Tomoki Yoshida

Evaluation of free energy landscape for base–amino acid interactions using ab initio force field and extensive sampling

Structural data of protein–DNA complex show redundancy and flexibility in base–amino acid interactions. To understand the origin of the specificity in protein–DNA recognition, we calculated the interaction free energy, enthalpy, entropy, and minimum energy maps for AT‐Asn, GC‐Asn, AT‐Ser, and GC‐Ser by means of a set of ab initio force field with extensive conformational sampling. We found that the most preferable interactions in these pairs are stabilized by hydrogen bonding, and are mainly enthalpy driven. However, minima in the free energy maps are not necessarily the same as those in the minimum energy map or enthalpy maps, due to the entropic effect. The effect of entropy is particularly important in the case of GC‐Asn. Experimentally observed structures of base–amino acid interactions are within preferable regions in the calculated free energy maps, where there are many different interaction configurations with similar energy. The full geometry optimization procedure using ab initio molecular orbital method was applied to get the optimal interaction geometries for AT‐Asn, GC‐Asn, AT‐Ser, and GC‐Ser. We found that there are various base–amino acid combinations with similar interaction energies. These results suggest that the redundancy and conformational flexibility in the base–amino acid interactions play an important role in the protein–DNA recognition.

Crystallographic and mutational analyses of cystathionine β-synthase in the H2S-synthetic gene cluster in Lactobacillus plantarum

Cystathionine β‐synthase (CBS) catalyzes the formation of l‐cystathionine from l‐serine and l‐homocysteine. The resulting l‐cystathionine is decomposed into l‐cysteine, ammonia, and α‐ketobutylic acid by cystathionine γ‐lyase (CGL). This reverse transsulfuration pathway, which is catalyzed by both enzymes, mainly occurs in eukaryotic cells. The eukaryotic CBS and CGL have recently been recognized as major physiological enzymes for the generation of hydrogen sulfide (H2S). In some bacteria, including the plant‐derived lactic acid bacterium Lactobacillus plantarum, the CBS‐ and CGL‐encoding genes form a cluster in their genomes. Inactivation of these enzymes has been reported to suppress H2S production in bacteria; interestingly, it has been shown that H2S suppression increases their susceptibility to various antibiotics. In the present study, we characterized the enzymatic properties of the L. plantarum CBS, whose amino acid sequence displays a similarity with those of O‐acetyl‐l‐serine sulfhydrylase (OASS) that catalyzes the generation of l‐cysteine from O‐acetyl‐l‐serine (l‐OAS) and H2S. The L. plantarum CBS shows l‐OAS‐ and l‐cysteine‐dependent CBS activities together with OASS activity. Especially, it catalyzes the formation of H2S in the presence of l‐cysteine and l‐homocysteine, together with the formation of l‐cystathionine. The high affinity toward l‐cysteine as a first substrate and tendency to use l‐homocysteine as a second substrate might be associated with its enzymatic ability to generate H2S. Crystallographic and mutational analyses of CBS indicate that the Ala70 and Glu223 residues at the substrate binding pocket are important for the H2S‐generating activity.

Knee-chest position improves pulmonary oxygenation in elderly patients undergoing lower spinal surgery with spinal anesthesia

STUDY OBJECTIVE To define the effect of the knee-chest position on pulmonary oxygenation in patients who underwent lower spinal operations under spinal anesthesia. DESIGN Clinical, prospective study. SETTING Inpatient anesthesia and orthopedic surgery clinic at a municipal hospital. PATIENTS Fifty-six patients (30 males and 26 females) who underwent lower spinal surgery under spinal anesthesia. INTERVENTIONS After administering hyperbaric tetracaine solution and fixing the anesthesia level in the supine position for 15 minutes, patients were turned to the knee-chest position. They breathed room air normally. MEASUREMENTS AND MAIN RESULTS Arterial blood gas tensions were measured in the supine position 15 minutes after administration of the tetracaine solution and 15 minutes after turning patients to the knee-chest position. Patients were classified into six groups according to their age: patients in their teens and 20s, 30s, 40s, 50s, 60s, and 70s. In the supine position, the mean values of the alveolar arterial oxygen tension difference (A-aDO2) of patients in their 50s, 60s, and 70s were significantly higher than those of patients in their teens and 20s, 30s, and 40s. In the knee-chest position, these high values of A-aDO2 in the older patient groups decreased significantly, thereby eliminating any significant difference in A-aDO2 among all age groups. To determine the mechanism of the improvement of pulmonary oxygenation in the elderly patients, the effect of the knee-chest position on lung volumes was studied in eight young volunteers. CONCLUSION A significant improvement of pulmonary oxygenation was seen in elderly patients who underwent lower spinal operation with spinal anesthesia when they were turned to the knee-chest position. The knee-chest position has a beneficial effect on pulmonary oxygenation in elderly patients who are given spinal anesthesia.

Digraphs in Chemistry: All Possible Structures and Temperature-Dependent Distribution of Water Clusters

Graphs, digraphs, and rooted digraphs play important roles in chemistry. We present a graph-theoretical procedure to generate all the topology-distinct structures for water clusters. The NVT ensemble of water clusters is divided into the configurational subsets, which correspond to the topology-distinct hydrogen-bonding patterns, and the relative molar Helmholtz energies of the hydrogen-bonding patterns are evaluated. The method is based on the combination of standard Monte Carlo techniques with defined hydrogen-bonding patterns. The structure distributions of water clusters at finite temperatures are presented on the basis of the hydrogen-bonding patterns instead of the inherent structures. The thermodynamically favored structures of water clusters are presented. A list of new potential energy functions for water is given. An assessment of potential energy functions for water is also presented. A rooted digraph is used to represent the features of protonated water clusters. From detailed investigation of the structural patterns obtained, several restrictions which should be satisfied in the stable structures of protonated water clusters are found. The generated hydrogen-bonding matrices of the restrictive rooted digraph are used as the theoretical framework to obtain all the local minima on the potential energy surfaces of those protonated water clusters using ab initio molecular orbital and density functional theory methods.