Surface salt bridges stabilize the GCN4 leucine zipper.


Abstract

We present a study of the role of salt bridges in stabilizing a simplified tertiary structural motif, the coiled-coil. Changes in GCN4 sequence have been engineered that introduce trial patterns of single and multiple salt bridges at solvent exposed sites. At the same sites, a set of alanine mutants was generated to provide a reference for thermodynamic analysis of the salt bridges. Introduction of three alanines stabilizes the dimer by 1.1 kcal/mol relative to the wild-type. An arrangement corresponding to a complex type of salt bridge involving three groups stabilizes the dimer by 1.7 kcal/ mol, an apparent elevation of the melting temperature relative to wild type of about 22 degrees C. While identifying local from nonlocal contributions to protein stability is difficult, stabilizing interactions can be identified by use of cycles. Introduction of alanines for side chains of lower helix propensity and complex salt bridges both stabilize the coiled-coil, so that combining the two should yield melting temperatures substantially higher than the starting species, approaching those of thermophilic sequences. Study holds ProTherm entries: 3425, 3426, 3427, 3428, 3429, 3430, 3431, 3432, 3433, 3434, 14215, 14216, 14217, 14218, 14219, 14220, 14221, 14222, 14223 Extra Details: GCN4; leucine zipper; salt bridge; thermal stability

Submission Details

ID: gRfVTChx

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:21 p.m.

Version: 1

Publication Details
Spek EJ;Bui AH;Lu M;Kallenbach NR,Protein Sci. (1998) Surface salt bridges stabilize the GCN4 leucine zipper. PMID:9828010
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
1ZTA 1993-04-15 THE SOLUTION STRUCTURE OF A LEUCINE-ZIPPER MOTIF PEPTIDE
1IHQ 2001-10-03 GLYTM1BZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF A RAT SHORT ALPHA TROPOMYOSIN WITH THE N-TERMINUS ENCODED BY EXON 1B
2OVN 2007-04-03 NMR structure of the GCN4 trigger peptide
1FMH 2000-11-01 NMR SOLUTION STRUCTURE OF A DESIGNED HETERODIMERIC LEUCINE ZIPPER
2LPB 2012-02-22 Structure of the complex of the central activation domain of Gcn4 bound to the mediator co-activator domain 1 of Gal11/med15
2K8X 2009-04-28 GlyTM1b(1-19)zip: A Chimeric Peptide Model of the N-Terminus of a Rat Short Alpha-Tropomyosin with the N-Terminus Encoded by Exon 1b in Complex with TM9d(252-284), a Peptide Model Containing the C Terminus of Alpha-Tropomyosin Encoded by Exon 9d
5IEW 2017-03-15 NMR Structures Show Unwinding of the GCN4p Coiled Coil Superhelix Accompanying Disruption of Ion Pairs at Acidic pH
2N9B 2016-06-15 Solution NMR Structure of Antiparallel Myosin-10:GCN4 Tandem Coiled-Coil
5IIR 2017-03-15 NMR Structures Show Unwinding of the GCN4p Coiled Coil Superhelix Accompanying Disruption of Ion Pairs at Acidic pH
2G9J 2006-11-07 Complex of TM1a(1-14)Zip with TM9a(251-284): a model for the polymerization domain ('overlap region') of tropomyosin, Northeast Structural Genomics Target OR9
5IIV 2017-03-15 GCN4p pH 1.5
1TMZ 1998-06-17 TMZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF ALPHA TROPOMYOSIN, NMR, 15 STRUCTURES
3AZD 2011-10-19 0.98 Crystal structure of tropomyosin N-terminal fragment at 0.98A resolution
2WQ1 2009-11-03 1.08 GCN4 leucine zipper mutant with three IxxNTxx motifs coordinating bromide
2WQ0 2009-11-03 1.12 GCN4 leucine zipper mutant with three IxxNTxx motifs coordinating chloride
4OWI 2014-05-21 1.2 peptide structure
2WQ3 2009-11-03 1.22 GCN4 leucine zipper mutant with three IxxNTxx motifs coordinating chloride and nitrate
2HY6 2006-10-24 1.25 A seven-helix coiled coil
2WPZ 2009-11-03 1.25 GCN4 leucine zipper mutant with two VxxNxxx motifs coordinating chloride
2YNY 2012-12-12 1.35 Salmonella enterica SadA 255-302 fused to GCN4 adaptors (SadAK1)
2IPZ 2007-01-16 1.35 A Parallel Coiled-Coil Tetramer with Offset Helices
5APU 2016-01-27 1.35 Sequence IANKEDKAD inserted between GCN4 adaptors - Structure A9b black
2WQ2 2009-11-03 1.36 GCN4 leucine zipper mutant with three IxxNTxx motifs coordinating iodide
5APS 2016-01-27 1.37 Sequence IENKKAD inserted between GCN4 adaptors - Structure A7
2NRN 2007-04-17 1.4 Self-assembly of coiled-coil tetramers in the 1.40 A structure of a leucine-zipper mutant
2YNZ 2012-12-12 1.4 Salmonella enterica SadA 823-947 fused to a GCN4 adaptor (SadAK5)
3M48 2011-02-16 1.45 GCN4 Leucine Zipper Peptide Mutant
5KHT 2017-06-21 1.5 Crystal structure of the N-terminal fragment of tropomyosin isoform Tpm1.1 at 1.5 A resolution
1LLM 2003-09-30 1.5 Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA
2BNI 2005-03-30 1.5 pLI mutant E20C L16G Y17H, antiparallel
2B1F 2006-01-31 1.5 Antiparallel four-stranded coiled coil specified by a 3-3-1 hydrophobic heptad repeat
5APZ 2016-01-27 1.6 Thermosinus carboxydivorans Nor1 Tcar0761 residues 68-101 and 191-211 fused to GCN4 adaptors
2CCN 2006-04-06 1.6 pLI E20C is antiparallel
5APW 2016-01-27 1.6 Sequence MATKDD inserted between GCN4 adaptors - Structure T6
3I1G 2009-07-07 1.6 Crystal structure of a GCN4 leucine zipper mutant at 1.6 A resolution
3CRP 2008-10-07 1.7 A heterospecific leucine zipper tetramer
1UO4 2004-10-13 1.7 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
2CCF 2006-04-06 1.7 Antiparallel Configuration of pLI E20S
1IJ2 2001-08-08 1.7 GCN4-pVTL Coiled-coil Trimer with Threonine at the a(16) position
3CK4 2008-10-07 1.7 A heterospecific leucine zipper tetramer
2WPY 2009-11-03 1.75 GCN4 leucine zipper mutant with one VxxNxxx motif coordinating chloride
5APT 2016-01-27 1.8 Sequence IENKADKAD inserted between GCN4 adaptors - Structure A9
2VNL 2009-02-10 1.8 MUTANT Y108Wdel OF THE HEADBINDING DOMAIN OF PHAGE P22 TAILSPIKE C- TERMINally fused to ISOLEUCINE ZIPPER pIIGCN4 (chimera II)
5APX 2016-01-27 1.8 Sequence MATKDDIAN inserted between GCN4 adaptors - Structure T9(6)
2EFR 2008-03-04 1.8 Crystal structure of the c-terminal tropomyosin fragment with N- and C-terminal extensions of the leucine zipper at 1.8 angstroms resolution
1GCM 1996-01-29 1.8 GCN4 LEUCINE ZIPPER CORE MUTANT P-LI
1PIQ 1998-09-30 1.8 CRYSTAL STRUCTURE OF GCN4-PIQ, A TRIMERIC COILED COIL WITH BURIED POLAR RESIDUES
6O2F 2019-06-26 1.8 GCN4 with NPEG4 at position 18
1CE9 1999-03-25 1.8 HELIX CAPPING IN THE GCN4 LEUCINE ZIPPER
2ZTA 1992-10-15 1.8 X-RAY STRUCTURE OF THE GCN4 LEUCINE ZIPPER, A TWO-STRANDED, PARALLEL COILED COIL
1IJ3 2001-08-08 1.8 GCN4-pVSL Coiled-coil trimer with Serine at the a(16) position
4TL1 2014-08-06 1.8 GCN4-p1 with mutation to 1-Aminocyclohexanecarboxylic acid at residue 10
1ZIK 1997-07-07 1.8 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16LYS IN THE DIMERIC STATE
1ZII 1997-07-07 1.8 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16ABA IN THE DIMERIC STATE
1GZL 2002-10-10 1.8 Crystal structure of C14linkmid/IQN17: a cross-linked inhibitor of HIV-1 entry bound to the gp41 hydrophobic pocket
3ZMF 2013-02-20 1.85 Salmonella enterica SadA 303-358 fused to GCN4 adaptors (SadAK2)
1IJ0 2001-08-08 1.86 Coiled Coil Trimer GCN4-pVLS Ser at Buried D Position
1IJ1 2001-08-08 1.86 GCN4-pVLT Coiled-coil Trimer with Threonine at the d(12) Position
2O7H 2007-11-27 1.86 Crystal structure of trimeric coiled coil GCN4 leucine zipper
4G2K 2012-09-12 1.9 Crystal structure of the Marburg Virus GP2 ectodomain in its post-fusion conformation
1GK6 2002-03-15 1.9 Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B)
3K7Z 2009-11-24 1.9 GCN4-Leucine zipper core mutant as N16A trigonal automatic solution
1RB5 2004-01-13 1.9 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TRIGONAL FORM
1RB4 2004-01-13 1.9 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TETRAGONAL AUTOMATIC SOLUTION
6O2E 2019-06-26 1.9 GCN4 with asparagine at position 18
2CCE 2006-04-06 1.9 Parallel Configuration of pLI E20S
4NJ0 2014-08-20 1.9 GCN4-p1 single Val9 to Ile mutant
1RB6 2004-01-13 1.9 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TETRAGONAL FORM
1UO3 2004-10-13 1.92 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
1W5K 2004-09-24 1.92 AN ANTI-PARALLEL FOUR HELIX BUNDLE
6E52 2019-02-27 1.93 Chimeric structure of Saccharomyces cerevisiae GCN4 leucine zipper fused to Staphylococcus aureus AgrC cytoplasmic histidine kinase module (dataset anisotropically truncated by STARANISO)
3I5C 2009-08-18 1.94 Crystal structure of a fusion protein containing the leucine zipper of GCN4 and the GGDEF domain of WspR from Pseudomonas aeruginosa
4C46 2013-09-11 1.95 ANDREI-N-LVPAS fused to GCN4 adaptors
1UO2 2004-10-13 1.99 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
1LD4 2002-11-04 11.4 Placement of the Structural Proteins in Sindbis Virus
4NJ1 2014-08-20 2.0 GCN4-p1 double Val9, 23 to Ile mutant
4NIZ 2014-08-20 2.0 GCN4-p1 single Val9 to aminobutyric acid mutant
5APV 2016-01-27 2.0 Sequence IANKEDKAD inserted between GCN4 adaptors - Structure A9b grey
1ZIJ 1997-07-07 2.0 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16ABA IN THE TRIMERIC STATE
2AHP 2006-08-01 2.0 GCN4 leucine zipper, mutation of Lys15 to epsilon-azido-Lys
5APY 2016-01-27 2.0 Sequence MATKDDIAN inserted between GCN4 adaptors - Structure T9(9)
2B22 2006-01-31 2.0 Antiparallel four-stranded coiled coil specified by a 3-3-1 hydrophobic heptad repeat
3G9R 2009-05-12 2.0 Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation
2EFS 2008-03-04 2.0 Crystal structure of the C-terminal tropomyosin fragment with N- and C-terminal extensions of the leucine zipper at 2.0 angstroms resolution
2YO3 2012-12-12 2.0 Salmonella enterica SadA 1185-1386 fused to GCN4 adaptors (SadAK14)
2YO2 2012-12-12 2.0 Salmonella enterica SadA 255-358 fused to GCN4 adaptors (SadAK12)
1ZIM 1997-07-07 2.0 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE TRIMERIC STATE
3GJP 2010-03-09 2.0 Crystal structure of mutant coiled coil GCN4 leucine zipper
4DMD 2012-11-14 2.0 GCN4 leucine zipper domain in a dimeric oligomerization state
2VKY 2009-02-10 2.05 Headbinding Domain of Phage P22 Tailspike C-Terminally Fused to Isoleucine Zipper pIIGCN4 (Chimera I)
1UNU 2004-10-13 2.07 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
1UO5 2004-10-13 2.07 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
1UNT 2004-10-13 2.07 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
5APQ 2016-01-27 2.1 Sequence IENKAD inserted between GCN4 adaptors - Structure A6
6H9M 2019-02-13 2.1 Coiled-coil domain-containing protein 90B residues 43-125 from Homo sapiens fused to a GCN4 adaptor
1GCL 1995-06-03 2.1 GCN4 LEUCINE ZIPPER CORE MUTANT P-LI
2WG5 2009-04-28 2.1 Proteasome-Activating Nucleotidase (PAN) N-domain (57-134) from Archaeoglobus fulgidus fused to GCN4
2Z5I 2008-04-22 2.1 Crystal structure of the head-to-tail junction of tropomyosin
1UNV 2004-10-13 2.14 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
1W5G 2004-09-24 2.16 An anti-parallel four helix bundle (acetimide modification).
1W5L 2004-09-24 2.17 An anti-parallel to parallel switch.
1W5J 2004-09-24 2.2 AN ANTI-PARALLEL FOUR HELIX BUNDLE
1UNW 2004-10-13 2.2 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
2DGC 1996-03-08 2.2 GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA
4NJ2 2014-08-20 2.2 GCN4-p1 triple Val9, 23,30 to Ile mutant
1ZIL 1997-07-07 2.25 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE DIMERIC STATE
6E95 2019-02-27 2.25 Chimeric structure of Saccharomyces cerevisiae GCN4 leucine zipper fused to Staphylococcus aureus AgrC cytoplasmic histidine kinase module (dataset isotropically truncated by HKL2000)
4HU6 2013-08-21 2.3 Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Cyclic product
3BAS 2008-01-08 2.3 Crystal structure of the N-terminal region of the scallop myosin rod, monoclinic (C2) form
4HU5 2013-08-21 2.3 Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Linear precursor
5APP 2016-01-27 2.3 Actinobacillus actinomycetemcomitans OMP100 residues 133-198 fused to GCN4 adaptors
1W5I 2004-09-24 2.3 ABA does not affect topology of pLI.
1UNZ 2004-10-13 2.3 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
3BAT 2008-01-08 2.3 Crystal structure of the N-terminal region of the scallop myosin rod, monoclinic (P21) form
1UNY 2004-10-13 2.3 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
1UO0 2004-10-13 2.4 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
1UNX 2004-10-13 2.4 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
2WG6 2009-04-28 2.5 Proteasome-Activating Nucleotidase (PAN) N-domain (57-134) from Archaeoglobus fulgidus fused to GCN4, P61A Mutant
1NKN 2003-07-22 2.5 VISUALIZING AN UNSTABLE COILED COIL: THE CRYSTAL STRUCTURE OF AN N-TERMINAL SEGMENT OF THE SCALLOP MYOSIN ROD
1UO1 2004-10-13 2.5 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
1W5H 2004-09-24 2.5 An anti-parallel four helix bundle.
1SWI 1996-11-08 2.6 GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A COMPLEXED WITH BENZENE
2D3E 2006-09-12 2.6 Crystal structure of the C-Terminal fragment of rabbit skeletal alpha-tropomyosin
1KQL 2002-05-29 2.7 Crystal structure of the C-terminal region of striated muscle alpha-tropomyosin at 2.7 angstrom resolution
2YO0 2012-12-12 2.8 Salmonella enterica SadA 1049-1304 fused to GCN4 adaptors (SadAK9-cfI)
2Z5H 2008-04-22 2.89 Crystal structure of the head-to-tail junction of tropomyosin complexed with a fragment of TnT
3P8M 2011-08-31 2.9 Human dynein light chain (DYNLL2) in complex with an in vitro evolved peptide dimerized by leucine zipper
1YSA 1993-10-31 2.9 THE GCN4 BASIC REGION LEUCINE ZIPPER BINDS DNA AS A DIMER OF UNINTERRUPTED ALPHA HELICES: CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX
1FAV 2000-08-23 3.0 THE STRUCTURE OF AN HIV-1 SPECIFIC CELL ENTRY INHIBITOR IN COMPLEX WITH THE HIV-1 GP41 TRIMERIC CORE
1DGC 1994-06-22 3.0 THE X-RAY STRUCTURE OF THE GCN4-BZIP BOUND TO ATF/CREB SITE DNA SHOWS THE COMPLEX DEPENDS ON DNA FLEXIBILITY
2YO1 2012-12-12 3.1 Salmonella enterica SadA 1049-1304 fused to GCN4 adaptors (SadAK9- cfII)
6HN5 2018-11-21 3.2 Leucine-zippered human insulin receptor ectodomain with single bound insulin - 'upper' membrane-distal part
6HN4 2018-11-21 4.2 Leucine-zippered human insulin receptor ectodomain with single bound insulin - 'lower' membrane-proximal part

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 General control protein GCN4 P03069 GCN4_YEAST