5 research outputs found
A detailed binding free energy study of 2 : 1 ligand–DNA complex formation by experiment and simulation
In 2004, we used NMR to solve the structure of the minor groove binder thiazotropsin A bound in a 2 : 1 complex to the DNA duplex, d(CGACTAGTCG)2. In this current work, we have combined theory and experiment to confirm the binding thermodynamics of this system. Molecular dynamics simulations that use polarizable or non-polarizable force fields with single and separate trajectory approaches have been used to explore complexation at the molecular level. We have shown that the binding process invokes large conformational changes in both the receptor and ligand, which is reflected by large adaptation energies. This is compensated for by the net binding free energy, which is enthalpy driven and entropically opposed. Such a conformational change upon binding directly impacts on how the process must be simulated in order to yield accurate results. Our MM-PBSA binding calculations from snapshots obtained from MD simulations of the polarizable force field using separate trajectories yield an absolute binding free energy (-15.4 kcal mol-1) very close to that determined by isothermal titration calorimetry (-10.2 kcal mol-1). Analysis of the major energy components reveals that favorable non-bonded van der Waals and electrostatic interactions contribute predominantly to the enthalpy term, whilst the unfavorable entropy appears to be driven by stabilization of the complex and the associated loss of conformational freedom. Our results have led to a deeper understanding of the nature of side-by-side minor groove ligand binding, which has significant implications for structure-based ligand development
Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions
A scoring
protocol based on implicit membrane-based scoring functions
and a new protocol for optimizing the positioning of proteins inside
the membrane was evaluated for its capacity to discriminate native-like
states from misfolded decoys. A decoy set previously established by
the Baker lab (<i>Proteins: Struct., Funct., Genet.</i> <b>2006</b>, <i>62</i>, 1010–1025) was used along
with a second set that was generated to cover higher resolution models.
The Implicit Membrane Model 1 (IMM1), IMM1 model with CHARMM 36 parameters
(IMM1-p36), generalized Born with simple switching (GBSW), and heterogeneous
dielectric generalized Born versions 2 (HDGBv2) and 3 (HDGBv3) were
tested along with the new HDGB van der Waals (HDGBvdW) model that
adds implicit van der Waals contributions to the solvation free energy.
For comparison, scores were also calculated with the distance-scaled
finite ideal-gas reference (DFIRE) scoring function. Z-scores for
native state discrimination, energy vs root-mean-square deviation
(RMSD) correlations, and the ability to select the most native-like
structures as top-scoring decoys were evaluated to assess the performance
of the scoring functions. Ranking of the decoys in the Baker set that
were relatively far from the native state was challenging and dominated
largely by packing interactions that were captured best by DFIRE with
less benefit of the implicit membrane-based models. Accounting for
the membrane environment was much more important in the second decoy
set where especially the HDGB-based scoring functions performed very
well in ranking decoys and providing significant correlations between
scores and RMSD, which shows promise for improving membrane protein
structure prediction and refinement applications. The new membrane
structure scoring protocol was implemented in the MEMScore web server
(http://feiglab.org/memscore)
Doing the methylene shuffle - further insights into the inhibition of mitotic kinesin Eg5 with S-trityl L-cysteine
S-Trityl L-cysteine (STLC) is an inhibitor of the mitotic kinesin Eg5 with potential as an antimitotic chemotherapeutic agent. We previously reported the crystal structure of the ligand protein complex, and now for the first time, have quantified the interactions using a molecular dynamics based approach. Based on these data, we have explored the SAR of the trityl head group using the methylene shuffle strategy to expand the occupation of one of the hydrophobic pockets. The most potent compounds exhibit strong (<100 nM) inhibition of Eg5 in the basal ATPase assay and inhibit growth in a variety of tumour-derived cell lines. (C) 2012 Elsevier Masson SAS. All rights reserved
Insights into Saquinavir Resistance in the G48V HIV-1 Protease: Quantum Calculations and Molecular Dynamic Simulations
The spread of acquired immune deficiency syndrome has increasingly become a great concern owing largely to the failure of chemotherapies. The G48V is considered the key signature residue mutation of HIV-1 protease developing with saquinavir therapy. Molecular dynamics simulations of the wild-type and the G48V HIV-1 protease complexed with saquinavir were carried out to explore structure and interactions of the drug resistance. The molecular dynamics results combined with the quantum-based and molecular mechanics Poisson-Boltzmann surface area calculations indicated a monoprotonation took place on D25, one of the triad active site residues. The inhibitor binding of the triad residues and its interaction energy in the mutant were similar to those in the wild-type. The overall structure of both complexes is almost identical. However, the steric conflict of the substituted valine results in the conformational change of the P2 subsite and the disruption of hydrogen bonding between the −NH of the P2 subsite and the backbone −CO of the mutated residue. The magnitude of interaction energy changes was comparable to the experimental K(i) data. The designing for a new drug should consider a reduction of steric repulsion on P2 to enhance the activity toward this mutant strain