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Biomedical subjects

Ranjan Mukhopadhyay

Publications and source records attributed to Ranjan Mukhopadhyay.

17 recordsLinked to original sources

A curvature-mediated mechanism for localization of lipids to bacterial poles.

Subcellular protein localization is a universal feature of eukaryotic cells, and the ubiquity of protein localization in prokaryotic species is now acquiring greater appreciation. Though some targeting anchors are known, the origin of polar and division-site localization remains mysterious for a large fraction of bacterial proteins. Ultimately, the molecular components responsible for such symmetry breaking must employ a high degree of self-organization. Here we propose a novel physical mechanism, based on the two-dimensional curvature of the membrane, for spontaneous lipid targeting to the poles and division site of rod-shaped bacterial cells. If one of the membrane components has a large intrinsic curvature, the geometrical constraint of the plasma membrane by the more rigid bacterial cell wall naturally leads to lipid microphase separation. We find that the resulting clusters of high-curvature lipids are large enough to spontaneously and stably localize to the two cell poles. Recent evidence of localization of the phospholipid cardiolipin to the poles of bacterial cells suggests that polar targeting of some proteins may rely on the membrane's differential lipid content. More generally, aggregates of lipids, proteins, or lipid-protein complexes may localize in response to features of cell geometry incapable of localizing individual molecules.

Bacillus subtilis↗

Palladium-mediated intramolecular aryl amination on furanose derivatives: an expedient approach to the synthesis of chiral benzoxazocine derivatives and tricyclic nucleosides.

Pd-catalyzed intramolecular arylamination on sugar derivatives has been accomplished by using bulky biaryl phosphine ligands. An application of this methodology on a variety of D-glucose-derived substrates, 2a-f, led to the synthesis of highly functionalized cis-fused tricyclic oxazocines, 3a-e. The products could subsequently be transformed to the optically active benzoxazocine derivative 4 and tricyclic nucleoside 6. This is the first example of the synthesis of eight-membered rings via intramolecular cycloamination of furanose derivatives, which provides a very useful method for the catalytic synthesis of medium-ring heterocycles.

Amination↗

General route to 4a-methylhydrofluorene diterpenoids: total syntheses of (+/-)-taiwaniaquinones d and h, (+/-)-taiwaniaquinol B, (+/-)-dichroanal B, and (+/-)-dichroanone.

A general and convergent route for the synthesis of the 4a-methylhydrofluorene diterpenoids has been established through a common hexahydrofluorenone intermediate (10) obtained via Pd(0)-catalyzed reductive cyclization of a substituted 2-(2-bromobenzyl) methylene cyclohexane (13). The strategy has been successfully utilized for the synthesis of (+/-)-taiwaniaquinones D (3) and H (5), (+/-)-taiwaniaquinol B (1), (+/-)-dichroanal B (7), and (+/-)-dichroanone (8).

Diterpenes↗

Divergent cycloaddition and ring-closing metathesis approaches to indolizidine and pyrrolo[1,2-a]azepine skeletons from a chiral precursor: an expeditious route to (-)-8-epi-swainsonine triacetate.

[reaction: see text] A divergent strategy for the synthesis of diverse azabicyclic ring systems has been developed in which a chiral N-allylpyrrolidine derivative, obtained from a carbohydrate precursor was converted to (-)-8-epi-swainsonine triacetate by RCM and to a pyrrolo[1,2-a]azepine derivative and a 3-hydroxymethyl-substituted indolizidine by N-allylcarbohydrate nitrone and nitrile oxide cycloadditions.

Alkaloids↗

Synthesis and intramolecular nitrile oxide cycloaddition of 3,5'-ether-linked pseudooligosaccharide derivatives: an approach to chiral macrooxacycles.

3,5'-ether-linked pseudooligopentose derivatives were synthesized for the first time from readily available carbohydrate precursors. The 1,2-isopropylidene-protected ether-linked oligopentoses are potentially important as precursors of novel RNA analogues. Intramolecular cycloaddition of the nitrile oxides prepared from these derivatives led to the diastereoselective formation of chiral isoxazolines fused to 10-16-membered oxacycles. The stereochemistry of some of these isoxazolines was established by X-ray diffraction and NOESY analysis.

Cyclization↗

Stereoselective syntheses of (+/-)-komaroviquinone and (+/-)-faveline methyl ether through intramolecular Heck reaction.

[reaction: see text] An efficient, flexible, and stereoselective convergent route for constructing the trans-10-hydroxy-1,1-dimethyloctahydrodibenzo[a,d]cyclohepten-7-ones (5a-c) was achieved via intramolecular Heck reaction. This strategy has been successfully implemented for the syntheses of (+/-)-komaroviquinone (3) through (+/-)-coulterone dimethyl ether (5c) and (+/-)-faveline methyl ether (1a).

Antineoplastic Agents, Phytogenic↗

Optimal path to epigenetic switching.

We use large deviation methods to calculate rates of noise-induced transitions between states in multistable genetic networks. We analyze a synthetic biochemical circuit, the toggle switch, and compare the results to those obtained from a numerical solution of the master equation.

Adaptation, Physiological↗

Flexibility of beta-sheets: principal component analysis of database protein structures.

Protein folds are built primarily from the packing together of two types of structures: alpha-helices and beta-sheets. Neither structure is rigid, and the flexibility of helices and sheets is often important in determining the final fold (e.g., coiled coils and beta-barrels). Recent work has quantified the flexibility of alpha-helices using a principal component analysis (PCA) of database helical structures (J. Mol. Bio. 2003, 327, pp. 229-237). Here, we extend the analysis to beta-sheet flexibility using PCA on a database of beta-sheet structures. For sheets of varying dimension and geometry, we find two dominant modes of flexibility: twist and bend. The distributions of amplitudes for these modes are found to be Gaussian and independent, suggesting that the PCA twist and bend modes can be identified as the soft elastic normal modes of sheets. We consider the scaling of mode eigenvalues with sheet size and find that parallel beta-sheets are more rigid than antiparallel sheets over the entire range studied. Finally, we discuss the application of our PCA results to modeling and design of beta-sheet proteins.

Databases, Protein↗

Statistical mechanics of RNA folding: importance of alphabet size.

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.

Base Composition↗

Fluctuating nematic elastomer membranes.

We study the flat phase of nematic elastomer membranes with rotational symmetry spontaneously broken by an in-plane nematic order. Such a state is characterized by a vanishing elastic modulus for simple shear and soft transverse phonons. At harmonic level, the in-plane orientational (nematic) order is stable to thermal fluctuations that lead to short-range in-plane translational (phonon) correlations. To treat thermal fluctuations and relevant elastic nonlinearities, we introduce two generalizations of two-dimensional membranes in a three-dimensional space to arbitrary D-dimensional membranes embedded in a d-dimensional space and analyze their anomalous elasticities in an expansion about D=4. We find a stable fixed point that controls long-scale properties of nematic elastomer membranes. It is characterized by singular in-plane elastic moduli that vanish as a power law eta(lambda)=4-D of a relevant inverse length scale (e.g., wave vector) and a finite bending rigidity. Our predictions are asymptotically exact near four dimensions.

Journal Article↗

Flexibility of alpha-helices: results of a statistical analysis of database protein structures.

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.

Databases, Protein↗

Stomatocyte-discocyte-echinocyte sequence of the human red blood cell: evidence for the bilayer- couple hypothesis from membrane mechanics.

Red-cell shape is encoded in the mechanical properties of the membrane. The plasma membrane contributes bending rigidity; the protein-based membrane skeleton contributes stretch and shear elasticity. When both effects are included, membrane mechanics can reproduce in detail the full stomatocyte-discocyte-echinocyte sequence by variation of a single parameter related to the bilayer couple originally introduced by Sheetz and Singer [Sheetz, M. P. & Singer, S. J. (1974) Proc. Natl. Acad. Sci. USA 71, 4457-4461].

Biomechanical Phenomena↗

Symmetries and elasticity of nematic gels.

A nematic liquid-crystal gel is a macroscopically homogeneous elastic medium with the rotational symmetry of a nematic liquid crystal. In this paper, we develop a general approach to the study of these gels that incorporates all underlying symmetries. After reviewing traditional elasticity and clarifying the role of broken rotational symmetries in both the reference space of points in the undistorted medium and the target space into which these points are mapped, we explore the unusual properties of nematic gels from a number of perspectives. We show how symmetries of nematic gels formed via spontaneous symmetry breaking from an isotropic gel enforce soft elastic response characterized by the vanishing of a shear modulus and the vanishing of stress up to a critical value of strain along certain directions. We also study the phase transition from isotropic to nematic gels. In addition to being fully consistent with approaches to nematic gels based on rubber elasticity, our description has the important advantages of being independent of a microscopic model, of emphasizing and clarifying the role of broken symmetries in determining elastic response, and of permitting easy incorporation of spatial variations, thermal fluctuations, and gel heterogeneity, thereby allowing a full statistical-mechanical treatment of these materials.

Journal Article↗

Two experimental tests of a fluctuation-induced first-order phase transition: intensity fluctuation microscopy at the nematic-smectic-A transition.

We have developed a new, extremely sensitive real-space technique (intensity fluctuation microscopy) to probe the order of the nematic-smectic-A (NA) transition. Using this technique, we show that the NA transition in 4'-n-octyl-4-cyanobiphenyl (8CB) is clearly first order, contrary to calorimetric studies but in agreement with conclusions drawn from front-velocity measurements. We characterize the strength of the discontinuity at the first-order transition by the dimensionless quantity t(0)=(T(NA)-T*)/T(*). By precisely measuring t(0), we have made the first detailed tests of predictions based on the Halperin-Lubensky-Ma (HLM) theory of fluctuation-induced, first-order phase transitions. First, we explore the effect of an external magnetic field on the NA transition. Although modest fields (of order 10 T) are predicted to drive the weakly first-order transition in pure 8CB second order, we observe no such effect; we establish instead that the lower bound on this critical field is approximately 30 T. Likewise, we observe no effect in mixtures of 8CB with its longer chemical homolog 4'-n-decyl-4-cyanobiphenyl (10CB). Second, we examine the dependence of t(0) as a function of 8CB-10CB mixture concentration and find that the data in mixtures with small nematic temperature range are well-fit by the parameters derived by Anisimov et al. based on calorimetric measurements. As we increase the nematic range (by using concentrations closer to pure 8CB), the measured t(0) deviates more and more from the HLM predictions. Smectic fluctuations, which are neglected in the HLM calculation, are an obvious candidate to explain such a discrepancy, but one's naive expectation is that they would reduce t(0) below the HLM levels, whereas the observed values are too large. However, a recent renormalization-group calculation concludes that smectic fluctuations, surprisingly, should indeed increase t(0), explaining the observations presented here.

Journal Article↗

Fractional quantum Hall effect in an array of quantum wires.

We demonstrate the emergence of the quantum Hall (QH) hierarchy in a 2D model of coupled quantum wires in a perpendicular magnetic field. At commensurate values of the magnetic field, the system can develop instabilities to appropriate interwire electron hopping processes that drive the system into a variety of QH states. Some of the QH states are not included in the Haldane-Halperin hierarchy. In addition, we find operators allowed at any field that lead to novel crystals of Laughlin quasiparticles. We demonstrate that any QH state is the ground state of a Hamiltonian that we explicitly construct.

Journal Article↗

Echinocyte shapes: bending, stretching, and shear determine spicule shape and spacing.

We study the shapes of human red blood cells using continuum mechanics. In particular, we model the crenated, echinocytic shapes and show how they may arise from a competition between the bending energy of the plasma membrane and the stretching/shear elastic energies of the membrane skeleton. In contrast to earlier work, we calculate spicule shapes exactly by solving the equations of continuum mechanics subject to appropriate boundary conditions. A simple scaling analysis of this competition reveals an elastic length Lambda(el), which sets the length scale for the spicules and is, thus, related to the number of spicules experimentally observed on the fully developed echinocyte.

Animals↗