Salt-bridges can stabilize but do not accelerate the folding of the homodimeric coiled-coil peptide GCN4-p1.


Abstract

Double mutant cycle analysis was employed to ascertain the role of intra- and interchain salt-bridges in the folding and stability of the dimeric coiled-coil peptide, GCN4-p1, the 33-residue leucine zipper domain of the transcriptional activator GCN4. Equilibrium circular dichroism studies of the urea-induced unfolding reaction at neutral pH revealed that both types of ionic interactions, localized primarily in the N-terminal portion of the molecule, enhance the stability of the native coiled-coil. By contrast, comparable stopped-flow circular dichroism studies indicate that the salt-bridge interactions, with one possible exception, are not well formed in the transition state for folding. Although the E22Q/R25A double mutant failed to fold, fragmentation studies suggest that the E22/R25 intramolecular salt-bridge may play a critical role in stabilizing C-terminal nascent helices that drive the association reaction. The remaining salt-bridges appear to stabilize the parallel-stranded coiled-coil architecture of GCN4-p1 only after the peptide traverses the rate-limiting, dimeric transition state. Study holds ProTherm entries: 17015, 17016, 17017, 17018, 17019, 17020, 17021, 17022, 17023, 17024, 17025, 17026, 17027, 17028, 17029 Extra Details: Pseudo wild type M2V. circular dichroism spectroscopy; electrostatics; ionic interactions; leucine zipper peptides; protein folding kinetics

Submission Details

ID: ZaCckz9Q

Submitter: Connie Wang

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

Version: 1

Publication Details
Ibarra-Molero B;Zitzewitz JA;Matthews CR,J. Mol. Biol. (2004) Salt-bridges can stabilize but do not accelerate the folding of the homodimeric coiled-coil peptide GCN4-p1. PMID:15037063
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
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
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
2N9B 2016-06-15 Solution NMR Structure of Antiparallel Myosin-10:GCN4 Tandem Coiled-Coil
1TMZ 1998-06-17 TMZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF ALPHA TROPOMYOSIN, NMR, 15 STRUCTURES
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
5IEW 2017-03-15 NMR Structures Show Unwinding of the GCN4p Coiled Coil Superhelix Accompanying Disruption of Ion Pairs at Acidic pH
1ZTA 1993-04-15 THE SOLUTION STRUCTURE OF A LEUCINE-ZIPPER MOTIF PEPTIDE
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
5IIV 2017-03-15 GCN4p pH 1.5
2OVN 2007-04-03 NMR structure of the GCN4 trigger peptide
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
2WPZ 2009-11-03 1.25 GCN4 leucine zipper mutant with two VxxNxxx motifs coordinating chloride
2HY6 2006-10-24 1.25 A seven-helix coiled coil
2IPZ 2007-01-16 1.35 A Parallel Coiled-Coil Tetramer with Offset Helices
2YNY 2012-12-12 1.35 Salmonella enterica SadA 255-302 fused to GCN4 adaptors (SadAK1)
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
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
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
5APW 2016-01-27 1.6 Sequence MATKDD inserted between GCN4 adaptors - Structure T6
2CCN 2006-04-06 1.6 pLI E20C is antiparallel
3I1G 2009-07-07 1.6 Crystal structure of a GCN4 leucine zipper mutant at 1.6 A resolution
5APZ 2016-01-27 1.6 Thermosinus carboxydivorans Nor1 Tcar0761 residues 68-101 and 191-211 fused to GCN4 adaptors
3CRP 2008-10-07 1.7 A heterospecific leucine zipper tetramer
3CK4 2008-10-07 1.7 A heterospecific leucine zipper tetramer
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
1UO4 2004-10-13 1.7 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
2WPY 2009-11-03 1.75 GCN4 leucine zipper mutant with one VxxNxxx motif coordinating chloride
1IJ3 2001-08-08 1.8 GCN4-pVSL Coiled-coil trimer with Serine at the a(16) position
1ZIK 1997-07-07 1.8 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16LYS IN THE DIMERIC STATE
1PIQ 1998-09-30 1.8 CRYSTAL STRUCTURE OF GCN4-PIQ, A TRIMERIC COILED COIL WITH BURIED POLAR RESIDUES
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
5APX 2016-01-27 1.8 Sequence MATKDDIAN inserted between GCN4 adaptors - Structure T9(6)
4TL1 2014-08-06 1.8 GCN4-p1 with mutation to 1-Aminocyclohexanecarboxylic acid at residue 10
1ZII 1997-07-07 1.8 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16ABA IN THE DIMERIC STATE
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)
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
2ZTA 1992-10-15 1.8 X-RAY STRUCTURE OF THE GCN4 LEUCINE ZIPPER, A TWO-STRANDED, PARALLEL COILED COIL
5APT 2016-01-27 1.8 Sequence IENKADKAD inserted between GCN4 adaptors - Structure A9
1CE9 1999-03-25 1.8 HELIX CAPPING IN THE GCN4 LEUCINE ZIPPER
6O2F 2019-06-26 1.8 GCN4 with NPEG4 at position 18
1GCM 1996-01-29 1.8 GCN4 LEUCINE ZIPPER CORE MUTANT P-LI
3ZMF 2013-02-20 1.85 Salmonella enterica SadA 303-358 fused to GCN4 adaptors (SadAK2)
2O7H 2007-11-27 1.86 Crystal structure of trimeric coiled coil GCN4 leucine zipper
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
1RB6 2004-01-13 1.9 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TETRAGONAL FORM
3K7Z 2009-11-24 1.9 GCN4-Leucine zipper core mutant as N16A trigonal automatic solution
6O2E 2019-06-26 1.9 GCN4 with asparagine at position 18
4NJ0 2014-08-20 1.9 GCN4-p1 single Val9 to Ile mutant
1RB4 2004-01-13 1.9 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TETRAGONAL AUTOMATIC SOLUTION
1GK6 2002-03-15 1.9 Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B)
2CCE 2006-04-06 1.9 Parallel Configuration of pLI E20S
4G2K 2012-09-12 1.9 Crystal structure of the Marburg Virus GP2 ectodomain in its post-fusion conformation
1RB5 2004-01-13 1.9 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TRIGONAL 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
5APY 2016-01-27 2.0 Sequence MATKDDIAN inserted between GCN4 adaptors - Structure T9(9)
3G9R 2009-05-12 2.0 Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation
4NIZ 2014-08-20 2.0 GCN4-p1 single Val9 to aminobutyric acid mutant
2YO2 2012-12-12 2.0 Salmonella enterica SadA 255-358 fused to GCN4 adaptors (SadAK12)
3GJP 2010-03-09 2.0 Crystal structure of mutant coiled coil GCN4 leucine zipper
4NJ1 2014-08-20 2.0 GCN4-p1 double Val9, 23 to Ile mutant
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)
1ZIJ 1997-07-07 2.0 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16ABA IN THE TRIMERIC STATE
1ZIM 1997-07-07 2.0 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE TRIMERIC STATE
5APV 2016-01-27 2.0 Sequence IANKEDKAD inserted between GCN4 adaptors - Structure A9b grey
4DMD 2012-11-14 2.0 GCN4 leucine zipper domain in a dimeric oligomerization state
2B22 2006-01-31 2.0 Antiparallel four-stranded coiled coil specified by a 3-3-1 hydrophobic heptad repeat
2AHP 2006-08-01 2.0 GCN4 leucine zipper, mutation of Lys15 to epsilon-azido-Lys
2VKY 2009-02-10 2.05 Headbinding Domain of Phage P22 Tailspike C-Terminally Fused to Isoleucine Zipper pIIGCN4 (Chimera I)
1UNT 2004-10-13 2.07 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
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
2WG5 2009-04-28 2.1 Proteasome-Activating Nucleotidase (PAN) N-domain (57-134) from Archaeoglobus fulgidus fused to GCN4
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
5APQ 2016-01-27 2.1 Sequence IENKAD inserted between GCN4 adaptors - Structure A6
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.
2DGC 1996-03-08 2.2 GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA
1UNW 2004-10-13 2.2 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
4NJ2 2014-08-20 2.2 GCN4-p1 triple Val9, 23,30 to Ile mutant
1W5J 2004-09-24 2.2 AN ANTI-PARALLEL FOUR HELIX BUNDLE
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)
1ZIL 1997-07-07 2.25 GCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE DIMERIC STATE
5APP 2016-01-27 2.3 Actinobacillus actinomycetemcomitans OMP100 residues 133-198 fused to GCN4 adaptors
1UNY 2004-10-13 2.3 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
4HU5 2013-08-21 2.3 Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Linear precursor
1UNZ 2004-10-13 2.3 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
1W5I 2004-09-24 2.3 ABA does not affect topology of pLI.
3BAS 2008-01-08 2.3 Crystal structure of the N-terminal region of the scallop myosin rod, monoclinic (C2) form
3BAT 2008-01-08 2.3 Crystal structure of the N-terminal region of the scallop myosin rod, monoclinic (P21) form
4HU6 2013-08-21 2.3 Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Cyclic product
1UNX 2004-10-13 2.4 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
1NKN 2003-07-22 2.5 VISUALIZING AN UNSTABLE COILED COIL: THE CRYSTAL STRUCTURE OF AN N-TERMINAL SEGMENT OF THE SCALLOP MYOSIN ROD
1W5H 2004-09-24 2.5 An anti-parallel four helix bundle.
2WG6 2009-04-28 2.5 Proteasome-Activating Nucleotidase (PAN) N-domain (57-134) from Archaeoglobus fulgidus fused to GCN4, P61A Mutant
1UO1 2004-10-13 2.5 Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
2D3E 2006-09-12 2.6 Crystal structure of the C-Terminal fragment of rabbit skeletal alpha-tropomyosin
1SWI 1996-11-08 2.6 GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A COMPLEXED WITH BENZENE
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
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
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
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