Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins.

Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology.

Structures and electronic spectra of CdSe-Cys complexes: density functional theory study of a simple peptide-coated nanocluster.

We present density functional theory (DFT) structures and time-dependent DFT electronic excitation energies of several small CdSe nanoclusters with the composition Cd(n)Se(n) (n = 3, 6, 10, 13). We examine the effects on the geometries and excitation spectra of the nanoclusters induced by two chemical changes: peptide-binding and ligand passivation. We use cysteine (Cys) and cysteine-cysteine dipeptide (Cys-Cys) as model peptides and hydrogen atoms as surface-bound solvent ligands (or stabilizing agents). By comparing the results calculated for bare, hydrogen-passivated (Cd(n)Se(n)H(2n)), as well as the corresponding Cys- and Cys-Cys- bound clusters (Cd(n)Se(n)-, Cd(n)Se(n)H(2n), -Cys, -Cys-Cys), we find that peptide-binding blue shifts the electronic excitations of bare nanoclusters, but red shifts those of hydrogen-passivated nanoclusters. The carboxyl oxygen and the sulfur atom tend to form a four-centered ring with adjacent two Cd atoms when the CdSe cluster forms covalent bonds with Cys or Cys-Cys. Further, this type of bonds may be distinguishable by significant red shifts of the excitation energies.

Adsorbate-induced absorption redshift in an organic-inorganic cluster conjugate: Electronic effects of surfactants and organic adsorbates on the lowest excited states of a methanethiol-CdSe conjugate.

Bioconjugated CdSe quantum dots are promising reagents for bioimaging applications. Experimentally, the binding of a short peptide has been found to redshift the optical absorption of nanoclusters [J. Tsay et al., J. Phys. Chem. B 109, 1669 (2005)]. This study examines this issue by performing density functional theory (DFT) and time-dependent-DFT calculations to study the ground state and low-lying excited states of (CdSe)(6)[SCH(3)](-), a transition metal complex built by binding methanethiolate to a CdSe molecular cluster. Natural bond orbital results show that the redshift is caused by ligand-inorganic cluster orbital interaction. The highest occupied molecular orbital (HOMO) of (CdSe)(6) is dominated by selenium 4p orbitals; in contrast, the HOMO of (CdSe)(6)[SCH(3)](-) is dominated by sulfur 3p orbitals. This difference shows that [SCH(3)](-) binding effectively introduces filled sulfur orbitals above the selenium 4p orbitals of (CdSe)(6). The resulting smaller HOMO-LUMO gap of (CdSe)(6)[SCH(3)](-) indeed leads to redshifts in its excitation energies compared to (CdSe)(6). In contrast, binding of multiple NH(3) destabilizes cadmium 5p orbitals, which contribute significantly to the lowest unoccupied molecular orbital (LUMO) of (CdSe)(6), while leaving the selenium 4p orbitals near the HOMO relatively unaffected. This has the effect of widening the HOMO-LUMO gap of (CdSe)(6)6NH(3) compared to (CdSe)(6). As expected, the excitation energies of the passivated (CdSe)(6)6NH(3) are also blueshifted compared to (CdSe)(6). As far as NH(3) is a faithful representation of a surfactant, the results clearly illustrate the differences between the electronic effects of an alkylthiolate versus those of surfactant molecules. Surface passivation of (CdSe)(6)[SCH(3)](-) is then simulated by coating it with multiple NH(3) molecules. The results suggest that the [SCH(3)](-) adsorption induces a redshift in the excitation energies in a surfactant environment.

Diffuse infiltrative primary cardiac lymphoma with delayed extracardiac involvement.

Primary cardiac lymphoma (PCL) is an extremely rare and fatal neoplasm of the heart. Traditionally, it is defined as lymphoma involving the heart or pericardium. PCL has a poor prognosis because of the diagnostic difficulty and its location. We present the case of a 48-year-old man who presented with pericardial effusion and diffuse cardiac wall thickening. We first suspected infiltrative heart disease. However, even after performing a biopsy, we could not establish an accurate diagnosis. After 20 months, primary cardiac diffuse large B cell lymphoma (DLBCL) was diagnosed by cervical lymph node biopsy. In this case, after chemotherapy, the DLBCL lesions, including cardiac wall thickening, improved. The treatment outcome suggests that the diagnosis was diffuse infiltrative PCL with delayed extracardiac involvement.

A case of late onset-acute tubulointerstitial nephritis with infliximab and mesalazine treatment in a patient with Crohn's disease.

Infliximab is a chimeric anti-tumor necrosis factor-alpha monoclonal antibody. Infusion related reactions and infection are well known side effects of infliximab; however, renal complications have not been well recognized. We report on a patient with late onset-acute tubulointerstitial nephritis (ATIN) after treatment with infliximab and mesalazine for Crohn's disease. A 25-year-old woman was admitted with a purpuric rash on both lower extremities and arthralgia. She had been diagnosed with Crohn's disease 5.6 years previously and had been treated with mesalazine and infliximab. Serum creatinine level, last measured one year ago, was elevated from 0.6 mg/dL to 1.9 mg/dL. Results of urinalysis, ultrasound, and serologic examinations were normal. With a tentative diagnosis of Henoch-Schonlein purpura, oral prednisolone was given, and serum creatinine decreased to 1.46 mg/dL, but was elevated to 2.6 mg/dL again at two months after discontinuation of prednisolone. Renal biopsy indicated that ATIN was probably induced by drug, considering significant infiltration of eosinophils. Concomitant use of infliximab with mesalazine was supposed to trigger ATIN. Oral prednisolone was administered, and serum creatinine level showed partial recovery. Thus, ATIN should be suspected as a cause of renal impairment in Crohn's disease even after a long period of maintenance treatment with infliximab and mesalazine.

Development of enterohepatic fistula after embolization in ileal gastrointestinal stromal tumor: a case report.

Gastrointestinal stromal tumor (GIST) is a rare mesenchymal tumor of the gastrointestinal tract that has been associated with the formation of fistulas to adjacent organs in few case reports. However, GIST with enterohepatic fistula has not been reported. Here we report the case of an enterohepatic fistula that occurred after embolization of a liver mass originating in the distal ileum. An 87-year-old woman was hospitalized for melena. On initial conventional endoscopy, a bleeding focus in the gastrointestinal tract was not found. Because of massive hematochezia, enteroscopy was performed through the anus. A protruding, ulcerative mass was found in the distal ileum that was suspected to be the source of the bleeding; a biopsy sample was taken. Electrocoagulation was not successful in controlling the bleeding; therefore, embolization was performed. After embolization, the patient developed a high fever and severe abdominal tenderness with rebound tenderness. Follow-up abdominopelvic computed tomography revealed an enterohepatic fistula between the liver and distal ileum. The fistula was treated surgically by segmental resection of the distal ileum and unlooping of the liver mass.

Effects of bioconjugation on the structures and electronic spectra of CdSe: density functional theory study of CdSe-adenine complexes.

We present density functional theory (DFT) and time-dependent DFT (TD-DFT) study of the structures and electronic spectra of small CdSe nanocluster-adenine complexes Cd(n)Se(n)-adenine (n = 3, 6, 10, 13). We examine the changes in the geometries and excitation spectra of the nanoclusters induced by DNA base-binding. By comparing the results calculated for the bare (Cd(n)Se(n)), hydrogen-passivated (Cd(n)Se(n)H(2n)), as well as the corresponding adenine (Ade)-bound clusters (Cd(n)Se(n)-Ade, Cd(n)Se(n)H(2n)-Ade, Cd(n)Se(n)H(2n-2)-Ade), we find that binding with Ade slightly blue-shifts (up to 0.18 eV) the electronic excitations of bare nanoclusters but strongly red-shifts (<1.2 eV) those of hydrogen-passivated nanoclusters. Natural bond orbital analysis shows that the LUMO of Cd(n)Se(n)H(2n)-Ade is a pi* orbital located on the purine ring.

Tautomerization of adenine facilitated by water: computational study of microsolvation.

We present calculations for the mechanism and the barrier heights of tautomerization of adenine. We find various pathways for the 9(H) <--> 7(H) and 9(H) <--> 3(H) tautomerization. One mechanism for the 9(H) --> 7(H) tautomerization involves an sp(3)- or carbene-type intermediate, whereas the other proceeds via imine intermediates. Tautomerization from the 9(H) tautomer to 7(H) or 3(H) is predicted to occur with a very large activation barrier (60-70 kcal/mol), indicating that the processes may not occur readily in the gas phase. Interactions with the water molecule(s) are found to lower the barrier tremendously. We suggest that dramatic lowering of the 9(H) --> 3(H) and 9(H) --> 7(H) barriers by microsolvating water molecules may facilitate the formation and observation of the 7(H) and 3(H) tautomers in the solution phase.

Facile S(N)2 reaction in protic solvent: quantum chemical analysis.

We study the effects of protic solvent (water, methanol, ethanol, and tert-butyl alcohol) and cation (Na+, K+, Cs+) on the unsymmetrical SN2 reaction X- + RY --> RX + Y- (X = F, Br; R = CH3,C3H7;Y = Cl, OMs). We describe a series of calculations for the S(N)2 reaction mechanism under the influence of cation and protic solvent, presenting the structures of pre- and postreaction complexes and transition states and the magnitude of the activation barrier. An interesting mechanism is proposed, in which the protic solvent molecules that are shielded from the nucleophile by the intervening cation act as a Lewis base to reduce the unfavorable Coulombic influence of the cation on the nucleophile. We predict that the reaction barrier for the S(N)2 reaction is significantly lowered by the cooperative effects of cation and protic solvent. We show that the cation and protic solvent, each of which has been considered to retard the SN2 reactivity of the nucleophile, can accelerate the reaction tremendously when they interact with the fluoride ion in an intricate, combined fashion. This alternative S(N)2 mechanism is discussed in relation to the recently observed phenomenal efficiency of fluorination in tert-alcohol media [Kim, D. W.; et al. J. Am. Chem. Soc. 2006, 128, 16394].