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BioSystems103 (2011) 18–26

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BioSystems

j o u r n a l h o m e p a g e:w w w.e l s e v i e r.c o m/l o c a t e/b i o s y s t e m

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Structure and dynamics of the‘protein folding code’inferred using Tlusty’s topological rate distortion approach

Rodrick Wallace

Division of Epidemiology,The New York State Psychiatric Institute,Box47,1051Riverside Dr.,New York,NY10032,United States

a r t i c l e i n f o

Article history:

Received9July2010

Received in revised form31August2010 Accepted11September2010

Keywords:

Amyloid

Catalysis

Groupoid

Information

Theory

Prion

Rate distortion

Symmetry a b s t r a c t

…… 此处隐藏2003字 ……

The basic spectrum of Fig.1for proteins having a hydrophobic core,in general,explains the necessity of the elaborate regulatory structures associated with the endoplasmic reticulum and its atten-E-mail address:wallace@pi.cpmc.columbia.edu.dant spectrum of chaperone proteins(e.g.,Scheuner and Kaufman, 2008),and the evolutionary pattern of protein sequences inferred by Goldschmidt et al.(2010).The inevitable corrosion of the cellular regulatory apparatus with age would then explain the subsequent onset of amyloid?bril and other aggregation disorders.

Most particularly,the spectrum of valleys in Fig.1characterizes a set of equivalence classes that de?nes a‘protein folding groupoid’, in the sense of Weinstein(1996).As we will argue below,both the native state and amyloid?bril have structured subdivisions, internal equivalence classes,that de?ne a nested set of groupoids. See Mathematical Appendix for a summary of standard material on groupoids.

With regard to the disjunction between‘native’and‘amyloid’protein forms,very early on,Astbury(1935)conjectured that glob-ular proteins could also have a linear state,based on pioneering X-ray studies.Chiti et al.(1999)argue that

...[P]rovided appropriate conditions are maintained over pro-longed periods of time,the formation of ordered amyloid proto?laments and?brils could be an intrinsic property of many polypeptide chains,rather than being a phenomenon limited to

a very few aberrant sequences.

Wang et al.(2008),in a an elegant series of experiments on bacterial inclusion bodies,conclude that

...[A]myloid aggregation appears to be a common property of protein segments and consequently is observed in both eukaryotes and prokaryotes...[Thus]there must be evolved

0303-2647/$–see front matter© 2010 Elsevier Ireland Ltd. All rights reserved. doi:10.1016/j.biosystems.2010.09.007