1
|
Ingram JA, Moog RS, Ito N, Biswas R, Maroncelli M. Solute Rotation and Solvation Dynamics in a Room-Temperature Ionic Liquid. J Phys Chem B 2003. [DOI: 10.1021/jp034231e] [Citation(s) in RCA: 278] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
|
22 |
278 |
2
|
Chellaiah MA, Kizer N, Biswas R, Alvarez U, Strauss-Schoenberger J, Rifas L, Rittling SR, Denhardt DT, Hruska KA. Osteopontin deficiency produces osteoclast dysfunction due to reduced CD44 surface expression. Mol Biol Cell 2003; 14:173-89. [PMID: 12529435 PMCID: PMC140236 DOI: 10.1091/mbc.e02-06-0354] [Citation(s) in RCA: 165] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2002] [Revised: 09/13/2002] [Accepted: 09/20/2002] [Indexed: 01/14/2023] Open
Abstract
Osteopontin (OPN) was expressed in murine wild-type osteoclasts, localized to the basolateral, clear zone, and ruffled border membranes, and deposited in the resorption pits during bone resorption. The lack of OPN secretion into the resorption bay of avian osteoclasts may be a component of their functional resorption deficiency in vitro. Osteoclasts deficient in OPN were hypomotile and exhibited decreased capacity for bone resorption in vitro. OPN stimulated CD44 expression on the osteoclast surface, and CD44 was shown to be required for osteoclast motility and bone resorption. Exogenous addition of OPN to OPN-/- osteoclasts increased the surface expression of CD44, and it rescued osteoclast motility due to activation of the alpha(v)beta(3) integrin. Exogenous OPN only partially restored bone resorption because addition of OPN failed to produce OPN secretion into resorption bays as seen in wild-type osteoclasts. As expected with these in vitro findings of osteoclast dysfunction, a bone phenotype, heretofore unappreciated, was characterized in OPN-deficient mice. Delayed bone resorption in metaphyseal trabeculae and diminished eroded perimeters despite an increase in osteoclast number were observed in histomorphometric measurements of tibiae isolated from OPN-deficient mice. The histomorphometric findings correlated with an increase in bone rigidity and moment of inertia revealed by load-to-failure testing of femurs. These findings demonstrate the role of OPN in osteoclast function and the requirement for OPN as an osteoclast autocrine factor during bone remodeling.
Collapse
|
research-article |
22 |
165 |
3
|
Fleming JG, Lin SY, El-Kady I, Biswas R, Ho KM. All-metallic three-dimensional photonic crystals with a large infrared bandgap. Nature 2002; 417:52-5. [PMID: 11986662 DOI: 10.1038/417052a] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Three-dimensional (3D) metallic crystals are promising photonic bandgap structures: they can possess a large bandgap, new electromagnetic phenomena can be explored, and high-temperature (above 1,000 degrees C) applications may be possible. However, investigation of their photonic bandgap properties is challenging, especially in the infrared and visible spectrum, as metals are dispersive and absorbing in these regions. Studies of metallic photonic crystals have therefore mainly concentrated on microwave and millimetre wavelengths. Difficulties in fabricating 3D metallic crystals present another challenge, although emerging techniques such as self-assembly may help to resolve these problems. Here we report measurements and simulations of a 3D tungsten crystal that has a large photonic bandgap at infrared wavelengths (from about 8 to 20 microm). A very strong attenuation exists in the bandgap, approximately 30 dB per unit cell at 12 microm. These structures also possess other interesting optical properties; a sharp absorption peak is present at the photonic band edge, and a surprisingly large transmission is observed in the allowed band, below 6 microm. We propose that these 3D metallic photonic crystals can be used to integrate various photonic transport phenomena, allowing applications in thermophotovoltaics and blackbody emission.
Collapse
|
|
23 |
140 |
4
|
Biswas R, Hamann DR. Interatomic potentials for silicon structural energies. PHYSICAL REVIEW LETTERS 1985; 55:2001-2004. [PMID: 10031984 DOI: 10.1103/physrevlett.55.2001] [Citation(s) in RCA: 125] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
|
|
40 |
125 |
5
|
Özbay E, Abeyta A, Tuttle G, Tringides M, Biswas R, Chan CT, Soukoulis CM, Ho KM. Measurement of a three-dimensional photonic band gap in a crystal structure made of dielectric rods. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 50:1945-1948. [PMID: 9976387 DOI: 10.1103/physrevb.50.1945] [Citation(s) in RCA: 116] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
|
31 |
116 |
6
|
Biswas R, Ghosh P, Banerjee N, Das JK, Sau T, Banerjee A, Roy S, Ganguly S, Chatterjee M, Mukherjee A, Giri AK. Analysis of T-cell proliferation and cytokine secretion in the individuals exposed to arsenic. Hum Exp Toxicol 2008; 27:381-6. [DOI: 10.1177/0960327108094607] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Over six million people in nine districts of West Bengal, India are exposed to very high levels of arsenic primarily through their drinking water. More than 300,000 people showed arsenic-induced skin lesions in these districts. This is regarded as the greatest arsenic calamity in the world. Chronic arsenicosis causes varied dermatological signs ranging from pigmentation changes, hyperkeratosis to non-melanocytic cancer of skin, and also malignancies in different internal organs. Higher incidences of opportunistic infections are found in the arsenic-exposed individuals, indicating that their immune systems may be impaired somehow. We have thus investigated the effect of arsenic on T-cell proliferation and cytokine secretion in 20 individuals with arsenic-induced skin lesions and compared the results with 18 arsenic-unexposed individuals. A marked dose-dependent suppression of Concanavalin A (Con A) induced T-cell proliferation was observed in the arsenic-exposed individuals compared with the unexposed ( P < 0.001) individuals. This correlated with a significant decrease in the levels of secreted cytokines by the T cells (TNF-α, IFN-γ, IL2, IL10, IL5, and IL4) in the exposed individuals ( P < 0.001). Thus it can be inferred that arsenic exposure can cause immunosuppression in humans.
Collapse
|
|
17 |
107 |
7
|
Song W, Biswas R, Maroncelli M. Intermolecular Interactions and Local Density Augmentation in Supercritical Solvation: A Survey of Simulation and Experimental Results. J Phys Chem A 2000. [DOI: 10.1021/jp000888d] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
|
25 |
106 |
8
|
Biswas R, Hamann DR. New classical models for silicon structural energies. PHYSICAL REVIEW. B, CONDENSED MATTER 1987; 36:6434-6445. [PMID: 9942353 DOI: 10.1103/physrevb.36.6434] [Citation(s) in RCA: 96] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
|
|
38 |
96 |
9
|
Biswas R, Hamann DR. Simulated annealing of silicon atom clusters in Langevin molecular dynamics. PHYSICAL REVIEW. B, CONDENSED MATTER 1986; 34:895-901. [PMID: 9939701 DOI: 10.1103/physrevb.34.895] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
|
|
39 |
86 |
10
|
Biswas R, Basu M, Sen-Majumdar A, Das M. Intrapeptide autophosphorylation of the epidermal growth factor receptor: regulation of kinase catalytic function by receptor dimerization. Biochemistry 1985; 24:3795-802. [PMID: 2994718 DOI: 10.1021/bi00335a056] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The epidermal growth factor (EGF) receptor is a transmembrane polypeptide of 170 000 daltons (Da) with a cytoplasmically facing protein kinase domain. The regulation of the tyrosine kinase activity of the EGF receptor by added EGF and by receptor association state was studied in an in vitro system. The rate of autophosphorylation of the solubilized and purified EGF receptor was found to be independent of receptor concentration. To determine whether the zero-order kinetics observed point to intrapeptide phosphorylation, we measured the sedimentation characteristics of the undenatured solubilized receptor. The receptor was found to exist in two association-dissociation states-a monomeric 7.7S form and a dimeric 12S form. The 7.7S form is an active tyrosine kinase; it has high basal activity, and the activity is not further stimulated by EGF; it appears to be an EGF-independent form of the receptor kinase. The 12S form is devoid of catalytic activity, but in the presence of EGF it dissociates into the active monomeric form. Freshly purified receptor preparations contain mainly the monomeric receptor, have high basal kinase activity, and show low EGF stimulatability (less than 1.3-fold). Aging of the receptor results in progressive dimerization and decay of EGF-independent kinase activity (and increase in EGF stimulatability). All of these processes are reversed in the presence of EGF or dithiothreitol.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
|
|
40 |
84 |
11
|
Lewis JE, Biswas R, Robinson AG, Maroncelli M. Local Density Augmentation in Supercritical Solvents: Electronic Shifts of Anthracene Derivatives. J Phys Chem B 2001. [DOI: 10.1021/jp0043672] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
|
24 |
80 |
12
|
Abstract
The epidermal growth factor (EGF) receptor and other growth factor receptors have been shown to possess tyrosine-specific protein kinase activity. Before the demonstration of kinase activity in growth factor receptors, tyrosine kinases of molecular weight (MW) 60,000 (60K) were found to be encoded by the src oncogene and other oncogenes related to src. Our earlier work on intracellular processing of the EGF receptor, a 170,000-MW polypeptide, provided evidence for proteolytic separation of well defined structural domains, and suggested to us the possibility of separating functional domains by limited proteolysis. The isolation of such kinase domains should facilitate comparison of the receptor/kinase with other well characterized kinases including those of oncogene origin. We report here the identification of a catalytically functional 42K kinase derived proteolytically from the isolated human EGF receptor. This fragment, comparable in size to pp60src, carries the kinase ATP-binding site, and functions catalytically even after detachment from the EGF-binding site and the major autophosphorylation region.
Collapse
|
|
41 |
79 |
13
|
Biswas R, Roy S, Bagchi B. Anomalous ion diffusion in dense dipolar liquids. PHYSICAL REVIEW LETTERS 1995; 75:1098-1101. [PMID: 10060205 DOI: 10.1103/physrevlett.75.1098] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
|
|
30 |
75 |
14
|
Dahl K, Biswas R, Ito N, Maroncelli M. Solvent Dependence of the Spectra and Kinetics of Excited-State Charge Transfer in Three (Alkylamino)benzonitriles. J Phys Chem B 2005; 109:1563-85. [PMID: 16851128 DOI: 10.1021/jp046605p] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Steady-state absorption and emission spectra and emission decay kinetics are reported for 4-aminobenzonitrile (ABN), 4-(1-azetidinyl)benzonitrile (P4C), 4-(1-pyrrolidinyl)benzonitrile (P5C), and 4-(1-piperidinyl)benzonitrile (P6C) in 24 room temperature solvents. In solvents of modest to high polarity, P4C, P5C, and P6C exhibit dual fluorescence and emission decays characteristic of the transformation from an initially prepared (LE) state to a more polar charge transfer (CT) state, whereas ABN does not undergo this reaction. The frequencies of the steady-state absorption and emission spectra of all of these solutes can be rationalized using a dielectric continuum description of the solvent and considering only the minima on the reactive surfaces, which are assumed to involve both an intramolecular (twisting) and a solvation coordinate. Characteristics of the gas-phase solutes deduced from this analysis are in good agreement with electronic structure calculations and indicate that differences in their spectra mainly reflect differences in the relative energies of the gas-phase LE and CT states. The relative yields of LE and CT emission are not described as satisfactorily by this model, and reasons for this failure are discussed. The kinetics of the LE --> CT reaction vary considerably with solute and solvent. In many solvents, the emission decays of P4C are reasonably described by a simple two-state kinetic scheme with time-independent rate constants. In P5C and P6C multiexponential decays are observed that reflect time-dependent shifts of the component spectra as well as time-dependent reaction rates. A simplified analysis of these complex dynamics provides estimates for both the free energy change Delta(r)G and (average) LE --> CT rate constant k(f) for a wide range of solute and solvent combinations. The driving force for reaction (-Delta(r)G) follows the order P6C > P5C > P4C and increases with increasing solvent polarity. The reaction rates are correlated to Delta(r)G and follow the opposite trend. The relationships observed between k(f) and Delta(r)G suggest that static solvent effects, i.e., barrier height changes, are the primary determinants of the solvent dependence in P4C. Correlations between barrier-corrected rates and solvation times suggest that dynamical solvent effects contribute substantially to the solvent dependence of the rates in P5C, and especially P6C.
Collapse
|
|
20 |
73 |
15
|
Biswas R, Lugo A, Akeroyd M, Schlee W, Gallus S, Hall D. Tinnitus prevalence in Europe: a multi-country cross-sectional population study. THE LANCET REGIONAL HEALTH. EUROPE 2022; 12:100250. [PMID: 34950918 PMCID: PMC8671623 DOI: 10.1016/j.lanepe.2021.100250] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
BACKGROUND Tinnitus prevalence studies report large variability across countries that might be due to inconsistent research methods. Our study aimed to report a single Pan-European estimate for tinnitus prevalence and investigate the effect of individual and country-level characteristics on prevalence. We explored the relationships of healthcare resource use and hearing difficulty with tinnitus symptoms. METHODS Between 2017-2018, a cross-sectional European Tinnitus Survey (ETS) was conducted in 12 European Union nations (Bulgaria, England, France, Germany, Greece, Ireland, Italy, Latvia, Poland, Portugal, Romania, and Spain), using a standardised set of tinnitus-related questions and response options in country-specific languages. We recruited 11,427 adults aged ≥18 years. FINDINGS Prevalence of any tinnitus was 14·7% (14·0% in men and 15·2% in women), ranging from 8·7% in Ireland to 28·3% in Bulgaria. Severe tinnitus was found in 1·2% participants (1·0% in men and 1·4% in women), ranging from 0·6% in Ireland to 4·2% in Romania. Tinnitus prevalence significantly increased with increasing age and worsening of hearing status. Healthcare resource use for tinnitus increased with increasing tinnitus symptom severity. INTERPRETATION This is the first multinational report of Pan-European tinnitus prevalence using standardised questions. The overall prevalence estimates refine previous findings, although widespread inter-country heterogeneity was noted. The results indicate that more than 1 in 7 adults in the EU have tinnitus. Extrapolating to the overall population, approximately 65 million adults in EU28 have tinnitus, 26 million have bothersome tinnitus and 4 million have severe tinnitus. FUNDING National Institute for Health Research, European Union's Horizon 2020, Medical Research Council, and GENDER-Net Co-Plus Fund.
Collapse
|
research-article |
3 |
70 |
16
|
Mosher J, Guy J, Kessler R, Astier P, Marriner J, Betoule M, Sako M, El-Hage P, Biswas R, Pain R, Kuhlmann S, Regnault N, Frieman JA, Schneider DP. COSMOLOGICAL PARAMETER UNCERTAINTIES FROM SALT-II TYPE IA SUPERNOVA LIGHT CURVE MODELS. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/0004-637x/793/1/16] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
|
11 |
60 |
17
|
Lee YH, Biswas R, Soukoulis CM, Wang CZ, Chan CT, Ho KM. Molecular-dynamics simulation of thermal conductivity in amorphous silicon. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 43:6573-6580. [PMID: 9998098 DOI: 10.1103/physrevb.43.6573] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
|
34 |
58 |
18
|
Biswas R, Grest GS, Soukoulis CM. Generation of amorphous-silicon structures with use of molecular-dynamics simulations. PHYSICAL REVIEW. B, CONDENSED MATTER 1987; 36:7437-7441. [PMID: 9942510 DOI: 10.1103/physrevb.36.7437] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
|
|
38 |
55 |
19
|
Biswas R, Grest GS, Soukoulis CM. Molecular-dynamics simulation of cluster and atom deposition on silicon (111). PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 38:8154-8162. [PMID: 9945567 DOI: 10.1103/physrevb.38.8154] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
|
|
37 |
50 |
20
|
Biswas R, Martin RM, Needs RJ, Nielsen OH. Stability and electronic properties of complex structures of silicon and carbon under pressure: Density-functional calculations. PHYSICAL REVIEW. B, CONDENSED MATTER 1987; 35:9559-9568. [PMID: 9941381 DOI: 10.1103/physrevb.35.9559] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
|
|
38 |
50 |
21
|
Shindo M, Di Bisceglie AM, Biswas R, Mihalik K, Feinstone SM. Hepatitis C virus replication during acute infection in the chimpanzee. J Infect Dis 1992; 166:424-7. [PMID: 1321863 DOI: 10.1093/infdis/166.2.424] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The events following experimental infection of 2 chimpanzees with the H strain of hepatitis C virus (HCV) were studied by quantitating the levels of HCV RNA in liver and serum. Serum and liver samples were tested every 1-3 weeks for up to 32 weeks. The genomic and antigenomic strands of HCV RNA were individually detected in liver and serum by strand-specific reverse transcription followed by polymerase chain reaction (PCR) using nested primers specific for the 5' noncoding region of the HCV genome and were quantitated by end-point dilution of the nucleic acid extract. Both genomic and antigenomic strands were detected in liver and serum within 1 week after inoculation and approximately 1 week before the development of elevated levels of alanine aminotransferase (ALT) activity. Changes in levels of antigenomic strand paralleled those of the genomic strand in both serum and liver. Titers of HCV RNA in serum and liver generally correlated with changes in ALT levels.
Collapse
|
|
33 |
48 |
22
|
Biswas R, Ledman DW, Fox RO, Altman S, Gopalan V. Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe. J Mol Biol 2000; 296:19-31. [PMID: 10656815 DOI: 10.1006/jmbi.1999.3443] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The protein subunit of Escherichia coli ribonuclease P (which has a cysteine residue at position 113) and its single cysteine-substituted mutant derivatives (S16C/C113S, K54C/C113S and K66C/C113S) have been modified using a sulfhydryl-specific iron complex of EDTA-2- aminoethyl 2-pyridyl disulfide (EPD-Fe). This reaction converts C5 protein, or its single cysteine-substituted mutant derivatives, into chemical nucleases which are capable of cleaving the cognate RNA ligand, M1 RNA, the catalytic RNA subunit of E. coli RNase P, in the presence of ascorbate and hydrogen peroxide. Cleavages in M1 RNA are expected to occur at positions proximal to the site of contact between the modified residue (in C5 protein) and the ribose units in M1 RNA. When EPD-Fe was used to modify residue Cys16 in C5 protein, hydroxyl radical-mediated cleavages occurred predominantly in the P3 helix of M1 RNA present in the reconstituted holoenzyme. C5 Cys54-EDTA-Fe produced cleavages on the 5' strand of the P4 pseudoknot of M1 RNA, while the cleavages promoted by C5 Cys66-EDTA-Fe were in the loop connecting helices P18 and P2 (J18/2) and the loop (J2/4) preceding the 3' strand of the P4 pseudoknot. However, hydroxyl radical-mediated cleavages in M1 RNA were not evident with Cys113-EDTA-Fe, perhaps indicative of Cys113 being distal from the RNA-protein interface in the RNase P holoenzyme. Our directed hydroxyl radical-mediated footprinting experiments indicate that conserved residues in the RNA and protein subunit of the RNase-P holoenzyme are adjacent to each other and provide structural information essential for understanding the assembly of RNase P.
Collapse
|
|
25 |
47 |
23
|
Biswas R, Wahl MC, Ban C, Sundaralingam M. Crystal structure of an alternating octamer r(GUAUGUA)dC with adjacent G x U wobble pairs. J Mol Biol 1997; 267:1149-56. [PMID: 9150403 DOI: 10.1006/jmbi.1997.0936] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The crystal structure of the RNA duplex, r(GUAUGUA)dC, with a 3'-terminal deoxy C residue, has been determined at 1.38 A resolution. The r(GUAUGU) hexameric consensus sequence is present at the exon-intron junction in pre-mRNAs of yeast and higher eukaryotic organisms. The crystal belongs to the rhombohedral space group R3. The hexagonal unit cell dimensions are a = b = 39.71 A, c = 68.15 A and gamma = 120 degrees with one duplex in the asymmetric unit. The structure was solved using the molecular replacement method. The final model contains 332 atoms of the duplex and 67 solvent molecules. The R-factor is 17.6% (Rfree of 23.1%) for 4035 reflections with F > or = 1.5sigma(F) in the resolution range 10.0 to 1.38 A. The duplex is of the A-type with a pseudodyad relating the two strands. The RNA helix is slightly distorted, in spite of the presence of two adjacent G x U wobble base-pairs located at the center of the helix. The twist angle between the wobble pairs, 38.1 degrees, is above the average value and those between the wobble base-pairs and the flanking Watson-Crick base-pairs, 26.7 degrees and 26.3 degrees, respectively, are lower than the average values. The twist between the junction base-pairs are about 24 degrees. The G x U wobble pairs are bridged by water molecules and solvated in the grooves. G x U base-pairs are as stable as the Watson-Crick A x U pairs and only slightly less stable than the G x C pairs accounting for their frequent occurrence in RNA.
Collapse
|
Comparative Study |
28 |
46 |
24
|
Kwon I, Biswas R, Wang CZ, Ho KM, Soukoulis CM. Transferable tight-binding models for silicon. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 49:7242-7250. [PMID: 10009461 DOI: 10.1103/physrevb.49.7242] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
|
31 |
44 |
25
|
Kwon I, Biswas R, Grest GS, Soukoulis CM. Molecular-dynamics simulation of amorphous and epitaxial Si film growth on Si(111). PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:3678-3687. [PMID: 9994168 DOI: 10.1103/physrevb.41.3678] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
|
35 |
42 |