Biomedical subjects

Ayaluru Murali

Publications and source records attributed to Ayaluru Murali.

5 recordsLinked to original sources

PubMed2007

Core-controlled polymorphism in virus-like particles.

This study concerns the self-assembly of virus-like particles (VLPs) composed of an icosahedral virus protein coat encapsulating a functionalized spherical nanoparticle core. The recent development of efficient methods for VLP self-assembly has opened the way to structural studies. Using electron microscopy with image reconstruction, the structures of several VLPs obtained from brome mosaic virus capsid proteins and gold nanoparticles were elucidated. Varying the gold core diameter provides control over the capsid structure. The number of subunits required for a complete capsid increases with the core diameter. The packaging efficiency is a function of the number of capsid protein subunits per gold nanoparticle. VLPs of varying diameters were found to resemble to three classes of viral particles found in cells (T=1, 2, and 3). As a consequence of their regularity, VLPs form three-dimensional crystals under the same conditions as the wild-type virus. The crystals represent a form of metallodielectric material that exhibits optical properties influenced by multipolar plasmonic coupling.

Crystallization↗

PubMed2006

De novo design and spectroscopic characterization of a dinucleating copper-binding pentadecapeptide.

A spectroscopic study of aqueous solutions of Ac-WGHGHGHGPGHGHGH-NH(2) (HGP) indicates that copper(II) binds to the peptide to form a 2:1 Cu(2+)/HGP complex with four nitrogen atoms in the copper coordination environment. Electron paramagnetic resonance (EPR) and UV-visible data suggest copper binding through the peptide backbone and imidazole nitrogen donors. Circular dichroism data show that HGP is unbound below pH 5.5 and is copper-saturated at pH 9 and above. The apo form of the peptide is unstructured in solution and is organized into a turn conformation in the presence of 2 mol equiv of Cu(2+) at basic pH. EPR measurements for 2:1 Cu(2+)/HGP solutions in the g = 2 region and within the pH range 7-11 exhibit axial spectra. A molecular-mechanics-minimized model of the Cu(2+)/HGP complex gave a Cu...Cu separation of 8 A.

Amino Acid Sequence↗

PubMed2006

Quantum dot encapsulation in viral capsids.

Incorporation of CdSe/ZnS semiconductor quantum dots (QDs) into viral particles provides a new paradigm for the design of intracellular microscopic probes and vectors. Several strategies for the incorporation of QDs into viral capsids were explored; those functionalized with poly(ethylene glycol) (PEG) can be self-assembled into viral particles with minimal release of photoreaction products and enhanced stability against prolonged irradiation.

Capsid↗

PubMed2005

Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme.

An extended hammerhead ribozyme derived from Schistosoma mansoni, including conserved loops in stems I and II, has been examined to directly monitor the relationship between docking of loops and its activity using site-directed spin labeling (SDSL) and EPR spectroscopy. Dynamics with EPR spectroscopy and fast-quench kinetics measurements have shown that the docking of stems I and II occurs at low Mg2+ concentrations ([Mg2+]1/2,dock = 0.7 mM, 0.1 M NaCl), but a much weaker Mg2+ interaction ([Mg2+]1/2,cat approximately 90 mM) increases activity to very high maximum rates of approximately 1 s-1 at 0.1 M Na+ and pH 7.0.

Animals↗

PubMed2004

A distance ruler for RNA using EPR and site-directed spin labeling.

As a basic model study for measuring distances in RNA molecules using continuous wave (CW) EPR spectroscopy, site-directed spin-labeled 10-mer RNA duplexes and HIV-1 TAR RNA motifs with various interspin distances were examined. The spin labels were attached to the 2'-NH2 positions of appropriately placed uridines in the duplexes, and interspin distances were measured from both molecular dynamics simulations (MD) and Fourier deconvolution methods (FD). The 10-mer duplexes have interspin distances ranging from 10 A to 30 A based on MD; however, dipolar line broadening of the CW EPR spectrum is only observed for the RNAs for predicted interspin distances of 10-21 A and not for distances over 25 A. The conformational changes in TAR (transactivating responsive region) RNA in the presence and in the absence of different divalent metal ions were monitored by measuring distances between two nucleotides in the bulge region. The predicted interspin distances obtained from the FD method and those from MD calculations match well for both the model RNA duplexes and the structural changes predicted for TAR RNA. These results demonstrate that distance measurement using EPR spectroscopy is a potentially powerful method to help predict the structures of RNA molecules.

Base Sequence↗