURE OF CYTOPLASMICALLY OPEN CONFORMATION OF BACTERIORHODOPSIN
1FBB 2000-08-09 3.2 CRYSTAL STRUCTURE OF NATIVE CONFORMATION OF BACTERIORHODOPSIN
1BM1 1999-04-27 3.5 CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN THE LIGHT-ADAPTED STATE
1BRD 1991-04-15 3.5 Model for the structure of Bacteriorhodopsin based on high-resolution Electron Cryo-microscopy
2BRD 1996-06-10 3.5 CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN PURPLE MEMBRANE

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Bacteriorhodopsin P02945 BACR_HALSA