Simple, yet powerful methodologies for conformational sampling of proteins

2015 ◽  
Vol 17 (9) ◽  
pp. 6155-6173 ◽  
Author(s):  
Ryuhei Harada ◽  
Yu Takano ◽  
Takeshi Baba ◽  
Yasuteru Shigeta
Keyword(s):  
Protein Folding ◽  
Large Amplitude ◽  
Sampling Methods ◽  
Substrate Binding ◽  
Conformational Sampling ◽  
T4 Lysozyme ◽  
Induced Fit ◽  
Feature Article ◽  
Loop Region ◽  
Small Proteins

This feature article reviews four different conformational sampling methods for proteins recently developed by us. We here deal with protein folding of small proteins, large amplitude domain motion of T4 lysozyme, and induced-fit motion of a loop region after substrate binding using our methods.

scholarly journals A Conserved Domain Is Crucial for Acceptor Substrate Binding in a Family of Glucosyltransferases

2014 ◽  
Vol 197 (3) ◽  
pp. 510-517 ◽  
Author(s):  
Fan Zhu ◽  
Hua Zhang ◽  
Hui Wu
Keyword(s):  
Bacterial Adhesion ◽  
Substrate Binding ◽  
Molecular Replacement ◽  
Bacterial Sepsis ◽  
Content Type ◽  
Acceptor Substrate ◽  
Loop Region ◽  
Conserved Domain ◽  
Substrate Binding Domain ◽  
Insight Into

Serine-rich repeat glycoproteins (SRRPs) are highly conserved in streptococci and staphylococci. Glycosylation of SRRPs is important for bacterial adhesion and pathogenesis.Streptococcus agalactiaeis the leading cause of bacterial sepsis and meningitis among newborns. Srr2, an SRRP fromS. agalactiaestrain COH1, has been implicated in bacterial virulence. Four genes (gtfA,gtfB,gtfC, and gtfD) located downstream ofsrr2share significant homology with genes involved in glycosylation of other SRRPs. We have shown previously thatgtfAandgtfBencode two glycosyltransferases, GtfA and GtfB, that catalyze the transfer of GlcNAc residues to the Srr2 polypeptide. However, the function of other glycosyltransferases in glycosylation of Srr2 is unknown. In this study, we determined that GtfC catalyzed the direct transfer of glucosyl residues to Srr2-GlcNAc. The GtfC crystal structure was solved at 2.7 Å by molecular replacement. Structural analysis revealed a loop region at the N terminus as a putative acceptor substrate binding domain. Deletion of this domain rendered GtfC unable to bind to its substrate Srr2-GlcNAc, concurrently abolished the glycosyltransferase activity of GtfC, and also altered glycosylation of Srr2. Furthermore, deletion of the corresponding regions from GtfC homologs also abolished their substrate binding and enzymatic activity, indicating that this region is functionally conserved. In summary, we have determined that GtfC is important for the glycosylation of Srr2 and identified a conserved loop region that is crucial for acceptor substrate binding from GtfC homologs in streptococci. These findings shed new mechanistic insight into this family of glycosyltransferases.

Toward a simplification of the protein folding problem: a stabilizing polyalanine .alpha.-helix engineered in T4 lysozyme

Biochemistry ◽  
1991 ◽  
Vol 30 (8) ◽  
pp. 2012-2017 ◽  
Author(s):  
X. J. Zhang ◽  
W. A. Baase ◽  
B. W. Matthews
Keyword(s):  
Protein Folding ◽  
Alpha Helix ◽  
T4 Lysozyme

Conformational Sampling and Polarization of Asp26 in pKa Calculations of Thioredoxin

2018 ◽  
Author(s):  
Aharon Gomez Llanos ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Force Field ◽  
Gibbs Free Energy ◽  
Conformational Sampling ◽  
Atomic Charges ◽  
Loop Region ◽  
Energy Cycle ◽  
Dynamics Simulations ◽  
Aspartate Residue

Thioredoxin is a protein that has been used as model system by various computational methods to predict the p<i>K<sub>a</sub></i> of aspartate residue Asp26 which is 3.5 units higher than a solvent exposed one (e.g Asp20). Here, we use extensive atomistic molecular dynamics simulations of two different protonation states of Asp26 in combination with conformational analysis based on RMSD clustering and principle component analysis to identify representative conformations of the protein in solution. For each conformation the Gibbs free energy of proton transfer between Asp26 and Asp20, which is fully solvated in a loop region of the protein, is calculated with the Amber99sb force field in alchemical transformations. The varying polarization of the two residues in different molecular environments and protonation states is described by Hirshfeld-I (HI) atomic charges obtained from the averaged polarized electron density. Our results show that the Gibbs free energy of proton transfer is dependent on the protein conformation, the proper sampling of the neighbouring Lys57 residue orientations and on water molecules entering the hydrophobic cavity upon deprotonating Asp26. The inclusion of the polarization of both aspartate residues in the free energy cycle by the HI atomic charges improves the results from the nonpolarizable force field and reproduces the experimental p<i>K<sub>a</sub></i> value of Asp26.<br>

Structure of Mammalian Cytochrome P450 2C5 Complexed with Diclofenac at 2.1 Å Resolution:  Evidence for an Induced Fit Model of Substrate Binding†,‡

Biochemistry ◽  
2003 ◽  
Vol 42 (31) ◽  
pp. 9335-9345 ◽  
Author(s):  
Michael R. Wester ◽  
Eric F. Johnson ◽  
Cristina Marques-Soares ◽  
Sylvie Dijols ◽  
Patrick M. Dansette ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Substrate Binding ◽  
Induced Fit
Sign in / Sign up

Export Citation Format

Share Document