Guanglei Cui

Importance of Dispersion and Electron Correlation in ab Initio Protein Folding

Dispersion is well-known to be important in biological systems, but the effect of electron correlation in such systems remains unclear. In order to assess the relationship between the structure of a protein and its electron correlation energy, we employed both full system Hartree-Fock (HF) and second-order Møller-Plesset perturbation (MP2) calculations in conjunction with the Polarizable Continuum Model (PCM) on the native structures of two proteins and their corresponding computer-generated decoy sets. Because of the expense of the MP2 calculation, we have utilized the fragment molecular orbital method (FMO) in this study. We show that the sum of the Hartree-Fock (HF) energy and force field (LJ6)-derived dispersion energy (HF + LJ6) is well correlated with the energies obtained using second-order Møller-Plesset perturbation (MP2) theory. In one of the two examples studied, the correlation energy as well as the empirical dispersive energy term was able to discriminate between native and decoy structures. On the other hand, for the second protein we studied, neither the correlation energy nor dispersion energy showed discrimination capabilities; however, the ab initio MP2 energy and the HF+LJ6 both ranked the native structure correctly. Furthermore, when we randomly scrambled the Lennard-Jones parameters, the correlation between the MP2 energy and the sum of the HF energy and dispersive energy (HF+LJ6) significantly drops, which indicates that the choice of Lennard-Jones parameters is important.

Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS.

Protein farnesyltransferase (FTase) catalyzes farnesylation of a variety of peptide substrates. (3)H α-secondary kinetic isotope effect (α-SKIE) measurements of two peptide substrates, CVIM and CVLS, are significantly different and have been proposed to reflect a rate-limiting S(N)2-like transition state with dissociative characteristics for CVIM, while, due to the absence of an isotope effect, CVLS was proposed to have a rate-limiting peptide conformational change. Potential of mean force quantum mechanical/molecular mechanical studies coupled with umbrella sampling techniques were performed to further probe this mechanistic dichotomy. We observe the experimentally proposed transition state (TS) for CVIM but find that CVLS has a symmetric S(N)2 TS, which is also consistent with the absence of a (3)H α-SKIE. These calculations demonstrate facile substrate-dependent alterations in the transition state structure catalyzed by FTase.

The Intrinsic Dynamics and Function of Nickel-Binding Regulatory Protein : Insights from Elastic Network Analysis

Nickel-responsive protein NikR regulates the nickel uptake in nickel-dependent bacteria by interacting with the operator of nikABCDE and subsequently repressing the transcription of NikABCDE, an ABC-type nickel transporter system. The function of NikR and its affinity for the operator DNA is highly conformation-dependent, which has been confirmed by three independent crystallographic studies on NikR proteins from different bacteria. Depending on the intracellular nickel concentration, NikR is able to adopt either the open form or one of the two closed forms (cis and trans) that differ in the domain-domain arrangement. Only the closed cis form is optimal for DNA binding. We examined the low-resolution vibrational spectrum of NikR in each conformational form using the elastic network model and observed large-scale domain-domain vibrations that are closely related to the conformational transitions required for function, particularly the symmetric bending mode and the asymmetric twisting mode. This analysis on the intrinsic dynamics coded in the three-dimensional molecular construct allows us to examine the proposed mechanisms of NikR regulation from the standpoint of protein collective motions. Our findings further support the three-state equilibrium hypothesis proposed by others, and imply that an isolated closed cis form may be dynamically unstable but can be stabilized by DNA binding. However, we also found that the simple C(alpha)-model used in the current analysis is insufficient to capture the impact of nickel binding on the protein dynamics, for which an all-atom model with detailed atom typing is more appropriate.

Interpreting The Observed Substrate Selectivity And The Product Regioselectivity In Orf2-Catalyzed Prenylation From X-Ray Structures

The combined QM/MM based X-ray crystallography technique is described. Its relevant strengths and weaknesses relative to traditional refinement protocols are discussed. The method is illustrated by refining Orf2 protein–ligand complexes and comparing the QM/MM based method to CNS derived results. It is shown that in this instance the QM/MM based approach give superior results to traditional MM based refinements methods as implemented in CNS