Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues.


Abstract

To elucidate the kinetic importance of structural intermediates in single-domain proteins, we measured the effect of solution conditions and amino-acid changes at a central core residue of ubiquitin (Val 26) on the kinetics of folding and unfolding. Kinetic analysis in terms of a sequential three-state mechanism provides insight into the contribution of specific interactions within the ubiquitin core to the structural stability of the native and intermediate states. The observations that disruptive mutations and/or addition of denaturants result in an apparent two-state folding process with slower rates is explained by the destabilization of a partially folded intermediate, which is in rapid equilibrium with unfolded states. The model predicts that under sufficiently stabilizing conditions kinetic intermediates may become populated even for proteins showing apparent two-state kinetics.

Submission Details

ID: wnXfeoVj3

Submitter: Connie Wang

Submission Date: Aug. 8, 2017, 1:46 p.m.

Version: 1

Publication Details
Khorasanizadeh S;Peters ID;Roder H,Nat Struct Biol (1996) Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. PMID:8564547
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
5L9U 2016-06-11T00:00:00+0000 6.4 Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with a cross linked Ubiquitin variant-substrate-UBE2C (UBCH10) complex representing key features of multiubiquitination
5OHM 2017-07-17T00:00:00+0000 3.8 K33-specific affimer bound to K33 diUb
6ZVK 2020-07-24T00:00:00+0000 3.49 The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism
2K39 2008-04-25T00:00:00+0000 0 Recognition dynamics up to microseconds revealed from RDC derived ubiquitin ensemble in solution
2KDE 2009-01-06T00:00:00+0000 0 NMR structure of major S5a (196-306):K48 linked diubiquitin species
1E0Q 2000-04-05T00:00:00+0000 0 Mutant Peptide from the first N-terminal 17 amino-acid of Ubiquitin
3AI5 2010-05-10T00:00:00+0000 1.4 Crystal structure of yeast enhanced green fluorescent protein-ubiquitin fusion protein
3J7O 2014-08-01T00:00:00+0000 3.5 Structure of the mammalian 60S ribosomal subunit
3J7P 2014-08-01T00:00:00+0000 3.5 Structure of the 80S mammalian ribosome bound to eEF2
3J7Q 2014-08-01T00:00:00+0000 3.5 Structure of the idle mammalian ribosome-Sec61 complex

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Polyubiquitin-C P63048 RL40_BOVIN
100.0 Polyubiquitin-C P63050 RL40_CANLF
100.0 Polyubiquitin-C P18101 RL40_DROME
100.0 Polyubiquitin-C P63052 RL40_FELCA
100.0 Polyubiquitin-C P62987 RL40_HUMAN
100.0 Polyubiquitin-C P0C273 RL40_MACFA
100.0 Polyubiquitin-C P62984 RL40_MOUSE
100.0 Polyubiquitin-C P68205 RL40_OPHHA
100.0 Polyubiquitin-C P63053 RL40_PIG
100.0 Polyubiquitin-C P0C275 RL40_PONPY
100.0 Polyubiquitin-C P62986 RL40_RAT
100.0 Polyubiquitin-C P0C276 RL40_SHEEP
100.0 Polyubiquitin-C P15357 RS27A_DROME
100.0 Polyubiquitin-C P29504 RS27A_MANSE
100.0 Polyubiquitin-C P68202 RS27A_PLUXY
100.0 Polyubiquitin-C P68203 RS27A_SPOFR
100.0 Polyubiquitin-C P0CG53 UBB_BOVIN
100.0 Polyubiquitin-C P0CG54 UBB_CAVPO
100.0 Polyubiquitin-C P0CG62 UBB_CHICK
100.0 Polyubiquitin-C P0CG67 UBB_GORGO
100.0 Polyubiquitin-C Q8MKD1 UBB_HORSE
100.0 Polyubiquitin-C P0CG47 UBB_HUMAN
100.0 Polyubiquitin-C P0CG49 UBB_MOUSE
100.0 Polyubiquitin-C P0CG65 UBB_PANTR
100.0 Polyubiquitin-C P0CG60 UBB_PONPY
100.0 Polyubiquitin-C P0CG51 UBB_RAT
100.0 Polyubiquitin-C P0CG55 UBB_SHEEP
100.0 Polyubiquitin-C P0CH28 UBC_BOVIN
100.0 Polyubiquitin-C P0CG66 UBC_GORGO
100.0 Polyubiquitin-C P0CG48 UBC_HUMAN
100.0 Polyubiquitin-C P0CG50 UBC_MOUSE
100.0 Polyubiquitin-C P0CG64 UBC_PANTR
100.0 Polyubiquitin-C P0CG68 UBC_PIG
100.0 Polyubiquitin-C P0CG61 UBC_PONPY
100.0 Polyubiquitin-C Q63429 UBC_RAT
100.0 Polyubiquitin-C P62976 UBIQP_CRIGR
100.0 Polyubiquitin-C P0CG69 UBIQP_DROME
100.0 Polyubiquitin-C P62972 UBIQP_XENLA
100.0 Polyubiquitin-C Q865C5 UBIQ_CAMDR
100.0 Polyubiquitin-C P68197 UBIQ_CERCA
100.0 Polyubiquitin-C P62975 UBIQ_RABIT
98.7 Polyubiquitin-C P46575 RL40_EIMBO
98.7 Polyubiquitin-C P23398 UBIQP_STRPU
98.7 Polyubiquitin-C Q8SWD4 UBIQ_ENCCU
100.0 Polyubiquitin-C P62992 RS27A_BOVIN
100.0 Polyubiquitin-C P62978 RS27A_CAVPO
100.0 Polyubiquitin-C P79781 RS27A_CHICK
100.0 Polyubiquitin-C P62979 RS27A_HUMAN
100.0 Polyubiquitin-C P68200 RS27A_ICTPU
100.0 Polyubiquitin-C P62983 RS27A_MOUSE
100.0 Polyubiquitin-C P62982 RS27A_RAT
98.7 Polyubiquitin-C P49632 RL40_CAEEL
98.7 Polyubiquitin-C P0CG71 UBIQ1_CAEEL
98.7 Polyubiquitin-C P59669 UBIQP_GEOCY
97.4 Polyubiquitin-C P69201 RL40_LEIMA
97.4 Polyubiquitin-C P0CH11 RL401_CHLRE
97.4 Polyubiquitin-C P0CH10 RL403_CHLRE
97.4 Polyubiquitin-C P33190 RL40_TETPY
97.4 Polyubiquitin-C P0DJ25 RL40_TETTS
97.4 Polyubiquitin-C P0CG82 UBIQP_TETPY
97.4 Polyubiquitin-C P19848 UBIQ_COPCO
97.4 Polyubiquitin-C P42740 UBIQP_AGLNE
96.1 Polyubiquitin-C P59271 R27AA_ARATH
96.1 Polyubiquitin-C P0CH06 RL401_SCHPO
96.1 Polyubiquitin-C P0CH07 RL402_SCHPO
96.1 Polyubiquitin-C B9DHA6 RL40A_ARATH
96.1 Polyubiquitin-C P0CH34 RL40A_ORYSJ
96.1 Polyubiquitin-C P0CH08 RL40A_YEAST
96.1 Polyubiquitin-C Q42202 RL40B_ARATH
96.1 Polyubiquitin-C P0CH35 RL40B_ORYSJ
96.1 Polyubiquitin-C P0CH09 RL40B_YEAST
96.1 Polyubiquitin-C P51423 RL40_BRARP
96.1 Polyubiquitin-C P40909 RL40_CRYNJ
97.4 Polyubiquitin-C P14794 RL40_DICDI
96.1 Polyubiquitin-C P49636 RL40_NICSY
96.1 Polyubiquitin-C P62980 RS27A_SOLLC
96.1 Polyubiquitin-C P62981 RS27A_SOLTU
96.1 Polyubiquitin-C Q9SHE7 RUB1_ARATH
96.1 Polyubiquitin-C P0C073 RUB1_DESAN
96.1 Polyubiquitin-C P0C030 RUB1_ORYSJ
96.1 Polyubiquitin-C Q8RUC6 RUB2_ARATH
96.1 Polyubiquitin-C P0C031 RUB2_ORYSJ
96.1 Polyubiquitin-C P0CG73 UBI1P_CANAX
96.1 Polyubiquitin-C P0CG85 UBI1P_NICSY
96.1 Polyubiquitin-C P0CH04 UBI1P_PETCR
96.1 Polyubiquitin-C P0CH05 UBI2P_PETCR
96.1 Polyubiquitin-C P0CG74 UBI4P_CANAX
96.1 Polyubiquitin-C P0CG75 UBI4P_KLULA
96.1 Polyubiquitin-C P0CG84 UBI4P_NICSY
96.1 Polyubiquitin-C P0CG72 UBI4P_SCHPO
96.1 Polyubiquitin-C P0CG63 UBI4P_YEAST
97.4 Polyubiquitin-C P0CG76 UBIQA_DICDI
97.4 Polyubiquitin-C P0CG77 UBIQD_DICDI
97.4 Polyubiquitin-C P0CG78 UBIQF_DICDI
97.4 Polyubiquitin-C P0CG79 UBIQG_DICDI
97.4 Polyubiquitin-C P0CG81 UBIQH_DICDI
97.4 Polyubiquitin-C P0CG80 UBIQI_DICDI
97.4 Polyubiquitin-C P0CG88 UBIQJ_DICDI
96.1 Polyubiquitin-C P69309 UBIQP_AVEFA
96.1 Polyubiquitin-C P0CG83 UBIQP_HORVU
96.1 Polyubiquitin-C P69315 UBIQP_LINUS
96.1 Polyubiquitin-C P69322 UBIQP_PEA
96.1 Polyubiquitin-C P69325 UBIQP_SOYBN
96.1 Polyubiquitin-C P69310 UBIQ_AVESA
96.1 Polyubiquitin-C P69313 UBIQ_HELAN
96.1 Polyubiquitin-C P69317 UBIQ_LUPPO
96.1 Polyubiquitin-C P69326 UBIQ_WHEAT
96.1 Polyubiquitin-C Q8H159 UBQ10_ARATH
96.1 Polyubiquitin-C P0CH33 UBQ11_ARATH
96.1 Polyubiquitin-C Q3E7T8 UBQ14_ARATH
96.1 Polyubiquitin-C Q1EC66 UBQ3_ARATH
96.1 Polyubiquitin-C Q58G87 UBQ3_ORYSJ
96.1 Polyubiquitin-C P0CH32 UBQ4_ARATH
94.7 Polyubiquitin-C P0C032 RUB3_ORYSJ
94.7 Polyubiquitin-C P42739 UBIQP_ACEPE
94.7 Polyubiquitin-C P22589 UBIQP_PHYIN
96.1 Polyubiquitin-C P0CH27 RL402_TRYCR
96.1 Polyubiquitin-C P49633 RL40_ACACA
96.1 Polyubiquitin-C P0C224 RL40_NEUCR
96.1 Polyubiquitin-C P14795 RL40_TRYCR
96.1 Polyubiquitin-C P0CG70 UBI4P_NEUCR
94.7 Polyubiquitin-C Q3E7K8 UBQ12_ARATH
93.4 Polyubiquitin-C Q9FHQ6 UBQ9_ARATH
94.7 Polyubiquitin-C P21899 RL40_TRYBB
96.0 Polyubiquitin-C P69061 RS27A_KLULA
96.0 Polyubiquitin-C P05759 RS31_YEAST
93.4 Polyubiquitin-C P23324 UBIQP_EUPEU
94.7 Polyubiquitin-C P69200 RL40_LEITA
96.0 Polyubiquitin-C P14799 RS27A_NEUCR
95.9 Polyubiquitin-C P14797 RS27A_DICDI
95.8 Polyubiquitin-C Q9ARZ9 R27AA_ORYSJ
95.8 Polyubiquitin-C P59232 R27AB_ARATH
95.8 Polyubiquitin-C P51431 R27AB_ORYSJ
95.8 Polyubiquitin-C P59233 R27AC_ARATH
95.8 Polyubiquitin-C P0CG86 RS271_HORVU
95.8 Polyubiquitin-C P0CG87 RS272_HORVU
95.8 Polyubiquitin-C P47905 RS27A_LUPAL
95.8 Polyubiquitin-C P27923 RS27A_MAIZE
95.8 Polyubiquitin-C P0C016 RS27A_SCHPO
95.8 Polyubiquitin-C P0C8R3 RS27B_SCHPO
95.7 Polyubiquitin-C P59272 RS27A_DAUCA
100.0 Polyubiquitin-C P84589 UBIQ_LUMTE
97.5 Polyubiquitin-C P31753 RS27A_ASPOF