Biomedical subjects
Publications and source records attributed to V Ramakrishnan.
Here we report the crystal structures of I.C and I.A wobble base pairs in the context of the ribosomal decoding center, clearly showing that the I.A base pair is of an I(anti).A(anti) conformation, as predicted by Crick. Additionally, the structures enable the observation of changes in the anticodon to allow purine-purine base pairing, the 'widest' base pair geometry allowed in the wobble position.
A possible new technique of endoscopic pharyngoplasty is described and has been developed in cadavers. The trans-nasal route is used for endoscopic visualisation of the velopharyngeal sphincter. Hynes pharyngoplasty is performed using both trans-oral and trans-nasal routes. This approach allows better visualisation and performance of the Hynes pharyngoplasty at the desired level, "high" in the nasopharynx, without splitting the soft palate.
The infrared and laser Raman spectra of L-methionine L-methioninium perchlorate monohydrate were recorded at room temperature and the vibrational assignments of the observed wave numbers were made. The presence of both the carbonyl and the ionized carboxylic groups has been identified in the title complex. The L-methionine and L-methioninium the cation have different conformations. This together with the different environment has seen by the two -CH(2)- groups in each skeleton cause several of the group wave numbers to occur as doublets or as broad bands. The perchlorate anion was found to be in the T(d) symmetry in the methionine environment. The coordination to other ligands in the crystal through hydrogen bonding does not affect this symmetry. The extensive intermolecular hydrogen bonding in the crystal was identified by the shifting of bands due to the stretching and bending modes of the various functional groups. Fermi resonance has also been observed.
The infrared and Raman spectra of bis(L-threoninium) sulphate monohydrate crystal have been recorded and analysed at room temperature. The proposed assignment of normal modes is based on group theoretical analysis. There is extensive intermolecular hydrogen bonding in the crystal and this is responsible for the changes in the position and intensity of several bands. The anion fundamentals continue to be degenerated which indicates that its symmetry is unaffected in the molecule.
Nano structured noble metals have very important applications in diverse fields as photovoltaics, catalysis, electronic and magnetic devices, etc. Here, we report the application of dual beam thermal lens technique for the determination of the effect of silver sol on the absolute fluorescence quantum yield (FQY) of the laser dye rhodamine 6G. A 532 nm radiation from a diode pumped solid state laser was used as the excitation source. It has been observed that the presence of silver sol decreases the fluorescence quantum efficiency. This is expected to have a very important consequence in enhancing Raman scattering which is an important spectrochemical tool that provides information on molecular structures. We have also observed that the presence of silver sol can enhance the thermal lens signal which makes the detection of the signal easier at any concentration.
The methods involved in determining the 850 kDa structure of the 30S ribosomal subunit from Thermus thermophilus were in many ways identical to those that are generally used in standard protein crystallography. This paper reviews and analyses the methods that can be used in phasing such large structures and shows that the anomalous signal collected from heavy-atom compounds bound to the RNA is both necessary and sufficient for ab initio structure determination at high resolution. In addition, measures to counter problems with non-isomorphism and radiation decay are described.
Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation then switches from the defective message to a short open reading frame on tmRNA that tags the defective nascent peptide chain for degradation. However, the mechanism by which tmRNA can enter and move through the ribosome is unknown. We present a cryo-electron microscopy study at approximately 13 to 15 angstroms of the entry of tmRNA into the ribosome. The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA.
Optical absorption, fluorescence emission and surface enhanced Raman spectra of 1,5-dipiperidino anthraquinone (1,5-DPAQ) have been examined to elucidate the nature of molecule in different environments. Fluorescence emission and optical absorption measurements show that the polarity of the solvent plays a vital role through intermolecular hydrogen bonding and reorientational motion of solvent molecule around excited state fluorophore. Anisotropy measurement gives the angle between absorption and emission transition dipoles. The vibrational features observed in surface enhanced Raman spectroscopy (SERS) suggest that the molecules are chemisorbed. The adsorption of the molecule is through pi electrons in the anthraquinone ring and the axial lone pair of electrons of nitrogen. The orientation of the molecule is found to be 'flat-on'.
During the decoding process, tRNA selection by the ribosome is far more accurate than expected from codon-anticodon pairing. Antibiotics such as streptomycin and paromomycin have long been known to increase the error rate of translation, and many mutations that increase or lower accuracy have been characterized. Recent crystal structures show that the specific recognition of base-pairing geometry leads to a closure of the domains of the small subunit around cognate tRNA. This domain closure is likely to trigger subsequent steps in tRNA selection. Many antibiotics and mutations act by making the domain closure more or less favourable. In conjunction with recent cryoelectron microscopy structures of the ribosome, a comprehensive structural understanding of the decoding process is beginning to emerge.
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The aim of this work was to quantify the ability to predict intrafraction diaphragm motion from an external respiration signal during a course of radiotherapy. The data obtained included diaphragm motion traces from 63 fluoroscopic lung procedures for 5 patients, acquired simultaneously with respiratory motion signals (an infrared camera-based system was used to track abdominal wall motion). During these sessions, the patients were asked to breathe either (i) without instruction, (ii) with audio prompting, or (iii) using visual feedback. A statistical general linear model was formulated to describe the relationship between the respiration signal and diaphragm motion over all sessions and for all breathing training types. The model parameters derived from the first session for each patient were then used to predict the diaphragm motion for subsequent sessions based on the respiration signal. Quantification of the difference between the predicted and actual motion during each session determined our ability to predict diaphragm motion during a course of radiotherapy. This measure of diaphragm motion was also used to estimate clinical target volume (CTV) to planning target volume (PTV) margins for conventional, gated, and proposed four-dimensional (4D) radiotherapy. Results from statistical analysis indicated a strong linear relationship between the respiration signal and diaphragm motion (p<0.001) over all sessions, irrespective of session number (p=0.98) and breathing training type (p=0.19). Using model parameters obtained from the first session, diaphragm motion was predicted in subsequent sessions to within 0.1 cm (1 sigma) for gated and 4D radiotherapy. Assuming a 0.4 cm setup error, superior-inferior CTV-PTV margins of 1.1 cm for conventional radiotherapy could be reduced to 0.8 cm for gated and 4D radiotherapy. The diaphragm motion is strongly correlated with the respiration signal obtained from the abdominal wall. This correlation can be used to predict diaphragm motion, based on the respiration signal, to within 0.1 cm (1 sigma) over a course of radiotherapy.
A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution. In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. As a result, the transition to a closed form of the 30S induced by cognate tRNA is unfavorable for near-cognate tRNA unless paromomycin induces part of the rearrangement. We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity.
We present a detailed analysis of the protein structures in the 30 S ribosomal subunit from Thermus thermophilus, and their interactions with 16 S RNA based on a crystal structure at 3.05 A resolution. With 20 different polypeptide chains, the 30 S subunit adds significantly to our data base of RNA structure and protein-RNA interactions. In addition to globular domains, many of the proteins have long, extended regions, either in the termini or in internal loops, which make extensive contact to the RNA component and are involved in stabilizing RNA tertiary structure. Many ribosomal proteins share similar alpha+beta sandwich folds, but we show that the topology of this domain varies considerably, as do the ways in which the proteins interact with RNA. Analysis of the protein-RNA interactions in the context of ribosomal assembly shows that the primary binders are globular proteins that bind at RNA multihelix junctions, whereas proteins with long extensions assemble later. We attempt to correlate the structure with a large body of biochemical and genetic data on the 30 S subunit.
The publication of crystal structures of the 50S and 30S ribosomal subunits and the intact 70S ribosome is revolutionizing our understanding of protein synthesis. This review is an attempt to correlate the structures with biochemical and genetic data to identify the gaps and limits in our current knowledge of the mechanisms involved in translation.
Electron paramagnetic resonance (EPR) studies have been carried out on Cu(II) doped Cd(C5H5NO)6(BF4)2 in single crystal and powder forms at 300 K. Angular variation of hyperfine structure lines shows the presence of two magnetic sites, indicating possible twinning in the Cd lattice. From the mean values of two sites, the angular variation plot is fitted to an orthorhombic spin Hamiltonian. The observed orthorhombic g values and the very low A11 value ([A11] = 107.8 x 10(-4) cm(-1)) are unusual for a hexakis coordinated system. This unique behavior is explicable in terms of the static Jahn-Teller (JT) effect.
Infrared and laser Raman spectral investigations of [Ni(II)(dppe)Cl2] and [Co(III)(dppe)2Cl2]PF6 have been made to determine the conformation and nature of bonding in Ni(II) and Co(III) dppe complexes. The stereochemistry of the two forms of these complexes has been confirmed. The role of steric interferences in cis-Planar [Ni(II)(dppe)Cl2] complex is interpreted in terms of reduction in symmetry upon coordination. The strong trans influence of the chelating dppe ligand is observed in the [Co(III)(dppe)2Cl2]PF6 complex. Both complexes exhibit the effect of crystalline field on molecular vibrations. The Fermi resonance overtone is also observed in these complexes.
Both crystals under study have two phenylalanine groups in the cationic part of the complex. In the L-phenylalanine L-phenylalaninium perchlorate crystal, two phenylalanine groups share one proton and become monoprotonated. In the bis(DL-phenylalaninium) sulphate monohydrate crystal, on the other hand, both the phenylalanine groups are protonated. This leads to several differences in the infrared and Raman spectra of these two crystals. The presence of both the carbonyl and the ionized carboxylic groups has been identified in the perchlorate crystal, while the sulphate crystal has only the carbonyl group. Extensive hydrogen bonding further leads to the shifting of bands due to several stretching and bending modes. It also reduces the Td symmetry of the anions to C2v symmetry causing the degeneracies of several modes to be removed.
Surface enhanced Raman spectrum of 1,4-dimethylamino anthraquinone (1,4-DMAAQ) adsorbed on silver particles has been analyzed to understand the interaction between the molecule and silver surface. By studying the band intensities, the orientation of the molecule is determined. The high intensity and frequency downshifted peak due to carbonyl stretching vibration plays a major role, which shows that the molecules are chemisorbed through coordinating sites. The new peaks observed due to C-N and N-H stretching vibrations also provide the evidence for adsorption through co-ordinating sites. Optical absorption and laser induced fluorescence spectra of this molecule have also been studied in different solvents to understand the effect of environment. Polarization and anisotropy measurements provide the change in orientation induced by solvent molecules between absorption and emission transition dipoles.