Group II chaperonins play important roles in protein homeostasis in the eukaryotic cytosol and in Archaea. These proteins assist in the folding of nascent polypeptides and also refold unfolded proteins in an ATP-dependent manner. Chaperonin-mediated protein folding is dependent on the closure and opening of a built-in lid, which is controlled by the ATP hydrolysis cycle. Recent structural studies suggest that the ring structure of the chaperonin twists to seal off the central cavity. In this study, we demonstrate ATP-dependent dynamics of a group II chaperonin at the single-molecule level with highly accurate rotational axes views by diffracted X-ray tracking (DXT). A UV light-triggered DXT study with caged-ATP and stopped-flow fluorometry revealed that the lid partially closed within 1 s of ATP binding, the closed ring subsequently twisted counterclockwise within 2–6 s, as viewed from the top to bottom of the chaperonin, and the twisted ring reverted to the original open-state with a clockwise motion. Our analyses clearly demonstrate that the biphasic lid-closure process occurs with unsynchronized closure and a synchronized counterclockwise twisting motion.

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TheBiophysicalSociety of JapanGeneral IncorporatedAssociation significantly slow.There is also a criticul hydration ]cycl below which proteins do not function. Those facts indicatc that the dynamics of water play an impertant rote for proteins to function. However its underlyillg molecular mechanism has not been clarified yet. To understand it, it is vital to understand the role ofwater molecule for protcins to change their conformations, since the function of the proteins can be understood as the consecutive collfoirnation changes ofthe proteins triggered by the external stimuli.In order to understand the mechanism, we do molecu]ar dynamics simu]ation ofa peptide. Met-Enkephalin, -'hich consists of 5 am{no acids, in explicit -,ater solvent. The conformation changes of the peptide can be classificd into thc foTlewing two cases. One is water assisting. that is, the surrounding water performs ma.ior mechanical work for the peptide to change its conformation. The other is water hindering, that is, the water prevents peptide from changing its conformation, The di fference between the two can be understood in tenns or thc cooperative behavior of the vL'ater. We extract the cooperative bchafoior from density, moinentum and encrgy density of the water by us{ng ouT coarse-grained mcthod, GAIO extended to non-stationary dynamical system due to Froyland. 2C1412Kengo Nishiumi Uniu, ?Fae. fftevetYV-71FFMEtzLOVI-LOV2iflfiSpt(YO veMreRMPhoto-induced strvctural change of the blue-light sensor photetropin "LOVI-LOV2 Demain" 'i, Tilo Mathes2, Masahide TerazimaL (LGi'ad. Sch. Sci., K}'oto Sei.,ve) Phototropin is a blue-light sensor protein which exists in plants and rcgulates phototropism or stomal opening and so on.Thc N-tennina] photosensory domain of the phototropins contains two very similar domains of 1 1O amino acids designatcd LOVI and LOV2. These domains bind the cot'actor fiavin mononucleotide (FMN) and act as b]ue-light sensors. For understanding the functional mechanism of the fu11-lengLh photorepin, the photochemistry ofthe LOV2 domain has been extensively studied, because this LOV2 demain is thought to play an important rolc in regulating photetropin activity. A next logieal step could be revealing the photochemistry of the extended domain "LOVl-LOV2 tandem". In this study, we used the LOVl-LOV2 tandem fromChlamydomonas reinhardtii, --34kDa and the transient grating (TG) method for this purpose. The LOV1 domain ofthe tandem was inactivated by mutation of the reactive cysteine 57 to serine to prevcnt ovcrcrowding or the spectra, The TG signal after the photoexcitation showed a typical `'LOV2 signal"rthe fonnation of cysteine adduct (--2 ps) and the thermal grating signa]. However, after the thermal grating. the behavior was different from that of the LOV2 domahi reaction. The signal consists ofseveral phascs ofprotein difTLision. One of sigiiificant diffbrences is the diffl!sion Tate of this protein. The rate is much slower than that of LOV2. This is thought to be caused by the fo"nation of higher aggregates {larger...

Free energy scale is essential for understanding membrane protein folding and for predicting membrane protein structures. Hydrophobicity scales for membrane proteins have been measured experimentally in lipid bilayer and biological membrane. However, they were based on measurement of model peptides. Recently, a new biological scale of water-to-bilayer transfer free energy of 20 amino acids was obtained by measurement in the context of a native b-barrel transmembrane protein OmpLA [Moon and Fleming, 2011]. Here we report results on computational transfer free energy. It is based on an energy function composed of three terms, single-body burial, inter-strand interaction and sequential nearest neighbor contact interaction. Using a mechanics and statistical model, we have computed the full partition function of OmpLA and the transfer free energy of residues. The computed result of free energy scale of 19 amino acid residues correlates well with experimental data (r2 >0.80). In addition, our results indicate that free energy changes are context dependant. Our computational results also show that the occurrence of Arg is depth dependant and is not be overly costly.