Primary Citation PubMed: 11274458
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Robust structure-based resonance assignment for functional protein studies by NMR.
(2010) J Biomol NMR 46
PubMed: 20024602 | PubMedCentral: PMC2813526 | DOI: 10.1007/s10858-009-9390-3
Experimental data for Lysozyme The H N – H N NOE-data set deposited in the PDB (1E8L) (Schwalbe et al.
Publication Year: 2010
What lessons can be learned from studying the folding of homologous proteins?
(2010) Methods 52
PubMed: 20570731 | PubMedCentral: PMC2965948 | DOI: 10.1016/j.ymeth.2010.06.003
Class (fold) Superfamily Protein (species) Method of investigation PDB code Experimental references Comparative references a All-α (Acyl-CoA binding protein-like) Acyl-CoA binding protein ACBP... (Cow) Φ-Value analysis 2ABD [93,94]  ACBP (Rat) WT kinetics 2ABD b  ACBP (Yeast) Φ-Value analysis 2ABD b 
All-α (Acyl carrier protein-like) Colicin E immunity proteins Im7 ( E. coli ) Φ-Value analysis 1AYI   Im9 ( E. coli ) Φ-Value analysis 1IMQ [29,30,95]
All-α (Cytochrome c ) Cytochrome c Cytochrome c (Horse) Hydrogen exchange 1HRC   Cytochrome c 2 ( R. capsulatus ) WT kinetics 1C2R  Cytochrome c 551 ( P. aeruginosa ) Minimal Φ-value analysis 2PAC  Cytochrome c 552 ( H. thermophilus ) WT kinetics 1AYG  Cytochrome c 552 ( T. thermophilus ) WT kinetics 1C52  Mitochondrial cytochrome c (Yeast) WT kinetics 1YCC 
All-α (Four-helical up-and-down bundle) Cytochromes Cytochrome b 562 ( E. coli ) Hydrogen exchange 1APC  FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) FRB (Human) WT kinetics 1AUE 
All-α (DNA/RNA-binding 3-helical bundle) Homeodomain-like DNA-binding domain of human telomeric protein hTRF1 (Human) WT kinetics 1BA5   En-Hd (Drosophila) Φ-Value analysis 1ENH [7,105] c-Myb DNA-binding domain (Mouse) Φ-Value analysis 1IDY  Rap1 (Human) WT kinetics 1FEX 
All-α (Globin-like) Globin-like Leghemoglobin (Soybean) Hydrogen exchange 1FSL   Myoglobin (Sperm whale) Hydrogen exchange 1A6M 
All-α (peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex) Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex E3 binding domain of dihydrolipoamide acetyltransferase [E3BD] ( B. stearothermophilus ) Φ-Value analysis 1EBD   E3-binding domain of dihydrolipoamide succinyltransferase [BBL] ( E. coli ) Φ-Value analysis 1BBL  POB ( P. aerophilium ) Φ-Value analysis 1BBL b 
All-α (ROP-like) ROP protein ROP ( E. agglomerans ) WT kinetics 1ROP b   ROP ( E. coli ) WT kinetics 1ROP  ROP ( P. vulgaris ) WT kinetics 1ROP b 
All-α (spectrin repeat-like) Spectrin repeat Alpha chain R15 (Chicken) Φ-Value analysis 1U5P   Alpha chain R16 (Chicken) Φ-Value analysis 1CUN  Alpha chain R17 (Chicken) Φ-Value analysis 1CUN 
α/β (α/β knot) α/β knot YbeA ( E. coli ) Φ-Value analysis 1NS5   YibK ( H. influenzae ) Φ-Value analysis 1J85 
α/β (Dihydrofolate reductase-like) Dihydrofolate reductase-like Dihydrofolate reductase ( E. coli ) WT kinetics, Ligand binding 1RA9   Dihyrofolate reductase ( L. casei ) WT kinetics, Ligand binding 3DFR  Dihydrofolate reductase (Human) WT kinetics, Ligand binding 1KMV 
α/β (flavodoxin-like) CheY-like CheY ( E. coli ) Φ-Value analysis 1EAY   Flavoproteins Apoflavodoxin ( A. vinelandii ) WT kinetics 1YOB  Flavodoxin ( Anabaena pcc 7119 ) Φ-Value analysis 1FTG 
α/β (Phosphoglycerate kinase) Phosphoglycerate kinase Phosphoglycerate kinase ( B. stearothermophilus ) Minimal Φ-value analysis 1PHP  Phosphoglycerate kinase (Yeast) WT kinetics 3PGK 
α/β (RNase-H-like Motif) RNase-H-like RNase-H ( E.coli ) Hydrogen exchange Limited mutagenesis 1F21 [168,169] RNase-H ( T. thermophilus ) Hydrogen exchange 1RIL  [170,171] RNase-H ( C. tepidum ) WT kinetics 3H08 
α/β (TIM β/α-barrel) Ribulose-phosphate binding barrel Trptophan synthase α-subunit [αTS] ( E. coli ) WT kinetics 1V7Y   Indole-3-glycerophosphate synthase [sIGPS] ( S. solfataricus ) WT kinetics, Hydrogen exchange 1IGS [118,119]
Xylose isomerase-like IOLI ( B. subtilis ) WT kinetics 1I60 
α + β (Ferredoxin-like) Acyl-phosphatase-like AcP (Human) Φ-Value analysis 1APS b [26,120] [26,65,121] HypF ( E. coli ) WT kinetics 1GXU  Protease propeptides/inhibitors Procarboxy-peptidase A2 (Human) Φ-Value analysis 1O6X  Ribosomal protein S6 S6 ( A. aeolicus ) Φ-Value analysis 2J5A  S6 ( T. thermophilus ) Φ-Value analysis 1RIS  RNA binding domain (RBD) U1A (Human) Φ-Value analysis 1FHT 
α + β (β-hairpin-α-hairpin repeat) Ankyrin repeat AnkyrinR D34 (Human) Minimal Φ-value analysis 1N11   Ankyrin repeats in tumor suppressor p16 (Human) Φ-Value analysis 1BI7  Cell-cycle inhibitor p19ink4D (Human) WT kinetics 1BD8  Myotrophin (Rat) Φ-Value analysis 2MYO  Neurogenic locus notch receptor domain (Drosophila) Minimal Φ-value analysis, WT redesign 1OT8 [125,126]
α + β (Cell-cycle regulatory proteins) Cell-cycle regulatory proteins CksHs1 (Human) Φ-Value analysis 1BUH   CksHs2 (Human) WT kinetics 1CKS  Suc1 ( S. pombe ) Φ-Value analysis 1PUC 
α + β (Lysozyme-like) Lysozyme-like Lysozyme (Hen Egg White) WT kinetics 1E8L   α-Lactalbumin (Bovine) WT kinetics 1F6S  α-Lactalbumin (Goat) Minimal Φ-value analysis, Hydrogen exchange 1HFY [131,132]  Milk lysozyme (Dog) Hydrogen exchange 1EL1 [131,133]
α + β (β-grasp: ubiquitin-like) Immunoglobulin-binding domains Protein G ( Streptococcus ) Φ-Value analysis 2IGD  [42,134,135] Immunoglobulin light chain-binding domain of Protein L ( P. magnus ) Φ-Value analysis 2PTL  Ubiquitin-like c-Raf1 RBD (Human) Φ-Value analysis 1RFA [134,135] Ubiquitin (Human) Minimal Φ-value analysis 1UBQ  Ubiquitin (Yeast) Φ-Value analysis 1Q0W 
All-β (Ig-like β-sandwich) Fibronectin type III CAfn2 ( B. circulans ) Φ-Value analysis 1K85  [15,19] FnIII-9 (Human) WT kinetics 1FNF  FnIII-10 (Human) Φ-Value analysis 1FNF  TNfn3 (Human) Φ-Value analysis 1TEN  Immunoglobulin TI I27 (Human) Φ-Value analysis 1TIT  CD2 (Rat) Minimal Φ-value analysis 1HNG  Various antibody domains (V L , C L , C H 2, C H 3) WT kinetics [139–142] 
All-β (Lipocalins) Lipocalins CRABP I (Mouse) WT kinetics 2CBR [143,144] [32,143] CRBP II (Rat) WT kinetics 1OPA  IFABP (Rat) Minimal Φ-value analysis 1IFC [31,32,143,145] ILBP (Rat) Minimal Φ-value analysis 1O1V b [31,32]
All-β (OB-fold) Nucleic acid-binding proteins Bc-Csp ( B. caldolyticus ) Φ-Value analysis 1C9O [146,147] [146,148] CspA ( E. coli ) Hydrogen exchange 1MJC  Bs-CspB ( B. subtilis ) Φ-Value analysis 1CSP  Tm-Csp ( T. maritima ) WT kinetics 1G6P 
All-β (PDZ domain-like) PDZ domain-like PDZ2 domain from PTP-BL (Mouse) Φ-Value analysis 1GM1   Third PDZ domain from synaptic protein PSD-95 (Rat) Hydrogen exchange Φ-value analysis 1BE9 [151,152]
All-β (SH3-like barrel) Chromo domain-like DNA-binding protein Sso7d ( S. solfataricus ) Φ-Value analysis 1SSO  [21,153] SH3-domain α-Spectrin SH3-domain (Chicken) Φ-Value analysis, WT redesign 1SHG [22,154] Fyn proto-oncogene tyrosine kinase SH3-domain (Chicken) Φ-Value analysis, NMR dispersion 1FYN b [23,24,155,156] Actin binding protein ABP1 (Yeast) NMR dispersion 1JO8  Phosphatidylinositol 3-kinase SH3-domain (Cow) WT kinetics 2PNI  c-src protein tyrosine kinase (Chicken) Φ-Value analysis 1SRM 
All-β (WW domain-like) WW domain Formin Binding Protein 28 (Mouse) Φ-Value analysis 1E0L [8,158] Mitotic rotamase PIN1 (Human) Φ-Value analysis 1PIN [48,159] Yap65 WW domain (Human) WT kinetics 1JMQ 
Coiled coil proteins (Parallel coiled-coil) Leucine zipper domain GCN4 (Yeast) WT kinetics, Minimal Φ-value analysis 2BNI [161,162] c-Jun (Human) Dimer thermodynamics 1JUN  c-Fos (Human) Dimer thermodynamics 1FOS  a Comparative references are those in which the folding mechanisms/pathways of homologous proteins are compared and discussed.
PubMed ID is not available.
Published in 2008
Materials and methods 1) Import native lysozyme sequence (gi:45384212) from NCBI and structure (PDB 1E8L ) from PDB websites 2) Run lysozyme in Ab initio mode to start folding independently from the o... iginal protein sequence.
Publication Year: 2008
Conformation-independent structural comparison of macromolecules with ProSMART.
(2014) Acta Crystallogr D Biol Crystallogr 70
PubMed: 25195761 | PubMedCentral: PMC4157452 | DOI: 10.1107/S1399004714016241
Multi-model comparative analysis of a solution NMR structure of hen egg-white lysozyme (PDB entry 1e8l ).
Publication Year: 2014
Published in 2015
In an interesting twist, the refined NMR structure of HEWL shows that the inward or buried conformation of Glu35 is popular in solution (PDB entry 1e8l ; Schwalbe et al. , 2001 ▶ ).
Publication Year: 2015
Structural images The structure of Lyz was represented with PyMOL (The PyMOL Molecular Graphics System, Version 188.8.131.52 Schrödinger, LLC) using the pdb-entry 1E8L of an NMR based solution stru... ture of hen egg white lysozyme [ 42 ] to visualize the most probable PEGylation sites as well as the protein residues relevant for evaluation of the experimental data.
g004 Fig 4 Ribbon structure of hen egg white lysozyme (pdb entry 1E8L).
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