Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 Lysozyme L99A

2000 ◽  
Vol 302 (4) ◽  
pp. 979-989 ◽  
Author(s):  
Geoffrey Mann ◽  
Jan Hermans
Keyword(s):  
Small Molecule ◽  
Noble Gases ◽  
T4 Lysozyme ◽  
Phage T4 ◽  
Mutant Phage ◽  
Molecule Interactions

Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme

2000 ◽  
Vol 302 (4) ◽  
pp. 955-977 ◽  
Author(s):  
Michael L Quillin ◽  
Wendy A Breyer ◽  
Ian J Griswold ◽  
Brian W Matthews
Keyword(s):  
Noble Gases ◽  
T4 Lysozyme ◽  
Protein Ligand Interactions ◽  
Phage T4 ◽  
Ligand Interactions

Small Molecule Interactions with Protein−Tyrosine Phosphatase PTP1B and Their Use in Inhibitor Design†

Biochemistry ◽  
1996 ◽  
Vol 35 (50) ◽  
pp. 15989-15996 ◽  
Author(s):  
Terrence R. Burke, ◽  
Bin Ye ◽  
Xinjian Yan ◽  
Shaomeng Wang ◽  
Zongchao Jia ◽  
...  
Keyword(s):  
Small Molecule ◽  
Protein Tyrosine Phosphatase ◽  
Tyrosine Phosphatase ◽  
Inhibitor Design ◽  
Protein Tyrosine ◽  
Molecule Interactions

scholarly journals Stabilization of phage T4 lysozyme by engineered disulfide bonds

1989 ◽  
Vol 86 (17) ◽  
pp. 6562-6566 ◽  
Author(s):  
M Matsumura ◽  
W J Becktel ◽  
M Levitt ◽  
B W Matthews
Keyword(s):  
Disulfide Bonds ◽  
Theoretical Calculations ◽  
Equilibrium Constants ◽  
T4 Lysozyme ◽  
Disulfide Bridges ◽  
Large Loop ◽  
Phage T4 ◽  
Flexible Part ◽  
Free Phage

Four different disulfide bridges (linking positions 9-164, 21-142, 90-122, and 127-154) were introduced into a cysteine-free phage T4 lysozyme at sites suggested by theoretical calculations and computer modeling. The new cysteines spontaneously formed disulfide bonds on exposure to air in vitro. In all cases the oxidized (crosslinked) lysozyme was more stable than the corresponding reduced (noncrosslinked) enzyme toward thermal denaturation. Relative to wild-type lysozyme, the melting temperatures of the 9-164 and 21-142 disulfide mutants were increased by 6.4 degrees C and 11.0 degrees C, whereas the other two mutants were either less stable or equally stable. Measurement of the equilibrium constants for the reduction of the engineered disulfide bonds by dithiothreitol indicates that the less thermostable mutants tend to have a less favorable crosslink in the native structure. The two disulfide bridges that are most effective in increasing the stability of T4 lysozyme have, in common, a large loop size and a location that includes a flexible part of the molecule. The results suggest that stabilization due to the effect of the crosslink on the entropy of the unfolded polypeptide is offset by the strain energy associated with formation of the disulfide bond in the folded protein. The design of disulfide bridges is discussed in terms of protein flexibility.

scholarly journals Identification of a Hydrophobic Cleft in the LytTR Domain of AgrA as a Locus for Small Molecule Interactions That Inhibit DNA Binding

Biochemistry ◽  
2012 ◽  
Vol 51 (50) ◽  
pp. 10035-10043 ◽  
Author(s):  
Paul G. Leonard ◽  
Ian F. Bezar ◽  
David J. Sidote ◽  
Ann M. Stock
Keyword(s):  
Dna Binding ◽  
Small Molecule ◽  
Molecule Interactions ◽  
Hydrophobic Cleft
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