Energy exchange network of inter‐residue interactions within a thermally fluctuating protein molecule: A computational study

Protein function is regulated not only by the structure but also by physical dynamics and thermal fluctuations. We have developed the computer program, CURrent calculation for proteins (CURP), for the flow analysis of physical quantities within thermally fluctuating protein media. The CURP program was used to calculate the energy flow within the third PDZ domain of the neuronal protein PSD‐95, and the results were used to illustrate the energy exchange network of inter‐residue interactions based on atomistic molecular dynamics simulations. The removal of the α3 helix is known to decrease ligand affinity by 21‐fold without changing the overall protein structure; nevertheless, we demonstrated that the helix constitutes an essential part of the network graph. © 2015 Wiley Periodicals, Inc.     

Label-Free Imaging of Intracellular Temperature by Using the O−H Stretching Raman Band of Water

We propose a label-free method for measuring intracellular temperature using a Raman image of a cell in the O−H stretching band. Raman spectra of cultured cells and the medium were first measured at various temperatures using a Raman microscope and the intensity ratio of the two regions of the O−H stretching band was calculated. The intensity ratio varies linearly with temperature in both the medium and cells, and the resulting calibration lines allow simultaneous visualization of both intracellular and extracellular temperatures in a label-free manner. We applied this method to the measurement of temperature changes after the introduction of FCCP (carbonyl cyanide-p-trifluoromethoxyphenylhydrazone) in living cells. We observed a temperature rise in the cytoplasm and succeeded in obtaining an image of the change in intracellular temperature after the FCCP treatment.     

Structure and bonding of the (C6H6)+ 2 radical

To elucidate the relative stability of various structures of the benzene dimer cation radical, (C₆H₆)⁺ ₂ in its ground and low-lying excited states, ab initio complete active space self-consistent field (CASSCF), multi-reference singly and doubly excited configuration interaction (MRSDCI), and multi-reference coupled pair approximation (MRCPA) calculations were performed. Full optimization was performed at the CASSCF level for various structures of the dimer cation, followed by MRSDCI and MRCPA calculations. It was found that the global minimum of the cation is at a slipped C_2h sandwich structure but there are some other sandwich structures with almost the same stability, being within about kcal mol^?1. T-shape structures are less stable than the sandwich structures, by more than 5 kcal mol^?1 by MRCPA calculations. Low lying electronic excited states in various structures are also discussed.     

Theoretical study of the prion protein based on the fragment molecular orbital method

We performed fragment molecular orbital (FMO) calculations to examine the molecular interactions between the prion protein (PrP) and GN8, which is a potential curative agent for prion diseases. This study has the following novel aspects: we introduced the counterpoise method into the FMO scheme to eliminate the basis set superposition error and examined the influence of geometrical fluctuation on the interaction energies, thereby enabling rigorous analysis of the molecular interaction between PrP and GN8. This analysis could provide information on key amino acid residues of PrP as well as key units of GN8 involved in the molecular interaction between the two molecules. The present FMO calculations were performed using an original program developed in our laboratory, called “Parallelized ab initio calculation system based on FMO (PAICS)”. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

The Progress of the Gait Impairment and Brain Activation in a Patient with Post-stroke Hemidystonia

Objective: We explore the effects of body weight-supported (BWS) treadmill training, including the change of cortical activation, on a patient with post-stroke hemidystonia. Patient: The patient was a 71-year-old man with left thalamus hemorrhage. His motor symptoms indicated slight impairment. There was no overactive muscle contraction in the supine, sitting, or standing positions. During his gait, the right initial contact was the forefoot, and his right knee showed an extension thrust pattern. These symptoms suggested that he had post-stroke hemidystonia. Methods: The patient performed BWS treadmill training 14 times over 3 weeks. The effects of the BWS training were assessed by a step-length analysis, electromyography and functional magnetic resonance imaging (fMRI). Results: The patient''s nonparetic step length was extended significantly in the Inter-BWS (p<0.001) and Post-BWS (p=0.025) periods compared to the Pre-BWS session. The excessive muscle activity of the right gastrocnemius medialis in the swing phase was decreased at the Inter-BWS, Post-BWS, and follow-up compared to the Pre-BWS session. The peak timing difference of the bilateral tibialis anterior muscle became significant (p<0.05) on the first day of the intervention. The fMRI revealed that the cortical areas activated by the motor task converged through the intervention (p<0.05, family-wise error corrected). Conclusion: These results suggest that there was improvement of the patient''s symptoms of post-stroke hemidystonia due to changes in the brain activity during voluntary movement after BWS intervention. Body weight-supported treadmill training may thus be an effective treatment for patients with poststroke hemidystonia.     

Electronic characteristics of sandwich-type lanthanide octaethylporphyrins

The electronic behavior of sandwich-type rare earth octaethylporphyrinates Ln(oep)2 and Ln2(oep)3 (Ln=Ce, Pr and Eu) was characterized by measurements of the UV-vis or near infrared spectra and D.C. conductivity. However, the conductivity values measured at room temperature were distributed in an order of 10-7 to 10-8 S.cm-1 even after the partial oxidation of complex with the complexes with iodine and no remarkable change was observed among the complexes such as LnIV(Por2-)2 (Ln=Ce) and LnIV(Por2-)(Por.-) (Ln=Ce) or Ln2III(Por2-)3 and LnIII2(Por2-)2(Por-).     

One-step preparation of 3-alkoxypyrazine-2-carbonitriles from pyrazine-2,3-dicarbonitriles and related reactions

A series of 5,6-disubstituted 3-alkoxypyrazine-2-carbonitriles ( 2a-i ) were prepared from 5,6-disubstituted pyrazine-2,3-dicarbonitriles ( 1a-d ) by direct substitution with alcohols. Treatment of 1 with amines gave either pyrrolopyrazines ( 3a,b ) or substitution products ( 4,5 ). In a low temperature range, 1 afforded imidates and related compounds ( 6–11 ). The preference among these reactions depended on the 5,6-substituents and on the reaction conditions.     

Stereoselective Mannich-type reaction of chiral aldimines with 2-silyloxybutadienes by using trifluoromethanesulfonic acid

Novel stereoselective Mannich-type reaction of chiral aldimines with 2-silyloxybutadienes in the presence of trifluoromethanesulfonic acid has been carried out to give the corresponding products, which are not obtained by general Lewis acid-promoted methods, with 70-92% de in 62-74% yield. No cycloadducts were detected in the crude product by ¹H NMR.