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3‐ Instead of 4‐Helix Formation in a De Novo Designed Protein in Solution Revealed by Small‐Angle X‐ray Scattering
Author(s) -
HøibergNielsen Rasmus,
Tofteng Shelton A. Pernille,
Sørensen Kasper K.,
Roessle Manfred,
Svergun Dimitri I.,
Thulstrup Peter W.,
Jensen Knud J.,
Arleth Lise
Publication year - 2008
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/cbic.200800263
Subject(s) - small angle x ray scattering , helix (gastropod) , crystallography , helix bundle , circular dichroism , folding (dsp implementation) , dimer , protein folding , chemistry , protein design , protein structure , peptide , topology (electrical circuits) , scattering , physics , biochemistry , biology , mathematics , ecology , electrical engineering , organic chemistry , combinatorics , snail , optics , engineering
De novo design and chemical synthesis of proteins and their mimics are central approaches for understanding protein folding and accessing proteins with novel functions. We have previously described carbohydrates as templates for the assembly of artificial proteins, so‐called carboproteins. Here, we describe the preparation and structural studies of three α ‐helical bundle carboproteins, which were assembled from three different carbohydrate templates and one amphiphilic hexadecapeptide sequence. This heptad repeat peptide sequence has been reported to lead to 4‐α‐helix formation. The low resolution solution structures of the three carboproteins were analyzed by means of small‐angle X‐ray scattering (SAXS) and synchrotron radiation circular dichroism (SRCD). The ab initio SAXS data analysis revealed that all three carboproteins adopted an unexpected 3+1‐helix folding topology in solution, while the free peptide formed a 3‐helix bundle. This finding is consistent with the calculated α‐helicities based on the SRCD data, which are 72 and 68 % for two of the carboproteins. The choice of template did not affect the overall folding topology (that is for the 3+1 helix bundle) the template did have a noticeable impact on the solution structure. This was particularly evident when comparing 4‐helix carboprotein monomers with the 2×2‐helix carboprotein dimer as the latter adopted a more compact conformation. Furthermore, the clear conformational differences observed between the two 4‐helix (3+1) carboproteins based on D ‐altropyranoside and D ‐galactopyranoside support the notion that folding is affected by the template, and subtle variations in template distance‐geometry design may be exploited to control the solution fold. In addition, the SRCD data show that template assembly significantly increases thermostability.