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Docking and virtual screening (VS) reach maximum potential when the receptor displays the structural changes needed for accurate ligand binding. Unfortunately, these conformational changes are often poorly represented in experimental structures or homology models, debilitating their docking performance. Recently, we have shown that receptors optimized with our LiBERO method (Ligand-guided Backbone Ensemble Receptor Optimization) were able to better discriminate active ligands from inactives in flexible-ligand VS docking experiments. The LiBERO method relies on the use of ligand information for selecting the best performing individual pockets from ensembles derived from normal-mode analysis or Monte Carlo. Here we present ALiBERO, a new computational tool that has expanded the pocket selection from single to multiple, allowing for automatic iteration of the sampling-selection procedure. The selection of pockets is performed by a dual method that uses exhaustive combinatorial search plus individual addition of pockets, selecting only those that maximize the discrimination of known actives compounds from decoys. The resulting optimized pockets showed increased VS performance when later used in much larger unrelated test sets consisting of biologically active and inactive ligands. In this paper we will describe the design and implementation of the algorithm, using as a reference the human estrogen receptor alpha.

This paper formalises the so-called Supply-Use Based Econometric (SUBE) approach that allows for the introduction of econometric analysis in the calculation of backward input–output multipliers of the Leontief-type quantity model, using rectangular supply and use tables. The SUBE approach does not require any kind of inverse matrix and incorporates the traditional approach (with square supply-use tables) as a particular case. The empirical analysis shows that the SUBE carbon dioxide multipliers for the EU27 are considerably lower than those obtained by the traditional Leontief inverse. In an application of the SUBE approach, the European economy appears to emit about 10% less carbon dioxide than in a situation in which it would not import any intermediate inputs from outside the EU27.

Climate change research is currently a topic of great interest for economic researchers. In particular, environmental input–output analysis increasingly plays an important role in measuring the economic and environmental effects of sustainable development policies in Europe. Other approaches also exist, such as econometric modelling, in which impacts are quantified on statistical grounds and with certain desirable properties (efficient estimates, confidence intervals, hypothesis testing, etc.) that are not found in the input–output approach. Consequently, this paper merges the two approaches to address the calculation of unbiased and consistent carbon dioxide emission multipliers for Denmark and their respective confidence intervals. The use of the supply and use system instead of the symmetric input–output table also presents the opportunity to avoid the common problems associated with the construction of technical coefficients (technology assumptions, negatives, etc.). Moreover, a new policy-relevant application of these multipliers is introduced: the quantification of the performance of the carbon dioxide emission reductions carried out by industries via external trading.

The representation of protein flexibility is still a challenge for the state-of-the-art flexible ligand docking protocols. In this article we use a large and diverse benchmark to prove that is possible to improve consistently the cross docking performance against a single receptor conformation by using an equilibrium ensemble of binding site conformers. The benchmark contained 28 proteins, and the top ranked near native poses for the ligand were found 20% more efficiently than using a single receptor. The multiple conformations were derived from the collective variable space defined by all heavy atom elastic network normal modes, including backbone and side chains. We have found that the binding site displacements for best positioning of the ligand seem rather independent from the global collective motions of the protein. We also found that the number of binding site conformations needed to represent non-redundant flexibility was less than one hundred. The ensemble of receptor conformations can be generated in our web site at http://abagyan.scripps.edu/MRC.

The dynamics of proteins in aqueous solution has been investigated through a massive approach based on “state of the art” molecular dynamics simulations performed for all protein metafolds using the four most popular force fields (OPLS, CHARMM, AMBER, and GROMOS). A detailed analysis of the massive database of trajectories (>1.5 terabytes of data obtained using ≈50 years of CPU) allowed us to obtain a robust-consensus picture of protein dynamics in aqueous solution.

The essential dynamics of different normal and chemically modified DNA duplexes pertaining to the B family have been extensively explored from molecular dynamics simulations using powerful data mining techniques. Some of them, which are presented here for the first time, might become standard, powerful tools to characterize the dynamical behavior of complex biomolecular structures such as nucleic acids. Their potential impact is illustrated by examining the extended trajectories sampled for the set of DNA duplexes considered in this study, which allows us to discuss the degree of conservation of the natural flexibility pattern of the different DNAs, which in specific cases contain severe chemical modifications.

The structure of noncovalent complexes of DNA duplex with minor groove binders (mG-binders) has been analyzed by state of the art molecular dynamics (MD) simulations. More than 3.3 micros of MD trajectories (including 4 x 0.5 micros trajectories) were collected for the Dickerson's dodecamer bound to DAPI, Hoechst 33258, and Netropsin. Comparison of these trajectories with control simulations in water allowed us to determine that the extreme dehydration and partial neutralization occurring during electrospray experiments does not produce the disruption of the DNA:mG-binder complexes or the dissociation of the two strands of the duplex. Irrespective of the drug and the simulation conditions the mG-binders remains bound to the DNA near the preferential binding position in aqueous conditions. Large distortions appear in the two DNA strands, which maintain however a memory of the original DNA duplex structure in water, and a general helical-like conformation.

The counterion distribution around a DNA dodecamer (5'-CGCGAATTCGCG-3') is analyzed using both standard and novel techniques based on state of the art molecular dynamics simulations. Specifically, we have explored the population of Na(+) in the minor groove of DNA duplex, and whether or not a string of Na(+) can replace the spine of hydration in the narrow AATT minor groove. The results suggest that the insertion of Na(+) in the minor groove is a very rare event, but that when once the ion finds specific sites deep inside the groove it can reside there for very long periods of time. According to our simulation the presence of Na(+) inside the groove does not have a dramatic influence in the structure or dynamics of the duplex DNA. The ability of current MD simulations to obtain equilibrated pictures of the counterion atmosphere around DNA is critically discussed.

The tautomeric preferences of cytosine and its derivatives substituted at position 5 (R = CH3, propynyl, Cl, and Br) have been analyzed both in the gas phase and in aqueous solution by using a comb...

SummaryThe study of protein binding mechanisms is a major topic of research in structural biology. Here, we implement a combination of metrics to systematically assess the cost of backbone conformational changes that protein domains undergo upon association. Through the analyses of 2090 unique unbound → bound transitions, from over 12,000 structures, we show that two-thirds of these proteins do not suffer significant structural changes upon binding, and could thus fit the lock-and-key model well. Among the remaining proteins, one-third explores the bound conformation in the unbound state (conformational selection model) and, while most transitions are possible from an energetic perspective, a few do require external help to break the thermodynamic barrier (induced fit model). We also analyze the relationship between conformational transitions and protein connectivity, finding that, in general, domains interacting with many partners undergo smaller changes upon association, and are less likely to freely explore larger conformational changes.

The use of multiple X-ray protein structures has been reported to be an efficient alternative for the representation of the binding pocket flexibility needed for accurate small molecules docking. However, the docking performance of the individual single conformations varies widely, and adding certain conformations to an ensemble is even counterproductive. Here we used a very large and diverse benchmark of 1068 X-ray protein conformations of 99 therapeutically relevant proteins, first, to compare the performance of the ensemble and single-conformation docking and, second, to find the properties of the best-performing conformers that can be used to select a smaller set of conformers for ensemble docking. The conformer selection has been validated through retrospective virtual screening experiments aimed at separating known ligand binders from decoys. We found that the conformers cocrystallized with the largest ligands displayed high selectivity for binders, and when combined in ensembles they consistently provided better results than randomly chosen protein conformations. The use of ensembles encompassing between 3 and 5 experimental conformations consistently improved the docking accuracy and binders vs decoys separation.

Several very extended (0.5-1 micros) molecular dynamics (MD) simulations of parallel and antiparallel G-quadruplex DNA strongly suggest that in the presence of suitable cations the quadruplex not only remains stable in the gas phase, but also displays a structure that closely resembles that found in extended (25-ns long) trajectories in aqueous solution. In the absence of the crucial cations, the trajectories become unstable and in general the quadruplex structure is lost. To our knowledge, this is the first physiologically relevant structure of DNA for which very large MD simulations suggest that the structure in water and in the gas phase are indistinguishable.

Oligonucleotides can interact in a very specific manner with homopurine–homopyrimidine sequences of double-stranded DNA by forming triple helices (triplexes) that can be used to design sequence-specific DNA-binding molecules with diagnostic or therapeutic purposes. 2] Depending on the orientation of the third strand with respect to the central polypurine Watson–Crick strand, the triplexes are classified into two main categories: i) parallel and ii) antiparallel. Parallel triplexes require protonation of N3 of cytosine to form proper Hoogsteen bonding with N7 of guanine; this implies that its formation is strongly pH dependent. On the other hand, antiparallel triplexes require no protonation and exhibit largely pH-independent binding. 8-Amino-2’-deoxyguanosine (8AG) can be found in cellular DNA as a possible intermediate in the mutagenesis of nitroalkanes. Moreover, it has been stated that 8AG stabilizes parallel and antiparallel triplexes as well as parallel duplexes, causing an increase in the free energy of formation of 1– 4 kcalmol 1 per substitution. By using parallel and antiparallel clamps carrying the 8AG-containing strand linked to the Hoogsteen strand, it is possible to obtain DNA probes with very high affinity to single-stranded polypyrimidine targets. 8] Unfortunately, G-rich oligonucleotides easily form undesired intraor intermolecular G-tetrad structures. Thus, the ability of antiparallel clamps to form a triple-helical structure with its polypyrimidine target can be reduced by the formation of Gquartets. This has fueled the design of modified nucleobases that can destabilize the tetraplex; unfortunately, in most cases, these nucleobases also destabilize the triplex. Considering the large triplex-stabilizing effect of 8AG, we decided to test whether G tetrads were affected by the presence of 8AG residues. We selected the 15-base-long thrombin aptamer 5’GGTTGGTGTGGTTGG-3’ as a model for quadruplex-forming oligonucleotides (Scheme 1). It was shown that this oligonucleotide adopts a monomeric chair quadruplex structure in the presence of potassium and is characterized by a denaturation–renaturation profile that is reversible and can be observed by different techniques.

The field of molecular dynamic simulations of nucleic acids is reviewed, with particular emphasis on recent methodological advances that have expanded the range of applicability and increased the accuracy of these techniques. Keywords: nucleic acids; molecular dynamics; molecular modeling; DNA; RNA

The impact of the transfer from water to the vacuum in the duplex DNA has been explored by using long molecular dynamic simulations. In opposition to chemical intuition, it is found that vaporization of DNA, even at high temperatures, does not lead to a total disruption of the double helix. Rather, the DNA duplex preserves gross structural, energetic, and dynamic features of the conformation of the double helix in aqueous solution. Thus, the two strands remain bound, the global structure has a slight helicity, and the total number of DNA-DNA interactions is not dramatically different from that found in solution. The results provide detailed structural and dynamic information useful to complement current mass spectroscopy studies of DNA structures.

The effect of remote amino groups in the H-bonding of complementary bases of duplex and triplex DNA has been investigated in the gas phase by means of density functional theory. It is found that amino groups incorporated in regions of the purine that are distant from the H-bonding sites might have a notable influence on the stability of H-bonded dimers. The results show that, in addition to primary and secondary interactions, polarization effects can be relevant for the determination of hydrogen bonding in nucleobases. © 2002 Wiley Periodicals, Inc. Biopoly (Nucleic Acid Sci) 61: 52–60, 2002; DOI 10.1002/bip.10046

The role of virtual ligand screening in modern drug discovery is to mine large chemical collections and to prioritize for experimental testing a comparatively small and diverse set of compounds with expected activity against a target. Several studies have pointed out that the performance of virtual ligand screening can be improved by taking into account receptor flexibility. Here, we systematically assess how multiple crystallographic receptor conformations, a powerful way of discretely representing protein plasticity, can be exploited in screening protocols to separate binders from non-binders. Our analyses encompass 36 targets of pharmaceutical relevance and are based on actual molecules with reported activity against those targets. The results suggest that an ensemble receptor-based protocol displays a stronger discriminating power between active and inactive molecules as compared to its standard single rigid receptor counterpart. Moreover, such a protocol can be engineered not only to enrich a higher number of active compounds, but also to enhance their chemical diversity. Finally, some clear indications can be gathered on how to select a subset of receptor conformations that is most likely to provide the best performance in a real life scenario.

To understand cellular processes at the molecular level we need to improve our knowledge of protein−protein interactions, from a structural, mechanistic, and energetic point of view. Current theoretical studies and computational docking simulations show that protein dynamics plays a key role in protein association and support the need for including protein flexibility in modeling protein interactions. Assuming the conformational selection binding mechanism, in which the unbound state can sample bound conformers, one possible strategy to include flexibility in docking predictions would be the use of conformational ensembles originated from unbound protein structures. Here we present an exhaustive computational study about the use of precomputed unbound ensembles in the context of protein docking, performed on a set of 124 cases of the Protein−Protein Docking Benchmark 3.0. Conformational ensembles were generated by conformational optimization and refinement with MODELLER and by short molecular dynamics trajectories with AMBER. We identified those conformers providing optimal binding and investigated the role of protein conformational heterogeneity in protein−protein recognition. Our results show that a restricted conformational refinement can generate conformers with better binding properties and improve docking encounters in medium-flexible cases. For more flexible cases, a more extended conformational sampling based on Normal Mode Analysis was proven helpful. We found that successful conformers provide better energetic complementarity to the docking partners, which is compatible with recent views of binding association. In addition to the mechanistic considerations, these findings could be exploited for practical docking predictions of improved efficiency.

After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing a set of 30 proteins (representative of all native folds) through extensive molecular dynamics simulations in denaturant (using a range of force-fields), we derived robust rules for urea unfolding that are valid at the proteome level. Irrespective of the protein fold, presence or absence of disulphide bridges, and secondary structure composition, urea concentrates in the first solvation shell of quasi-native proteins, but with a density lower than that of the fully unfolded state. The presence of urea does not alter the spontaneous vibration pattern of proteins. In fact, it reduces the magnitude of such vibrations, leading to a counterintuitive slow down of the atomic-motions that opposes unfolding. Urea stickiness and slow diffusion is, however, crucial for unfolding. Long residence urea molecules placed around the hydrophobic core are crucial to stabilize partially open structures generated by thermal fluctuations. Our simulations indicate that although urea does not favor the formation of partially open microstates, it is not a mere spectator of unfolding that simply displaces to the right of the folded←→unfolded equilibrium. On the contrary, urea actively favors unfolding: it selects and stabilizes partially unfolded microstates, slowly driving the protein conformational ensemble far from the native one and also from the conformations sampled during thermal unfolding., Author Summary The delicate equilibrium between the folded and functional structure of a protein and its unfolded state is highly dependent on environmental variables such as the solvent. For example the co-solvent urea is a well-known protein denaturant that displaces the equilibrium towards unstructured and non-functional conformations of proteins. However the molecular mechanism behind its ability remains an enigma and the interpretation of the experimental data is still ambiguous. By analyzing a set of representative proteins through extensive molecular dynamics simulations in urea, we provide a robust and consensus picture of the first stages of urea-driven protein unfolding and elucidate the role of urea in accelerating protein unfolding. Our results suggest that urea, thanks to its stickiness and slow diffusion, benefits from the intrinsic flexibility of proteins and stabilizes partially open-states, slowly driving the protein toward unfolding.