Molecular Modeling of human molecular chaperone Hsp40 DjA1 as monomer and dimer
Domingues, M.N.1; Arcuri, H.A.1; Gava, L.M.1; Ramos, C.H.I.2; de Azevedo, W.F.3; Ruggiero, J.1; Borges J.C.1
1Departamento de Física, IBILCE-UNESP, São José do Rio Preto, SP, Brasil; 2Laboratório Nacional de Luz Síncrotron, LNLS, Campinas, SP, Brasil; 3Faculdade de Biociências, PUCRS, Porto Alegre, RS, Brasil.
Hsp40
are the main co-chaperones from the Hsp70 system, which plays a central
role in protein folding. They work selecting and presenting substrate
to the Hsp70 and also increasing its ATPase activity. Hsp40 may contain
four characteristic domains: the N-terminal J-domain; the adjacent
Gly/Phe-rich region; the Cys-rich domain and the C-terminal domain rich
in β-sheet structure. The last ~70 amino-acids are involved in the
Hsp40 dimerization. The Cys-rich and C-terminal domains participate in
substrate binding process. Based on domain content, Hsp40 proteins may
be classified in three subfamilies: A) contains all domains described,
B) lacks the Cys-rich domain and C) contains only the J-domain.
Low-resolution studies have showed that Hsp40 from subfamily A and B
are structurally unrelated, suggesting that this feature may explain
differences in chaperone functions (Borges, J.C., Hannes, F.,
Craievich, A.F., Ramos, C.H.I. (2005). J. Biol. Chem. 280,
13671-13681). Although crystallographic structures from Hsp40 domains
are available, there are not structures of whole Hsp40. To get further
information about Hsp40 proteins from subfamily A, this work aims to
develop molecular models of DjA1, a human Hsp40, from crystallographic
structures of solved domains and from low resolution data obtained by
small angle X ray scattering (SAXS). We used the restrained-based
modeling implemented in the program MODELLER for modeling the DjA1
structure in monomeric and dimeric form. A total of 1000 models were
generated and the final model was selected based on stereochemical
quality. The programs PROCHECK and WHATCHECK were used to check bond
lengths, bond angles, peptide bonds and side-chain ring planarities,
chirality, main-chain and side-chain torsion angles. VERIFY 3D program,
which measures the compatibility of a protein model with its sequence
using a 3D profile, also was used for analysis. The RMSD from ideal
geometry was extracted for each model using the program X-PLOR. The
selected models presented all these parameters in acceptable values.
The final models will be used for rigid body simulations relative of
settle previously obtained SAXS data for DjA1 monomer and dimer. These
final models will be important to our knowledge of how the Hsp40
domains interact with each other in the DjA1 dimer and monomer and also
with Hsp70, features that are lacking for this kind of proteins. Supported by FAPESP, CNPq/MCT, and LNLS.
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