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Arindam Banerjee

Publications and source records attributed to Arindam Banerjee.

13 recordsLinked to original sources

A short water-soluble self-assembling peptide forms amyloid-like fibrils.

A water-soluble tripeptide Val-Ile-Ala (VIA) , bearing sequence identity with the C-terminal portion of the Alzheimer Abeta-peptide (Abeta(40-42)), self-assembles, in crystalline form, to produce an intermolecularly hydrogen bonded supramolecular beta-sheet structure which self-associates to form straight, unbranched nanofibrils exhibiting amyloid-like behavior; in contrast, the synthetic tripeptide Ala-Val-Ile (AVI) self-assembles to produce a beta-sheet structure that forms branched nanofibrils which do not show any characteristic features of amyloid-like fibrils.

Journal Article↗

Formation of triple helical nanofibers using self-assembling chiral benzene-1,3,5-tricarboxamides and reversal of the nanostructure's handedness using mirror image building blocks.

Intertwining triple helical nanofibers with an overall handedness have been formed from self-assembling chiral benzene-1,3,5-tricarboxamides , and , whereas the achiral benzene-1,3,5-tricarboxamide upon self-association gives rise to straight nanofibers without any twist and transmission electron microscopy images of chiral compounds clearly demonstrate that the handedness of the triple helical nanofibers can be reversed by using the enantiomeric benzene-1,3,5-tricarboxamide building blocks.

Amides↗

Dendron-like growth of silver nanoparticles using a water-soluble oligopeptide.

A dendron-like nanostructure of silver was grown in solution using a water-soluble tetrapeptide Tyr-Aib-Tyr-Val (Aib, alpha-amino isobutyric acid), silver nitrate, and methanol. These structures are composed of silver nanoparticles having a bimodal size distribution with the median diameters around 2.0 and 19.5 nm, respectively. The dendron-like growth is ascribed to the effect of the local electric field generated by the dipoles associated with the peptide molecules. The optical absorption spectra have been analyzed by Mie scattering theory, which shows that there is a metal-nonmetal transition in silver particles having diameters less than approximately 2.0 nm.

Dendrimers↗

A mechanistic and kinetic study of the formation of metal nanoparticles by using synthetic tyrosine-based oligopeptides.

Synthetic oligopeptides containing redox-active tyrosine residues have been employed to prepare gold and silver nanoparticles. In this reduction process an electron from the tyrosinate ion of the peptide is transferred to the metal ion at basic pH through the formation of a tyrosyl radical, which is eventually converted to its dityrosine form during the reaction. This reaction mechanism was confirmed from UV-visible, fluorescence, and EPR spectroscopy and was found to be pH-dependent. Transmission electron microscopy measurement shows that the average size and the monodispersity of gold nanoparticles increase as the number of tyrosine residues in the peptide increases. The kinetic study, based on spectrophotometric measurements of the surface plasmon resonance optical property, shows that the rate of formation of gold nanoparticles was much faster at higher pH than at lower pH and was also dependent on the number of tyrosine residues present in the peptide. The dityrosine form of the peptide was found to retain reducing properties like those of tyrosine in basic medium.

Gold↗

Experimental verification of near-wall hindered diffusion for the Brownian motion of nanoparticles using evanescent wave microscopy.

A total internal reflection fluorescence microscopy technique coupled with three-dimensional tracking of nanoparticles is used to experimentally verify the theory on near-wall hindered Brownian motion [Goldman et al., Chem. Eng. Sci. 22, 637 (1967); Brenner, Chem. Eng. Sci. 16, 242 (1967)] very close to the solid surface (within approximately 1 microm). The measured mean square displacements (MSDs) in the lateral x-y directions show good agreement with the theory for all tested nanoparticles of radii 50, 100, 250, and 500 nm. However, the measured MSDs in the z direction deviate substantially from the theory particularly for the case of smaller particles of 50 and 100 nm radius. Since the theory considers only the hydrodynamic interaction of moving particles with a stationary solid wall, additionally possible interaction forces like gravitational forces, van der Waals forces, and electro-osmotic forces have been examined to delineate the physical reasons for the discrepancy.

Journal Article↗

The role of the disulfide bond in amyloid-like fibrillogenesis in a model peptide system.

Three terminally protected short peptides Bis[Boc-D-Leu1-Cys2-OMe] 1, Bis[Boc-Leu1-Cys2-OMe] and Bis[Boc-Val1-Cys2-OMe] 3 exhibit amyloid-like fibrillar morphology. Single crystal X-ray diffraction analysis of peptide 1 clearly demonstrates that it adopts an overall extended backbone molecular conformation that self-assembles to form an intermolecular hydrogen-bonded antiparallel supramolecular beta-sheet structure in crystals. Scanning electron microscopic (SEM) images, transmission electron microscopic (TEM) images and Congo red binding studies vividly demonstrate the amyloid-like fibril formation of peptides 1, 2 and 3. However, after reduction of the disulfide bridge of peptides 1, 2 and 3, three newly generated peptides Boc-D-Leu1-Cys2-OMe 4, Boc-Leu1-Cys2-OMe 5 and Boc-Val1-Cys2-OMe 6 are formed and all of them failed to form any kind of fibril under the same conditions, indicating the important role of the disulfide bond in amyloid-like fibrillogenesis in a peptide model system.

Amyloid↗

X-ray crystallographic signature of supramolecular triple helix formation from a water soluble synthetic tetrapeptide.

Single crystal X-ray diffraction studies on the water soluble, synthetic tetrapeptide Tyr(1)-Aib(2)-Tyr(3)-Val(4) with a non-coded amino acid residue (Aib: [small alpha]-amino isobutyric acid) reveal that the peptide adopts an "S"-shaped molecular structure which self-assembles to form a supramolecular triple helix using various non-covalent interactions including water mediated hydrogen bonds in the solid state.

Crystallography, X-Ray↗

Peptide-assisted synthesis of gold nanoparticles and their self-assembly.

A novel gold nanoparticle-tripeptide (GNP-tripeptide) conjugate was prepared by peptide in-situ redox technique at ambient temperatureusing a newly designed tripeptide. This new tripeptide was nso designed that it has a C-terminus tyrosine residue, which reduced Au+3 to Au, and the terminally located free amino group was bound to the gold nanoparticle (GNP) surface resulting in highly stable Au colloids. The average diameter of the tripeptide-stabilized GNP is 8.7 +/- 2.3 nm. Tripeptide bound gold nanoparticles formed three-dimensional assemblies in the presence of an excess of similar or disimilar tripeptides. The aggregation of GNPs results in a red shift in the surface plasmon resonance from lambda max = 527 to 556 nm. The effect of the solvent, concentration, and nature of the tripeptides on the assembly process were investigated by TEM and UV-visible spectroscopy.

Colloids↗

A new motif in the formation of peptide nanotubes: the crystallographic signature.

Terminally protected acyclic tripeptides Boc-Tyr(1)-Val(2)-Tyr(3)-OMe 1 and Boc-Tyr(1)-Ile(2)-Tyr(3)-OMe 2 self-assemble into nanotubes in crystals through various noncovalent interactions with an average internal diameter of 5 A (0.5 nm), and the tubular ensemble is developed through the hydrogen-bonded side chains of tyrosine residues. The inside of the hollow nanotubular structures is hydrophilic; however, no solvent molecules have been crystallographically detected. [structure: see text]

Crystallization↗

Frequency-sensitive competitive learning for scalable balanced clustering on high-dimensional hyperspheres.

Competitive learning mechanisms for clustering, in general, suffer from poor performance for very high-dimensional (>1000) data because of "curse of dimensionality" effects. In applications such as document clustering, it is customary to normalize the high-dimensional input vectors to unit length, and it is sometimes also desirable to obtain balanced clusters, i.e., clusters of comparable sizes. The spherical kmeans (spkmeans) algorithm, which normalizes the cluster centers as well as the inputs, has been successfully used to cluster normalized text documents in 2000+ dimensional space. Unfortunately, like regular kmeans and its soft expectation-maximization-based version, spkmeans tends to generate extremely imbalanced clusters in high-dimensional spaces when the desired number of clusters is large (tens or more). This paper first shows that the spkmeans algorithm can be derived from a certain maximum likelihood formulation using a mixture of von Mises-Fisher distributions as the generative model, and in fact, it can be considered as a batch-mode version of (normalized) competitive learning. The proposed generative model is then adapted in a principled way to yield three frequency-sensitive competitive learning variants that are applicable to static data and produced high-quality and well-balanced clusters for high-dimensional data. Like kmeans, each iteration is linear in the number of data points and in the number of clusters for all the three algorithms. A frequency-sensitive algorithm to cluster streaming data is also proposed. Experimental results on clustering of high-dimensional text data sets are provided to show the effectiveness and applicability of the proposed techniques. Index Terms-Balanced clustering, expectation maximization (EM), frequency-sensitive competitive learning (FSCL), high-dimensional clustering, kmeans, normalized data, scalable clustering, streaming data, text clustering.

Artificial Intelligence↗

First crystallographic signature of an acyclic peptide nanorod: molecular mechanism of nanorod formation by a self-assembled tetrapeptide.

A terminally protected acyclic tetrapeptide Boc-Aib-Val-Aib-beta-Ala-OMe 1 (Aib: alpha-aminoisobutyric acid, beta-Ala: beta-Alanine) self-assembles into a continuous hydrogen-bonded supramolecular helix with an average diameter of 10 A (1 nm) starting from a double bend molecular conformation in crystals and further self-assembly of this supramolecular architecture leads to the formation of polydisperse nanorods of diameters 10-40 nm.

Crystallography, X-Ray↗

Peptide design using omega-amino acids: unusual turn structures nucleated by an N-terminal single gamma-aminobutyric acid residue in short model peptides.

Incorporation of omega-amino acids into peptide sequences plays an important role in designing peptides with modified backbone conformation and enhanced stability against proteolysis. The present study establishes the presence of unusual turns involving 12-membered hydrogen bonded rings in terminally blocked tri- and tetrapeptides. X-ray diffraction analysis of single crystals and NMR studies have been used to probe the three-dimensional structures of two terminally protected short peptides, Boc-gamma-Abu(1)-Aib(2)-Ala(3)-OMe 1 and Boc-gamma-Abu(1)-Aib(2)-Ala(3)-Aib(4)-OMe 2 (gamma-Abu = gamma-aminobutyric acid), in which conformationally flexible omega-amino acids (gamma-Abu) and conformationally restricted alpha-aminoisobutyric acid (Aib) residues are positioned contiguously. The crystal structures of both peptides 1 and 2 exhibit unusual turns composed of 12-membered hydrogen bonded rings involving C [double bond] O from the Boc-group and Ala(3) NH. A type I' beta-turn was observed in the structure of peptide 2 adjacent to the unusual turn with a hydrogen bond between gamma-Abu(1) C [double bond] O and Aib(4) NH. The crystals of peptide 1 are in the space group P2(1), a = 9.3020(10) A, b = 23.785(2) A, c = 10.022(3) A, beta = 101.35 degrees(4), Z = 4, R = 5.7%, and R(w) = 14.5%. Similarly, the crystals of peptide 2 are in the space group C2, a = 19.0772(6) A, b = 8.7883(2) A, c = 16.7758(3) A, beta = 110.7910 degrees(10), Z = 4, R = 6.71%, and R(w) = 15.11%. The unusual turn in both peptides 1 and 2 are retained in solution as is evident from NMR studies in CDCl(3). The role of the adjacently located Aib residue to nucleate the 12-membered hydrogen bonded ring is also addressed.

Amino Acids↗