Kunihiro Kuwajima

Hydrogen-exchange behavior of the L20A mutant of the protein A B domain in guanidinium chloride: evidence for persistent native-like contacts

Seiichiro Hayashi, Saeko Yanaka, Maho Yagi‐Utsumi, Yukiko Isono et autres

Residual structure in unfolded proteins plays a crucial role in directing folding pathways. Here, we examined the unfolded state of the B domain of staphylococcal protein A carrying the L20A mutation, which disrupts native hydrophobic contacts between Leu20 and helix H3 (residues …

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The Folding Problem and the Random-coil Theory of Proteins

Kunihiro Kuwajima

談 話 室 リレーエッセイ：シン・私が影響を受けた論文(7) 蛋白質のフォールディング問題と

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The B domain of protein A retains residual structures in 6 M guanidinium chloride as revealed by hydrogen/deuterium‐exchange NMR spectroscopy

Saeko Yanaka, Maho Yagi‐Utsumi, Koichi Kato, Kunihiro Kuwajima

The characterization of residual structures persistent in unfolded proteins is an important issue in studies of protein folding, because the residual structures present, if any, may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the residual …

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DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science

Kunihiro Kuwajima, Maho Yagi‐Utsumi, Saeko Yanaka, Koichi Kato

Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy has been widely used for studying the structure, stability, and dynamics of proteins. When we apply the H/D-exchange method to investigate non-native states of proteins such as equilibrium and kinetic folding intermediates, H/D-exchange …

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Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR

Maho Yagi‐Utsumi, Mahesh S. Chandak, Saeko Yanaka, Methanee Hiranyakorn et autres

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The Molten Globule, and Two-State vs. Non-Two-State Folding of Globular Proteins

Kunihiro Kuwajima

From experimental studies of protein folding, it is now clear that there are two types of folding behavior, i.e., two-state folding and non-two-state folding, and understanding the relationships between these apparently different folding behaviors is essential for fully elucidating the molecular mechanisms …

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The Molten Globule, and Two-State vs. Non-Two-State Folding of Globular Proteins

Kunihiro Kuwajima

From experimental studies of protein folding, it is now clear that there are two types of folding behavior, i.e., two-state folding and non-two-state folding, and understanding the relationships between these apparently different folding behaviors is essential for fully elucidating the molecular mechanisms …

kr, jp (code pays fourni par la source)

Exploring the Folding Mechanism of Small Proteins GB1 and LB1

Qianyi Cheng, InSuk Joung, Juyong Lee, Kunihiro Kuwajima

The computational atomistic description of the folding reactions of the B1 domains, GB1 and LB1, of protein G and protein L, respectively, is an important challenge in current protein folding studies. Although the two proteins have overall very similar backbone structures (β-hairpin-α-helix-β-hairpin), …

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Determination of the structural ensemble of the molten globule state of a protein by computer simulations

Masahiro Shimizu, Yukihito Kajikawa, Kunihiro Kuwajima, Christopher Martin Dobson et autres

We have used computer simulations to investigate the structural nature of the molten globule (MG) state of canine milk lysozyme. To sample the conformational space efficiently, we performed replica-exchange umbrella sampling simulations with the radius of gyration as a reaction coordinate. We …

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PFDB: A standardized protein folding database with temperature correction

Balachandran Manavalan, Kunihiro Kuwajima, Jooyoung Lee

We constructed a standardized protein folding kinetics database (PFDB) in which the logarithmic rate constants of all listed proteins are calculated at the standard temperature (25 °C). A temperature correction based on the Eyring-Kramers equation was introduced for proteins whose folding kinetics …

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Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR

Mahesh S. Chandak, Takashi Nakamura, Maho Yagi‐Utsumi, Tomoko Yamaguchi et autres

Abstract The characterization of residual structures persistent in unfolded proteins in concentrated denaturant solution is currently an important issue in studies of protein folding, because the residual structure present, if any, in the unfolded state may form a folding initiation site and …

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An Overlapping Region between the Two Terminal Folding Units of the Outer Surface Protein A (OspA) Controls Its Folding Behavior

Koki Makabe, Takashi Nakamura, Debanjan Dhar, Teikichi Ikura et autres

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