A gradient‐directed Monte Carlo approach for protein design

We develop a new global optimization strategy, gradient‐directed Monte Carlo (GDMC) sampling, to optimize protein sequence for a target structure using RosettaDesign. GDMC significantly improves the sampling of sequence space, compared to the classical Monte Carlo search protocol, for a fixed backbone conformation as well as for the simultaneous optimization of sequence and structure. As such, GDMC sampling enhances the efficiency of protein design. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Dynamic docking and electron transfer between Zn-myoglobin and cytochrome b(5)

We present a broad study of the effect of neutralizing the two negative charges of the Mb propionates on the interaction and electron transfer (ET) between horse Mb and bovine cyt b(5), through use of Zn-substituted Mb (ZnMb, 1) to study the photoinitiated reaction, ((3)ZnP)Mb + Fe(3+)cyt b(5) --> (ZnP)(+)Mb + Fe(2+)cyt b(5). The charge neutralization has been carried out both by replacing the Mb heme with zinc-deuteroporphyrin dimethylester (ZnMb(dme), 2), which replaces the charges by small neutral hydrophobic patches, and also by replacement with the newly prepared zinc-deuteroporphyrin diamide (ZnMb(diamide), 3), which converts the charged groups to neutral, hydrophilic ones. The effect of propionate neutralization on the conformation of the zinc-porphyrin in the Mb heme pocket has been studied by multinuclear NMR with an (15)N labeled zinc porphyrin derivative (ZnMb((15)N-diamide), 4). The rates of photoinitiated ET between the Mb's (1-3) and cyt b(5) have been measured over a range of pH values and ionic strengths. Isothermal titration calorimetry (ITC) and NMR methods have been used to independently investigate the effect of charge neutralization on Mb/b(5) binding. The neutralization of the two heme propionates of ZnMb by formation of the heme diester or, for the first time, the diamide increases the second-order rate constant of the ET reaction between ZnMb and cyt b(5) by as much as several 100-fold, depending on pH and ionic strength, while causing negligible changes in binding affinity. Brownian dynamic (BD) simulations and ET pathway calculations provide insight into the protein docking and ET process. The results support a new "dynamic docking" paradigm for protein-protein reactions in which numerous weakly bound conformations of the docked complex contribute to the binding of cyt b(5) to Mb and Hb, but only a very small subset of these are ET active, and this subset does not include the conformations most favorable for binding; the Mb surface is a large "target" with a small "bullseye" for the cyt b(5) "arrow". This paradigm differs sharply from the more familiar, "simple" docking within a single, or narrow range of conformations, where binding strength and ET reactivity increase in parallel. Likewise, it is distinct from, although complementary to, the well-known picture of conformational control of ET through "gating", or a related picture of "conformational coupling". The new model describes situations in which tight binding does not correlate with efficient ET reactivity, and explains how it is possible to modulate reactivity without changing affinity. Such "decoupling" of reactivity from binding clearly is of physiological relevance for the reduction of met-Mb in muscle and of met-Hb in a red cell, where tight binding of cyt b(5) to the high concentration of ferrous-Mb/Hb would prevent the cytochrome from finding and reducing the oxidized proteins; it likely is of physiological relevance in other situations, as well.     

Nucleic Acid Charge Transfer: Black, White and Gray

Theoretical studies of charge transport in deoxyribonucleic acid (DNA) and peptide nucleic acid (PNA) indicate that structure and dynamics modulate the charge transfer rates, and that different members of a structural ensemble support different charge transport mechanisms. Here, we review the influences of nucleobase geometry, electronic structure, solvent environment, and thermal conformational fluctuations on the charge transfer mechanism. We describe an emerging framework for understanding the diversity of charge transport mechanisms seen in nucleic acids.     

A gradient-directed Monte Carlo approach to molecular design

The recently developed linear combination of atomic potentials (LCAP) approach [M. Wang et al., J. Am. Chem. Soc. 128, 3228 (2006)] allows continuous optimization in a discrete chemical space, and thus is useful in the design of molecules for targeted properties. To address further challenges arising from the rugged, continuous property surfaces in the LCAP approach, we develop a gradient-directed Monte Carlo (GDMC) strategy as an augmentation to the original LCAP optimization method. The GDMC method retains the power of exploring molecular space by utilizing local gradient information computed from the LCAP approach to jump between discrete molecular structures. It also allows random MC moves to overcome barriers between local optima on property surfaces. The combined GDMC-LCAP approach is demonstrated here for optimizing nonlinear optical properties in a class of donor-acceptor substituted benzene and porphyrin frameworks. Specifically, one molecule with four nitrogen atoms in the porphyrin ring was found to have a larger first hyperpolarizability than structures with the conventional porphyrin motif.     

Effect of backbone flexibility on charge transfer rates in peptide nucleic acid duplexes

Charge transfer (CT) properties are compared between peptide nucleic acid structures with an aminoethylglycine backbone (aeg-PNA) and those with a γ-methylated backbone (γ-PNA). The common aeg-PNA is an achiral molecule with a flexible structure, whereas γ-PNA is a chiral molecule with a significantly more rigid structure than aeg-PNA. Electrochemical measurements show that the CT rate constant through an aeg-PNA bridging unit is twice the CT rate constant through a γ-PNA bridging unit. Theoretical calculations of PNA electronic properties, which are based on a molecular dynamics structural ensemble, reveal that the difference in the CT rate constant results from the difference in the extent of backbone fluctuations of aeg- and γ-PNA. In particular, fluctuations of the backbone affect the local electric field that broadens the energy levels of the PNA nucleobases. The greater flexibility of the aeg-PNA gives rise to more broadening, and a more frequent appearance of high-CT rate conformations than in γ-PNA.     

Electron transfer between cofactors in protein domains linked by a flexible tether

Some key electron-transfer (ET) proteins have domains containing redox cofactors connected by a flexible tether. The relative motion of the domains is essential for reaction because of the strong ET rate dependence on distance. The constrained conformational flexibility produces a kinetic regime intermediate between “unimolecular” and “bimolecular”. We used a simple model for ET coupled to conformational diffusion to explore the structure dependence of the ET kinetics. The model describes the evolution of an initially prepared reduced donor state, and recovers the diffusion and electron tunneling-limited regimes. The restriction of the conformational space imposed by the tether introduces an entropic component to the effective donor–acceptor interaction potential. As such, the tether length may control the transition between the electron tunneling and diffusion-limited regimes.     

Chiral action at a distance: remote substituent effects on the optical activity of calyculins A and B

[structure--see text] Calyculins A and B differ only by the (E)- vs (Z)-configuration at C(2). Yet, they show a large difference in optical rotations. We demonstrate a new strategy that provides a physical analysis of this long-range chiro-optical effect by Boltzmann-averaged atomic contribution mapping. The polarizability characteristics of the CN substituent rather than the perturbation of the stereogenic centers or the introduction of asymmetry into the polyene chain give rise to the remarkable difference in rotation angles.     

PNA versus DNA: effects of structural fluctuations on electronic structure and hole-transport mechanisms

The effects of structural fluctuations on charge transfer in double-stranded DNA and peptide nucleic acid (PNA) are investigated. A palindromic sequence with two guanine bases that play the roles of hole donor and acceptor, separated by a bridge of two adenine bases, was analyzed using combined molecular dynamics (MD) and quantum-chemical methods. Surprisingly, electronic structure calculations on individual MD snapshots show significant frontier orbital electronic population on the bridge in approximately 10% of the structures. Electron-density delocalization to the bridge is found to be gated by fluctuations of the covalent conjugated bond structure of the aromatic rings of the nucleic bases. It is concluded, therefore, that both thermal hopping and superexchange should contribute significantly to charge transfer even in short DNA/PNA fragments. PNA is found to be more flexible than DNA, and this flexibility is predicted to produce larger rates of charge transfer.