Publications

2004
Endres, Robert G, Thomas C Schulthess, and Ned S Wingreen. “Toward an atomistic model for predicting transcription-factor binding sites.”. Proteins 57.2 (2004): , 57, 2, 262-8. Web.Abstract
Identifying the specific DNA-binding sites of transcription-factor proteins is essential to understanding the regulation of gene expression in the cell. Bioinformatics approaches are fast compared to experiments, but require prior knowledge of multiple binding sites for each protein. Here, we present an atomistic force-field method to predict binding sites based only on the X-ray structure of a related bound complex. Specific flexible contacts between the protein and DNA are modeled by a library of amino acid side-chain rotamers. Using the example of the mouse transcription factor, Zif268, a well-studied zinc-finger protein, we show that the protein sequence alone, without the detailed experimental structure, gives a strong bias toward the consensus binding site.
2003
Huang, Kerwyn Casey, Yigal Meir, and Ned S Wingreen. “Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones.”. Proc Natl Acad Sci U S A 100.22 (2003): , 100, 22, 12724-8. Web.Abstract
In Escherichia coli, division site selection is regulated in part by the Min-protein system. Oscillations of the Min proteins from pole to pole every approximately 40 sec have been revealed by in vivo studies of GFP fusions. The dynamic oscillatory structures produced by the Min proteins, including a ring of MinE protein, compact polar zones of MinD, and zebra-striped oscillations in filamentous cells, remain unexplained. We show that the Min oscillations, including mutant phenotypes, can be accounted for by in vitro-observed interactions involving MinD and MinE, with a crucial role played by the rate of nucleotide exchange. Recent discoveries suggest that protein oscillations may play a general role in proper chromosome and plasmid partitioning.
Emberly, Eldon G, et al.Flexibility of alpha-helices: results of a statistical analysis of database protein structures.”. J Mol Biol 327.1 (2003): , 327, 1, 229-37. Print.Abstract
Alpha-helices stand out as common and relatively invariant secondary structural elements of proteins. However, alpha-helices are not rigid bodies and their deformations can be significant in protein function (e.g. coiled coils). To quantify the flexibility of alpha-helices we have performed a structural principal-component analysis of helices of different lengths from a representative set of protein folds in the Protein Data Bank. We find three dominant modes of flexibility: two degenerate bend modes and one twist mode. The data are consistent with independent Gaussian distributions for each mode. The mode eigenvalues, which measure flexibility, follow simple scaling forms as a function of helix length. The dominant bend and twist modes and their harmonics are reproduced by a simple spring model, which incorporates hydrogen-bonding and excluded volume. As an application, we examine the amount of bend and twist in helices making up all coiled-coil proteins in SCOP. Incorporation of alpha-helix flexibility into structure refinement and design is discussed.
Hirose, Kenji, Yigal Meir, and Ned S Wingreen. “Local moment formation in quantum point contacts.”. Phys Rev Lett 90.2 (2003): , 90, 2, 026804. Web.Abstract
Spin-density-functional theory of quantum point contacts (QPCs) reveals the formation of a local moment with a net of one electron spin in the vicinity of the point contact-supporting the recent report of a Kondo effect in a QPC. The hybridization of the local moment to the leads decreases as the QPC becomes longer, while the on site Coulomb-interaction energy remains almost constant.
Wingreen, Ned S, Jonathan Miller, and Edward C Cox. “Scaling of mutational effects in models for pleiotropy.”. Genetics 164.3 (2003): , 164, 3, 1221-8. Print.Abstract
Mutation-selection models provide a framework to relate the parameters of microevolution to properties of populations. Like all models, these must be subject to test and refinement in light of experiments. The standard mutation-selection model assumes that the effects of a pleiotropic mutation on different characters are uncorrelated. As a consequence of this assumption, mutations of small overall effect are suppressed. For strong enough pleiotropy, the result is a nonvanishing fraction of a population with the "perfect" phenotype. However, experiments on microorganisms and experiments on protein structure and function contradict the assumptions of the standard model, and Kimura's observations of heterogeneity within populations contradict its conclusions. Guided by these observations, we present an alternative model for pleiotropic mutations. The new model allows mutations of small overall effect and thus eliminates the finite fraction of the population with the perfect phenotype.
Mukhopadhyay, Ranjan, et al.Statistical mechanics of RNA folding: importance of alphabet size.”. Phys Rev E Stat Nonlin Soft Matter Phys 68.4 Pt 1 (2003): , 68, 4 Pt 1, 041904. Web.Abstract
We construct a base-stacking model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four- or six-letter alphabets. With only two kinds of bases, most sequences have many alternative folding configurations and are consequently thermally unstable. Stable ground states are found only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.
Mok, Kenny C, Ned S Wingreen, and Bonnie L Bassler. “Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression.”. EMBO J 22.4 (2003): , 22, 4, 870-81. Web.Abstract
In a process called quorum sensing, bacteria communicate with one another by exchanging chemical signals called autoinducers. In the bioluminescent marine bacterium Vibrio harveyi, two different auto inducers (AI-1 and AI-2) regulate light emission. Detection of and response to the V.harveyi autoinducers are accomplished through two two-component sensory relay systems: AI-1 is detected by the sensor LuxN and AI-2 by LuxPQ. Here we further define the V.harveyi quorum-sensing regulon by identifying 10 new quorum-sensing-controlled target genes. Our examination of signal processing and integration in the V.harveyi quorum-sensing circuit suggests that AI-1 and AI-2 act synergistically, and that the V.harveyi quorum-sensing circuit may function exclusively as a 'coincidence detector' that discriminates between conditions in which both autoinducers are present and all other conditions.
2002
Miller, Jonathan, et al.Emergence of highly designable protein-backbone conformations in an off-lattice model.”. Proteins 47.4 (2002): , 47, 4, 506-12. Web.Abstract
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally suitable for design. Rather, certain structures are distinguished by unusually high designability: the number of amino acid sequences for which they represent the unique lowest energy state; sequences associated with such structures possess both robustness to mutation and thermodynamic stability. Here we report that highly designable backbone conformations also emerge in a realistic off-lattice model. The highly designable conformations of a chain of 23 amino acids are identified and found to be remarkably insensitive to model parameters. Although some of these conformations correspond closely to known natural protein folds, such as the zinc finger and the helix-turn-helix motifs, others do not resemble known folds and may be candidates for novel fold design.
Emberly, Eldon G, et al.Identifying proteins of high designability via surface-exposure patterns.”. Proteins 47.3 (2002): , 47, 3, 295-304. Print.Abstract
Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique lowest-energy conformation. We find that designability is closely correlated with the pattern of surface exposure of the folded structure. For longer chains, complete enumeration of structures is impractical. Instead, structures can be randomly sampled, and relative designability estimated either from designability within the random sample, or directly from surface-exposure pattern. We compare the surface-exposure patterns of those structures identified as highly designable to the patterns of naturally occurring proteins.
Emberly, Eldon G, Ned S Wingreen, and Chao Tang. “Designability of alpha-helical proteins.”. Proc Natl Acad Sci U S A 99.17 (2002): , 99, 17, 11163-8. Web.Abstract
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested on structures composed of four alpha-helices connected by short turns. All such natural four-helix bundles that are connected by short turns seen in nature are reproduced to closer than 3.6 A per residue within the ensemble. Because structures with no natural counterpart may be targets for ab initio structure design, the designability of each structure in the ensemble-defined as the number of sequences with that structure as their lowest-energy state-is evaluated using a hydrophobic energy. For the case of four alpha-helices, a small set of highly designable structures emerges, most of which have an analog among the known four-helix fold families; however, several packings and topologies with no analogs in protein database are identified.
Li, Hao, Chao Tang, and Ned S Wingreen. “Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.”. Proteins 49.3 (2002): , 49, 3, 403-12. Web.Abstract
We study the designability of all compact 3 x 3 x 3 and 6 x 6 lattice-protein structures using the Miyazawa-Jernigan (MJ) matrix. The designability of a structure is the number of sequences that design the structure, i.e., sequences that have that structure as their unique lowest-energy state. Previous studies of hydrophobic-polar (HP) models showed a wide distribution of structure designabilities. Recently, questions were raised concerning the use of a two-letter (HP) code in such studies. Here, we calculate designabilities using all 20 amino acids, with empirically determined interaction potentials (MJ matrix) and compare with HP model results. We find good qualitative agreement between the two models. In particular, highly designable structures in the HP model are also highly designable in the MJ model-and vice versa-with the associated sequences having enhanced thermodynamic stability.
Meir, Yigal, Kenji Hirose, and Ned S Wingreen. “Kondo model for the "0.7 anomaly" in transport through a quantum point contact.”. Phys Rev Lett 89.19 (2002): , 89, 19, 196802. Web.Abstract
Experiments on quantum point contacts have highlighted an anomalous conductance plateau around 0.7(2e(2)/h), with features suggestive of the Kondo effect. Here, an Anderson model for transport through a point contact analyzed in the Kondo limit. Hybridization to the band increases abruptly with energy but decreases with valence, so that the background conductance and the Kondo temperature T(K) are dominated by different valence transitions. This accounts for the high residual conductance above T(K). The model explains the observed gate-voltage, temperature, magnetic field, and bias-voltage dependences. A spin-polarized current is predicted even for low magnetic fields.

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