Takada S - Search Results

1

Folding energy landscape and network dynamics of small globular proteins.

Hori N, Chikenji G, Berry RS, Takada S. Hori N, et al. Among authors: takada s. Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):73-8. doi: 10.1073/pnas.0811560106. Epub 2008 Dec 29. Proc Natl Acad Sci U S A. 2009. PMID: 19114654 Free PMC article.

2

Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: dynamics.

Kinjo AR, Takada S. Kinjo AR, et al. Among authors: takada s. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Nov;66(5 Pt 1):051902. doi: 10.1103/PhysRevE.66.051902. Epub 2002 Nov 7. Phys Rev E Stat Nonlin Soft Matter Phys. 2002. PMID: 12513518

We have presented a theoretical framework for describing equilibrium properties of proteins in crowded solutions [A. R. Kinjo and S. Takada, Phys. Rev. E (to be published)]. In the present paper, we extend the theory to describe nonequilibrium properties of proteins …

We have presented a theoretical framework for describing equilibrium properties of proteins in crowded solutions [A. R. Kinjo and S. …

3

De novo design of foldable proteins with smooth folding funnel: automated negative design and experimental verification.

Jin W, Kambara O, Sasakawa H, Tamura A, Takada S. Jin W, et al. Among authors: takada s. Structure. 2003 May;11(5):581-90. doi: 10.1016/s0969-2126(03)00075-3. Structure. 2003. PMID: 12737823 Free article.

4

How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations.

Takagi F, Koga N, Takada S. Takagi F, et al. Among authors: takada s. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11367-72. doi: 10.1073/pnas.1831920100. Epub 2003 Aug 28. Proc Natl Acad Sci U S A. 2003. PMID: 12947041 Free PMC article.

5

Optimizing physical energy functions for protein folding.

Fujitsuka Y, Takada S, Luthey-Schulten ZA, Wolynes PG. Fujitsuka Y, et al. Among authors: takada s. Proteins. 2004 Jan 1;54(1):88-103. doi: 10.1002/prot.10429. Proteins. 2004. PMID: 14705026

6

SimFold energy function for de novo protein structure prediction: consensus with Rosetta.

Fujitsuka Y, Chikenji G, Takada S. Fujitsuka Y, et al. Among authors: takada s. Proteins. 2006 Feb 1;62(2):381-98. doi: 10.1002/prot.20748. Proteins. 2006. PMID: 16294329

7

Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study.

Chikenji G, Fujitsuka Y, Takada S. Chikenji G, et al. Among authors: takada s. Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3141-6. doi: 10.1073/pnas.0508195103. Epub 2006 Feb 17. Proc Natl Acad Sci U S A. 2006. PMID: 16488978 Free PMC article.

8

Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase.

Koga N, Takada S. Koga N, et al. Among authors: takada s. Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5367-72. doi: 10.1073/pnas.0509642103. Epub 2006 Mar 27. Proc Natl Acad Sci U S A. 2006. PMID: 16567655 Free PMC article.

9

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations.

Okazaki K, Koga N, Takada S, Onuchic JN, Wolynes PG. Okazaki K, et al. Among authors: takada s. Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11844-9. doi: 10.1073/pnas.0604375103. Epub 2006 Jul 28. Proc Natl Acad Sci U S A. 2006. PMID: 16877541 Free PMC article.

10

Secondary structure provides a template for the folding of nearby polypeptides.

Kameda T, Takada S. Kameda T, et al. Among authors: takada s. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17765-70. doi: 10.1073/pnas.0602632103. Epub 2006 Nov 13. Proc Natl Acad Sci U S A. 2006. PMID: 17101976 Free PMC article.

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