Structural Analyses of Designed α-Helix and β-Sheet Peptide Nanofibers Using Solid-State Nuclear Magnetic Resonance and Cryo-Electron Microscopy and Introduction of Structure-Based Metal-Responsive Properties

The 21-residue peptide α3, which is artificially designed and consists of three repeats of 7 residues, is known to rapidly assemble into the α-helix nanofiber. However, its molecular structure within the fiber has not yet been fully elucidated. Thus, we conducted a thorough investigation of the fiber's molecular structure using solid-state NMR and other techniques. The molecules were found to be primarily composed of the α-helix structure, with some regions near the C- and N-terminal adopting a 310-helix structure. Furthermore, it was discovered that β-sheet hydrogen bonds were formed between the molecules at both ends. These intermolecular interactions caused the molecules to assemble parallelly in the same direction, forming helical fibers. In contrast, we designed two molecules, CaRP2 and βKE, that can form β-sheet intermolecular hydrogen bonds using the entire molecule instead of just the ends. Cryo-EM and other measurements confirmed that the nanofibers formed in a cross β structure, albeit at a slow rate, with the formation times ranging from 1 to 42 days. To create peptide nanofibers that instantaneously respond to changes in the external environment, we designed several molecules (HDM1-3) based on α3 by introducing metal-binding sites. One of these molecules was found to be highly responsive to the addition of metal ions, inducing α-helix formation and simultaneously assembling into nanofibers. The nanofibers lost their structure upon removal of the metal ion. The change occurred promptly and was reversible, demonstrating that the intended level of responsiveness was attained.

Hyper Thermostability and Liquid-Crystal-Like Properties of Designed α-Helical Peptide Nanofibers

Structural and thermodynamic transitions of artificially designed α-helical nanofibers were investigated using eight peptide variants, including four peptides with amide-modified carboxyl termini (CB peptides) and four unmodified peptides (CF peptides). Temperature-dependent circular dichroism spectroscopy and differential scanning calorimetry showed that CB peptides exhibit thermostability up to 50 °C higher than CF peptides. As a result, one of the denaturation temperatures approached nearly 130 °C, which is exceptionally high for a biomacromolecule. Thermodynamic analysis and microscopy observations also showed that CB peptides undergo a thermal transition similar to the phase transition in liquid crystals. In addition, one of the peptides showed a sharp and highly cooperative transition with a small enthalpy change at around 25 °C, which was ascribed to a giga-bundle burst of the molecular assembly. These macroscopic changes in the thermostability and crystallinity of CB peptides may be attributed to an increased amphiphilicity of the molecule in the direction of the helix axis, originating from the microscopic modification of the carboxyl-terminus.

In Situ Synthesis of an Anticancer Peptide Amphiphile Using Tyrosine Kinase Overexpressed in Cancer Cells

Cell-selective killing using molecular self-assemblies is an emerging concept for cancer therapy. Reported molecular self-assemblies are triggered by hydrolysis of well-designed molecules inside or outside cancer cells. This hydrolysis can occur in cancer and normal cells because of the abundance of water in living systems. Here, we report the in situ synthesis of a self-assembling molecule using a tyrosine kinase overexpressed in cancer cells. We designed a tyrosine-containing peptide amphiphile (C16-E4Y) that is transformed into a phosphorylated peptide amphiphile (C16-E4pY) by the overexpressed tyrosine kinase. Phosphorylation of C16-E4Y promoted self-assembly to form nanofibers in cancer cells. C16-E4Y exhibited selective cytotoxicity toward cancer cells overexpressing the tyrosine kinase. Self-assembled C16-E4pY induced endoplasmic reticulum stress that caused apoptotic cell death. Animal experiments revealed that C16-E4Y has antitumor activity. These results show that an enzyme overexpressed in cancer cells is available for intracellular synthesis of an antitumor self-assembling drug that is cell-selective.

Inhibition of Melittin Activity Using a Small Molecule with an Indole Ring

We investigated d-amino acids as potential inhibitors targeting l-peptide toxins. Among the l- and d-amino acids tested, we found that d-tryptophan (d-Trp) acted as an inhibitor of melittin-induced hemolysis. We then evaluated various Trp derivatives and found that 5-chlorotryptamine (5CT) had the largest inhibitory effect on melittin. The indole ring, amino group, and steric hindrance of an inhibitor played important roles in the inhibition of melittin activity. Despite the small size and simple molecular structure of 5CT, its IC₅₀ was approximately 13 μg/mL. Fluorescence quenching, circular dichroism measurements, and size-exclusion chromatography revealed that 5CT interacted with Trp19 in melittin and affected the formation of the melittin tetramer involved in hemolysis. Molecular dynamics simulation of melittin also indicated that the interaction of 5CT with Trp19 in melittin affected the formation of the tetramer.

Pathway Dependence of the Formation and Development of Prefibrillar Aggregates in Insulin B Chain

Amyloid fibrils have been an important subject as they are involved in the development of many amyloidoses and neurodegenerative diseases. The formation of amyloid fibrils is typically initiated by nucleation, whereas its exact mechanisms are largely unknown. With this situation, we have previously identified prefibrillar aggregates in the formation of insulin B chain amyloid fibrils, which have provided an insight into the mechanisms of protein assembly involved in nucleation. Here, we have investigated the formation of insulin B chain amyloid fibrils under different pH conditions to better understand amyloid nucleation mediated by prefibrillar aggregates. The B chain showed strong propensity to form amyloid fibrils over a wide pH range, and prefibrillar aggregates were formed under all examined conditions. In particular, different structures of amyloid fibrils were found at pH 5.2 and pH 8.7, making it possible to compare different pathways. Detailed investigations at pH 5.2 in comparison with those at pH 8.7 have suggested that the evolution of protofibril-like aggregates is a common mechanism. In addition, different processes of evolution of the prefibrillar aggregates have also been identified, suggesting that the nucleation processes diversify depending on the polymorphism of amyloid fibrils.

Microenvironment pH-Induced Selective Cell Death for Potential Cancer Therapy Using Nanofibrous Self-Assembly of a Peptide Amphiphile

Self-assembly of synthetic molecules has been drawing broad attention as a novel emerging approach in drug discovery. Here, we report selective cell death induced by a novel peptide amphiphile that self-assembles to form entangled nanofibers (hydrogel) based on intracellular pH (pH_i). We found that a palmitoylated hexapeptide (C₁₆-VVAEEE) formed a hydrogel below pH 7. The formation of the nanofibrous self-assembly was responsive to a small pH change around pH 7. The cytotoxicity of C₁₆-VVAEEE was correlated with pH_i of cells. Microscope observation demonstrated the self-assembly of C₁₆-VVAEEE inside HEK293 cells. In vivo experiments revealed that the transcutaneous administration of C₁₆-VVAEEE showed remarkable anti-tumor activity. This study proposes that distinct microenvironment inside living cells can be used as a trigger for the intracellular self-assembly of a peptide amphiphile, which provide a new clue to drug discovery.

Rechallenge of voriconazole successfully tolerated after hepatic toxicity

Infections caused by Aspergillus species are often life-threatening. Drugs effective for Aspergillus infection are limited. Voriconazole is one of the most important drugs, however, considerable portion of patients experience liver toxicity and have to stop the drug administration. We frequently experience liver toxicity even though the serum concentration of voriconazole is within the target range. Historically, in some life-threatening situations like tuberculosis, where a suitable alternative is unavailable, rechallenge has been attempted. However, there have been no report on the rechallenge of voriconazole. We report cases of successful re-administration of voriconazole after liver toxicity.

P2623Measurement of liver fibrosis marker: type IV collagen 7S among patients with acute heart failure and its relationship with the Enhanced Liver Fibrosis (ELF) score

Background

Hemodynamic disturbance in acute heart failure (HF) can cause injury to extra-cardiac organs such as the liver. Organ injury in HF might evoke a profibrotic response, which could adversely affect the prognosis.

Methods

Among 189 patients with acute HF, we simultaneously determined the liver fibrosis marker, type IV collagen 7S (P4NP 7S) and the Enhanced Liver Fibrosis (ELF) Score consisting of tissue inhibitor of metalloproteinases 1 (TIMP-1), amino-terminal propeptide of type III procollagen (PIIINP) and hyaluronic acid (HA) on admission and at discharge.

Results

During hospitalization, P4NP 7S and ELF score significantly decreased from 7.1 ng/mL to 6.1 ng/mL (P<0.001) and 10.39 to 10.13 (P<0.001), respectively. P4NP 7S and ELF score were correlated with each other on admission (r=0.4, P<0.001) and at discharge (r=0.4, P<0.001). %Change of (Δ) P4NP 7S during hospitalization was correlated with ΔBNP and ΔELF score (r=0.3, P<0.001 and r=0.4, P<0.001, respectively). Among the components of ELF score, PIIINP and HA were correlated with P4NP 7S on admission (r=0.5, P<0.001 and r=0.3, P<0.001, respectively) and at discharge (r=0.4, P<0.001 and r=0.3, P<0.001, respectively). ΔP4NP 7S was also correlated with ΔTIMP-1, ΔPIIINP and ΔHA (r=0.3, P<0.001, r=0.4, P<0.001 and r=0.3, P<0.001, respectively). Each patient was followed up up to 365 days after discharge. 69 patients died or were hospitalized for HF. When the patients were divided into two groups according to the median value of each marker at discharge, the cumulative 1-year incidences of all cause death or HF hospitalization were 32.0% and 45.5% in P4NP 7S-low and P4NP 7S-high group, respectively (log-rank P=0.051) and 43.2% and 34.9% in ELF score-low and ELF score-high group, respectively (log-rank P=0.44). After adjustment by the clinically relevant factors including age, sex, hemoglobin, sodium and left ventricular ejection fraction, P4NP 7S showed independent prognostic value (adjusted hazard ratio: 1.12, P=0.02), while ELF score did not (adjusted hazard ratio: 1.04, P=0.79).

Conclusion

Parallel elevation of P4NP 7S and ELF score were documented during acute phase of HF. P4NP 7S at discharge may identify patients at high risk for subsequent HF related events.

A specific form of prefibrillar aggregates that functions as a precursor of amyloid nucleation

Non-fibrillar protein aggregates that appear in the earlier stages of amyloid fibril formation are sometimes considered to play a key role in amyloid nucleation; however, the structural features of these aggregates currently remain unclear. We herein identified a characteristic pathway of fibril formation by human insulin B chain, in which two major species of prefibrillar aggregates were identified. Based on the time-resolved tracking of this pathway with far-UV circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and ¹H-NMR spectroscopy, the first prefibrillar aggregate with a hydrodynamic diameter of approximately 70 nm accumulated concomitantly with the formation of a β-sheet structure, and the size further evolved to 130 nm with an additional structural development. These prefibrillar aggregates were metastable and survived at least 24 hours as long as they were maintained under quiescent conditions. The energy barrier for nucleation was overcome by shaking or even by applying a single short ultrasonic pulse. Furthermore, an investigation where nucleation efficiency was monitored by fibrillation rates with varying the timing of the ultrasonic-pulse treatment revealed that the second prefibrillar aggregate specifically produced amyloid nuclei. These results suggest that the second form of the prefibrillar aggregates acts as a direct precursor for the amyloid nucleation.

Changes of superoxide dismutase activity and ascorbic acid in focal cerebral ischaemia in rats

Free radical reactions are supposed to cause ischaemic brain damage, and active oxygens can initiate these chains reaction. If active oxygens play important roles in ischaemic brain damage, the activity of superoxide dismutase, scavenger of superoxide anion, is supposed to decrease in ischaemic brain. The reduced form of ascorbic acid also scavenges superoxide anion. In rat middle cerebral artery focal ischaemia, we investigated the changes in superoxide dismutase activity and the concentration of reduced ascorbate up to 48 hours. Middle cerebral artery territory of each cerebral hemisphere was homogenized. The supernatant was divided into two aliquots; one was dialysed to remove ascorbate and the other was not. The enzyme activity of the dialysed specimen from the ischaemic hemisphere did not decrease within 4 h after the arterial occlusion. The activity of the dialysed specimen from the nonischaemic side remained unchanged during the examination. Reduced ascorbate levels in nondialysed samples showed similar changes to the superoxide dismutase activities in the dialysed samples. Our data suggest that ascorbic acid may exert the enzyme activity and that the enzyme activity remains at the normal level in the early phase of ischaemia despite the irreversible ischaemic changes that take place within 4 h after the onset of ischaemia.

Change of xanthine dehydrogenase and xanthine oxidase activities in rat brain following complete ischaemia

We studied the activities of xanthine dehydrogenase and xanthine oxidase in rat forebrain after complete ischaemia. Complete ischaemia was induced by decapitation after transcardiac infusion with saline. The activities of xanthine dehydrogenase and xanthine oxidase immediately after ischaemia were 93.3 +/- 38.7 and 18.8 +/- 7.7 microU/mg protein, respectively, and at 24 h after ischaemia were 183.5 +/- 75.1 and 60.8 +/- 15.2 microU/mg protein, respectively. The ratios of xanthine dehydrogenase/xanthine oxidase immediately and 24 h after ischaemia were 5.04 +/- 1.03 and 3.04 +/- 0.99, respectively. These data indicate that xanthine dehydrogenase and xanthine oxidase activities were maintained even 24 h after complete ischaemia. Conversion of xanthine dehydrogenase to xanthine oxidase proceeds slowly during complete ischaemia.

Broadband Dielectric Spectroscopy on Lysozyme in the Sub-Gigahertz to Terahertz Frequency Regions: Effects of Hydration and Thermal Excitation

We have performed dielectric spectral measurements of lysozyme in a solid state to understand the effects of hydration and thermal excitation on the low-frequency dynamics of protein. Dielectric measurements were performed under changing hydration conditions at room temperature in the frequency region of 0.5 GHz to 1.8 THz. We also studied the temperature dependence (83 to 293 K) of the complex dielectric spectra in the THz frequency region (0.3 THz to 1.8 THz). Spectral analyses were performed using model functions for the complex dielectric constant. To reproduce the spectra, we found that two relaxational modes and two underdamped modes are necessary together with an ionic conductivity term in the model function. At room temperature, the two relaxational modes have relaxation times of ∼20 ps and ∼100 ps. The faster component has a major spectral intensity and is suggested to be due to coupled water-protein motion. The two underdamped modes are necessary to reproduce the temperature dependence of the spectra in the THz region satisfactorily. The protein dynamical transition is a well-known behavior in the neutron-scattering experiment for proteins, where the atomic mean-square displacement shows a sudden change in the temperature dependence at approximately 200 K, when the samples are hydrated. A similar behavior has also been observed in the temperature dependence of the absorption spectra of protein in the THz frequency region. From our broadband dielectric spectroscopic measurements, we conclude that the increase in the spectral intensities in the THz region at approximately 200 K is due to a spectral blue-shift of the fast relaxational mode.

Relationship between Cnm-positive Streptococcus mutans and cerebral microbleeds in humans

OBJECTIVE

Cerebral hemorrhage has been shown to occur in animals experimentally infected with Streptococcus mutans carrying the collagen-binding Cnm gene. However, the relationship between cerebral microbleeds and oral hygiene, with a focus on Cnm gene-positive S. mutans infection, remains unclear.

MATERIAL AND METHODS

One hundred and thirty-nine subjects participated. The presence or absence of Cnm-positive S. mutans and its collagen-binding activity were investigated using saliva samples, and relationship with cerebral microbleeds detected on MRI investigated, including clinical information and oral parameters.

RESULTS

Fifty-one subjects were identified as Cnm-positive S. mutans carriers (36.7%), with cerebral microbleeds being detected in 43 (30.9%). A significantly larger number of subjects carried Cnm-positive S. mutans in the cerebral microbleeds (+) group. S. mutans with Cnm collagen-binding ability was detected in 39 (28.1%) of all subjects, and the adjusted odds ratio for cerebral microbleeds in the Cnm-positive group was 14.4. Regarding the presence of cerebral microbleeds, no significant differences were noted in the number of remaining teeth, dental caries, or in classic arteriosclerosis risk factors.

CONCLUSIONS

The occurrence of cerebral microbleeds was higher in subjects carrying Cnm-positive S. mutans, indicating that the presence of Cnm-positive S. mutans increases cerebral microbleeds, and is an independent risk for the development of cerebrovascular disorders.

Temperature and Hydration Dependence of Low-Frequency Spectra of Lipid Bilayers Studied by Terahertz Time-Domain Spectroscopy

We have studied temperature and hydration dependent low-frequency spectra of lipid bilayers of 1,2-dimyristoyl-sn-glycero-3-phosphoryl-3'-rac-glycerol (DMPG) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) by terahertz time-domain spectroscopy (THz-TDS). We measured X-ray diffraction patterns and mid-infrared spectra of these lipid bilayers and found that the lipid bilayers have two different types of phases, i.e., the gel phase and the crystalline phase, depending on the preparation methods of the samples. In both phases, a few distinct bands were observed in the THz region. For DMPG, the peak wavenumbers of the absorption bands did not change upon hydration, while the bandwidth in the crystalline phase was smaller than that in the gel phase. We performed spectral analyses for the complex dielectric spectra for DMPG and DMPC with a model function, mainly to determine the peak wavenumbers of the absorption bands. In contrast to the case of the DMPG bilayers, the peak wavenumber of the absorption band of the DMPC bilayer shifts upon hydration. In the hydrated DMPC bilayer, it was suggested fast reorienting water molecules exist with a relaxation time of sub-picoseconds. It is suggested that the THz absorption patterns reflect the lipid packing pattern in the bilayers. The temperature dependence of the absorption band was analyzed by an empirical equation, and the anharmonicity of the vibrational potential of the low-frequency mode was quantitatively evaluated.

Designing cell-aggregating peptides without cytotoxicity

We have designed α-helical peptides de novo that can induce aggregation of various kinds of cells by focusing on physicochemical properties such as hydrophobicity, net charges, and amphipathicity. It is shown that peptide hydrophobicity is the key factor to determine capabilities for cell aggregation while peptide net charges contribute to nonspecific electrostatic interactions with cells. On the other hand, amphipathic peptides tend to exhibit cytotoxicity such as antimicrobial activity and hemolysis, which are competitive with cell-aggregation capabilities. Different from the cases of living cells, aggregation of artificial anionic liposomes appears to be mainly determined by electrostatic interactions. This discrepancy might be due to the complex structure of surfaces of cell membranes consisting of macromolecular chains such as peptidoglycans, polysaccharides, or glycocalyx, which coexist with lipid bilayers. Our design strategy would pave the way to design peptides that lead aggregation of living cells without cytotoxicity.

Mg-doped TiO2 nanorods improving open-circuit voltages of ammonium lead halide perovskite solar cells

Mg-doped TiO₂ nanorods were synthesized from colloidal titanate by a microwave hydrothermal reaction. Use of such TiO₂ having an elevated conduction band edge as an electron extracting material for ammonium lead halide perovskite solar cells resulted in a marked improvement of V_oc.

Salivary alpha-amylase and cortisol responsiveness following electrical stimulation stress in patients with the generalized type of social anxiety disorder

INTRODUCTION

Social anxiety disorder is believed to be a stress-induced disease. Although it can be inferred from the symptoms during attacks that there exists some abnormality of autonomic nervous system in any of the stress systems in social anxiety disorder, little evidence has been reported. This study focused on comparing the reactivity of 2 stress systems, the autonomic nervous system (ANS) and the hypothalamic-pituitary-adrenal (HPA) axis in patients with social anxiety disorder.

METHODS

32 patients with the generalized type of social anxiety disorder were compared with 80 age- and gender-matched controls. We collected saliva samples from patients and controls before and after electrical stimulation to measure the concentrations of salivary alpha-amylase (sAA) and salivary cortisol. Profile of Mood State (POMS) and State-Trait Anxiety Inventory (STAI) scores and Heart Rate Variability (HRV) were also determined following stimulation.

RESULTS

SAA in patients displayed a significantly higher level at baseline and a significantly larger response to electrical stimulation as compared to controls, whereas no group differences were seen in any HRV. Neither within-subject nor group differences were seen in salivary cortisol levels.

CONCLUSIONS

These results suggest that SAD patients displayed enhanced ANS (but not HPA axis) activity vs. healthy controls.

Long insular artery infarction: characteristics of a previously unrecognized entity

BACKGROUND AND PURPOSE

The infarctions arising in the long insular arteries of the M2 segment have been poorly described in the past. The purpose of this study was to investigate the incidence, clinical characteristics, and pathogenesis of long insular artery infarcts.

MATERIALS AND METHODS

Patients with acute isolated infarcts in territories of the long insular arteries and lenticulostriate arteries were retrospectively reviewed. The long insular artery territory was defined as the area above the lenticulostriate artery territory at the level of centrum semiovale. On the coronal section, it lies between the tip of the anterior horn and the top of the superior limb of the insular cleft. Clinical features and prevalence of embolic sources were compared between the 2 groups.

RESULTS

Of 356 consecutive patients with acute ischemic stroke, 8 (2.2%) had a long insular artery infarct (long insular artery group) and 50 (14.0%) had a lenticulostriate artery infarct (lenticulostriate artery group). There were no differences in age, sex, prevalence of risk factors, neurologic deficit, or incidence of lacunar syndromes between these groups. Abrupt onset was more common in the long insular artery than in the lenticulostriate artery group (P = .004). The prevalence of embolic high-risk sources (eg, atrial fibrillation) was not significantly different between these groups, but the combined prevalence of all embolic sources, including moderate-risk sources, was significantly higher in the long insular artery group (P = .048).

CONCLUSIONS

Isolated infarction caused by long insular artery occlusion is not rare. Abrupt onset is more common for long insular artery infarction, and this finding could be attributed to the higher incidence of an embolic etiology as the pathogenesis of infarction.

Can the opportunity of cardio-pulmonary bypass be useful in complex general thoracic surgery problems? A report of nine cases

AIM

We report on nine highly selected patients in whom the resection of the tumor was only possible with cardiopulmonary bypass (CPB).

METHODS

Between November 1996 and November 2009, nine patients with non-cardiac tumors underwent surgery under CPB. Indications were: infiltration of the pulmonary vein in the left atrium (four cases), one case where the tumor (a paraganglioma apparently located in the subcarinal space) was actually in the atrium wall, one mediastinal liposarcoma with massive infiltration of the pericardium and the main pulmonary artery, and three tracheal tumors (2 cylindromas and 1 carcinoid).

RESULTS

Indication for CPB was decided preoperatively in 7 cases and intraoperatively in the other 2 patients. Cardiac infiltration was confirmed with intraoperative transesophageal cardiac echography in 2 patients, which proved to be very useful. Concerning postoperative complications, one patient died intraoperatively because it was impossible to stop the CPB after reconstruction of the bifurcation of the main pulmonary artery. Although the duration of the operation was significantly increased by the use of cardiopulmonary by-pass, it did not influence postoperative recovery in any of the other eight patients, as far as bleeding or infection was concerned. In one patient, a thoracic drain had to be replaced due to a partial pneumothorax. In another patient a partial dehiscence of the neo-carina was conservatively treated. Long-term results were influenced by the initial pathology of the patient.

CONCLUSION

CPB provides the possibility of safely resecting intrathoracic tumors invading cardiac structures that were previously inoperable. This can be achieved with an acceptable level of risk and - in very selected cases - may achieve long-term survival.

Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants

GTP-bound Ras adopts two interconverting conformations, "inactive" state 1 and "active" state 2. However, the tertiary structure of wild-type (WT) state 1 remains unsolved. Here we solve the state 1 crystal structures of H-Ras WT together with its oncogenic G12V and Q61L mutants. They assume open structures characterized by impaired interactions of both Thr-35 in switch I and Gly-60 in switch II with the γ-phosphate of GTP and possess two surface pockets of mutually different shapes unseen in state 2, a potential target for selective inhibitor development. Furthermore, they provide a structural basis for the low GTPase activity of state 1.

Solution structure of the state 1 conformer of GTP-bound H-Ras protein and distinct dynamic properties between the state 1 and state 2 conformers

Ras small GTPases undergo dynamic equilibrium of two interconverting conformations, state 1 and state 2, in the GTP-bound forms, where state 2 is recognized by effectors, whereas physiological functions of state 1 have been unknown. Limited information, such as static crystal structures and (31)P NMR spectra, was available for the study of the conformational dynamics. Here we determine the solution structure and dynamics of state 1 by multidimensional heteronuclear NMR analysis of an H-RasT35S mutant in complex with guanosine 5'-(β, γ-imido)triphosphate (GppNHp). The state 1 structure shows that the switch I loop fluctuates extensively compared with that in state 2 or H-Ras-GDP. Also, backbone (1)H,(15)N signals for state 2 are identified, and their dynamics are studied by utilizing a complex with c-Raf-1. Furthermore, the signals for almost all the residues of H-Ras·GppNHp are identified by measurement at low temperature, and the signals for multiple residues are found split into two peaks corresponding to the signals for state 1 and state 2. Intriguingly, these residues are located not only in the switch regions and their neighbors but also in the rigidly structured regions, suggesting that global structural rearrangements occur during the state interconversion. The backbone dynamics of each state show that the switch loops in state 1 are dynamically mobile on the picosecond to nanosecond time scale, and these mobilities are significantly reduced in state 2. These results suggest that multiconformations existing in state 1 are mostly deselected upon the transition toward state 2 induced by the effector binding.

Cross-city comparison of indoor air temperatures in air-conditioned spaces

Field measurements were collected through physical measurements and observations in the cities of Seoul, Korea; Eugene and Portland, Oregon; and Yokohama, Japan, during the fall, winter, and summer seasons from 2005 to 2006. A total of 1733 data sets were collected (Seoul - 713; Oregon - 807; Yokohama - 213) in variety of multi-use buildings with the goal of examining operative temperatures and conditions encountered during everyday life. Of the four cities measured, winter and autumn indoor operative temperatures were highest in Seoul and lowest in Yokohama when normalized to outdoor conditions. In contrast, summer indoor operative temperatures were highest in Yokohama and lowest in Oregon. Clothing levels changed seasonally, and differences were observed between 'long-term occupants', 'residents', and 'transients.'

Critical roles of interactions among switch I-preceding residues and between switch II and its neighboring alpha-helix in conformational dynamics of the GTP-bound Ras family small GTPases

GTP-bound forms of Ras family small GTPases exhibit dynamic equilibrium between two interconverting conformations, "inactive" state 1 and "active" state 2. A great variation exists in their state distribution; H-Ras mainly adopts state 2, whereas M-Ras predominantly adopts state 1. Our previous studies based on comparison of crystal structures representing state 1 and state 2 revealed the importance of the hydrogen-bonding interactions of two flexible effector-interacting regions, switch I and switch II, with the γ-phosphate of GTP in establishing state 2 conformation. However, failure to obtain both state structures from a single protein hampered further analysis of state transition mechanisms. Here, we succeed in solving two crystal structures corresponding to state 1 and state 2 from a single Ras polypeptide, M-RasD41E, carrying an H-Ras-type substitution in residue 41, immediately preceding switch I, in complex with guanosine 5'-(β,γ-imido)triphosphate. Comparison among the two structures and other state 1 and state 2 structures of H-Ras/M-Ras reveal two new structural features playing critical roles in state dynamics; interaction of residues 31/41 (H-Ras/M-Ras) with residues 29/39 and 30/40, which induces a conformational change of switch I favoring its interaction with the γ-phosphate, and the hydrogen-bonding interaction of switch II with its neighboring α-helix, α3-helix, which induces a conformational change of switch II favoring its interaction with the γ-phosphate. The importance of the latter interaction is proved by mutational analyses of the residues involved in hydrogen bonding. These results define the two novel functional regions playing critical roles during state transition.