Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles

The stability, activity, and solubility of a protein sequence are determined by a delicate balance of molecular interactions in a variety of conformational states. Even so, most computational protein design methods model sequences in the context of a single native conformation. Simulations that model the native state as an ensemble have been mostly neglected due to the lack of sufficiently powerful optimization algorithms for multistate design. Here, we have applied our multistate design algorithm to study the potential utility of various forms of input structural data for design. To facilitate a more thorough analysis, we developed new methods for the design and high-throughput stability determination of combinatorial mutation libraries based on protein design calculations. The application of these methods to the core design of a small model system produced many variants with improved thermodynamic stability and showed that multistate design methods can be readily applied to large structural ensembles. We found that exhaustive screening of our designed libraries helped to clarify several sources of simulation error that would have otherwise been difficult to ascertain. Interestingly, the lack of correlation between our simulated and experimentally measured stability values shows clearly that a design procedure need not reproduce experimental data exactly to achieve success. This surprising result suggests potentially fruitful directions for the improvement of computational protein design technology

Mapping the genetic architecture of gene expression in human liver

Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order disease traits. Therefore, identifying the molecular phenotypes that vary in response to changes in DNA and that also associate with changes in disease traits has the potential to provide the functional information required to not only identify and validate the susceptibility genes that are directly affected by changes in DNA, but also to understand the molecular networks in which such genes operate and how changes in these networks lead to changes in disease traits. Toward that end, we profiled more than 39,000 transcripts and we genotyped 782,476 unique single nucleotide polymorphisms (SNPs) in more than 400 human liver samples to characterize the genetic architecture of gene expression in the human liver, a metabolically active tissue that is important in a number of common human diseases, including obesity, diabetes, and atherosclerosis. This genome-wide association study of gene expression resulted in the detection of more than 6,000 associations between SNP genotypes and liver gene expression traits, where many of the corresponding genes identified have already been implicated in a number of human diseases. The utility of these data for elucidating the causes of common human diseases is demonstrated by integrating them with genotypic and expression data from other human and mouse populations. This provides much-needed functional support for the candidate susceptibility genes being identified at a growing number of genetic loci that have been identified as key drivers of disease from genome-wide association studies of disease. By using an integrative genomics approach, we highlight how the gene RPS26 and not ERBB3 is supported by our data as the most likely susceptibility gene for a novel type 1 diabetes locus recently identified in a large-scale, genome-wide association study. We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process. © 2008 Schadt et al

Four small puzzles that Rosetta doesn't solve

A complete macromolecule modeling package must be able to solve the simplest structure prediction problems. Despite recent successes in high resolution structure modeling and design, the Rosetta software suite fares poorly on deceptively small protein and RNA puzzles, some as small as four residues. To illustrate these problems, this manuscript presents extensive Rosetta results for four well-defined test cases: the 20-residue mini-protein Trp cage, an even smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies, several lines of evidence indicate that conformational sampling is not the major bottleneck in modeling these small systems. Instead, approximations and omissions in the Rosetta all-atom energy function currently preclude discriminating experimentally observed conformations from de novo models at atomic resolution. These molecular "puzzles" should serve as useful model systems for developers wishing to make foundational improvements to this powerful modeling suite.Comment: Published in PLoS One as a manuscript for the RosettaCon 2010 Special Collectio

Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

A Supramolecular Ice Growth Inhibitor

Safranine O, a synthetic dye, was found to inhibit growth of ice at millimolar concentrations with an activity comparable to that of highly evolved antifreeze glycoproteins. Safranine inhibits growth of ice crystals along the crystallographic a-axis, resulting in bipyramidal needles extended along the directions as well as and plane-specific thermal hysteresis (TH) activity. The interaction of safranine with ice is reversible, distinct from the previously reported behavior of antifreeze proteins. Spectroscopy and molecular dynamics indicate that safranine forms aggregates in aqueous solution at micromolar concentrations. Metadynamics simulations and aggregation theory suggested that as many as 30 safranine molecules were preorganized in stacks at the concentrations where ice growth inhibition was observed. The simulations and single-crystal X-ray structure of safranine revealed regularly spaced amino and methyl substituents in the aggregates, akin to the ice-binding site of antifreeze proteins. Collectively, these observations suggest an unusual link between supramolecular assemblies of small molecules and functional proteins

Structure, Energetics, and Dynamics of Screw Dislocations in Even n-Alkane Crystals

Spiral hillocks on n-alkane crystal surfaces were observed immediately after Frank recognized the importance of screw dislocations for crystal growth, yet their structures and energies in molecular crystals remain ill-defined. To illustrate the structural chemistry of screw dislocations that are responsible for plasticity in organic crystals and upon which the organic electronics and pharmaceutical industries depend, molecular dynamics was used to examine heterochiral dislocation pairs with Burgers vectors along [001] in n-hexane, n-octane, and n-decane crystals. The cores were anisotropic and elongated in the (110) slip plane, with significant local changes in molecular position, orientation, conformation, and energy. This detailed atomic level picture produced a distribution of strain consistent with linear elastic theory, giving confidence in the simulations. Dislocations with doubled Burgers vectors split into pairs with elementary displacements. These results suggest a pathway to understanding the mechanical properties and failure associated with elastic and plastic deformation in soft crystals

Silver(I), gold(I) and palladium(II) complexes of a NHC-pincer ligand with an aminotriazine core: a comparison with pyridyl analogues

Dinuclear silver, di- and tetra-nuclear gold, and mononuclear palladium complexes with chelating C,N,C diethylaminotriazinyl-bridged bis(NHC) pincer ligands were prepared and characterised. The silver and gold complexes exist in a twisted, helical conformation in both the solution- and the solid state. In contrast, an analogous dinuclear gold complex with pyridyl-bridged NHCs exists in a linear conformation. Computational studies have been performed to rationalise the formation of twisted/helical vs. linear forms

Structural Correspondence of Solution, Liquid Crystal, and Crystalline Phases of the Chromonic Mesogen Sunset Yellow

The azo dye, sunset yellow, is a prototypical, chromonic liquid crystal in which assembly in aqueous solution at high volume fraction leads to lyotropic mesophases with a “package of properties distinct in almost every aspect” (Lydon, J. Curr. Opin. Colloid Interface Sci. 2004, 8, 480). In particular, the isotropic to nematic transition in such phases, the consequence of stacking of dye molecules in chains, is difficult to bring into correspondence with athermal theories for rigid rods as well as modifications that consider chain interactions with one another. Chromonic mesogens, small molecules that stack to form lyotropic liquid crystals, prompt structural questions that have yet to be answered; a full understanding of structure should inform colligative properties. Herein, the single crystal structure of a guanidinium salt of the sunset yellow dianion, a known chromonic mesogen, is reported. The compound crystallizes as a dihydrate, tetrahydrofuran solvate in the orthorhombic space group Pnna, with a = 6.8426(5) Å, b = 20.048(1) Å, c = 21.466(2) Å. The sunset yellow molecules, point group approximately Cs, are disordered about a crystallographic diad axis.The structure is informative because pairwise interactions in the disordered crystal structure show a remarkable correspondence with the stereochemistry of sunset yellow molecules in solution and in the liquid crystal phase. The solution structure is here simulated by the combination of molecular dynamics,metadynamics, and quantum chemical computations. The comparable disorder in the fluid and solid states suggests the possibility that stacked aggregates adhere to growing crystals intact. Computations were used to evaluate proposals that stacking faults and branching points lower the X-ray correlation lengths while preserving extended structures. Evidence is found forstacking faults but not branches. The solution stereochemistry and stereodynamics has implications for the geometry of long rods, for which understanding is a prerequisite for reckoning properties of vexing chromonic mesophases

Dislocation-Actuated Growth and Inhibition of Hexagonal L-Cystine Crystallization at the Molecular Level

Crystallization of L-cystine is a critical process in the pathogenesis of kidney stone formation in cystinuria, a disorder affecting more than 20 000 individuals in the United States alone. In an effort to elucidate the crystallization of L-cystine and the mode of action of tailored growth inhibitors that may constitute effective therapies, real-time in situ atomic force microscopy has been used to investigate the surface micromorphology and growth kinetics of the {0001} faces of L-cystine at various supersaturations and concentrations of the growth inhibitor L-cystine dimethylester (CDME). Crystal growth is actuated by screw dislocations on the {0001} L-cystine surface, producing hexagonal spiral hillocks that are a consequence of six interlacing spirals of anisotropic molecular layers. The high level of elastic stress in the immediate vicinity around the dislocation line results in a decrease in the step velocities and a corresponding increase in the spacing of steps. The kinetic curves acquired in the presence of CDME conform to the classical Cabrera–Vermilyea model. Anomalous birefringence in the {101̅0} growth sectors, combined with computational modeling, supports a high fidelity of stereospecific binding of CDME, in a unique orientation, exclusively at one of the six crystallographically unique projections on the {1010} plane

Difference Hirshfeld fingerprint plots: A tool for studying polymorphs

A new tool has been developed to help elucidate the differences in packing between different polymorphs, especially when the differences of interest are small. The technique builds upon the Hirshfeld fingerprint plot pioneered by Spackman and co-workers by subtracting the value at every point in a fingerprint plot from the value at every point in another. This is found to reveal differences that are not readily apparent to the eye. By summing the absolute values of these differences, a quantitative measure of the difference between two fingerprint plots can be obtained. The technique was applied to Ni and Cu trans-bis(2-hydroxy-5-methylphenonethanoneoximato) complexes determined at two temperatures, with the Ni complex displaying temperature-dependent polymorphism. Difference Hirshfeld fingerprint plots were also generated for calculated structures from DFT simulations that were performed on the experimental structures. These demonstrated that the simulations reproduced the fine detail of the packing