Spin Physics

We review recent experimental and theoretical progress in spin physics, as presented in the spin parallel session of DIS2006. In particular, we discuss the status of the nucleon spin structure, transverse polarized asymmetries, and recent developments such as DVCS, polarized fragmentation and polarized resummation.Comment: 14 pages, 10 figures, latex with ws-procs9x6.cls (included), convenors' summary of the spin working group at DIS2006 (Tsukuba, Japan

X-ray solution scattering studies of protein folding

Protein folding is a reaction in which an extended polypeptide chain acquires maximal packing through formation of secondary and tertiary structures. Compactness and shape are, therefore, critical properties characterizing the process of protein folding. Because the stability of the native state is determined by the subtle free energy balance between the native and denatured states, the characterization of the denatured state is also essential to understand the conformational stability of the native state. We show that solution X-ray scattering is the best technique available today to address these problems. Although the structural resolution of the unfolded or compact denatured states elucidated from solution X-ray scattering is low, it provides a variety of information complementary to that obtained by NMR or X-ray crystallography

Special Lagrangian fibrations, Berkovich retraction, and crystallographic groups

We explicitly construct special Lagrangian fibrations on finite quotients of maximally degenerating abelian varieties, glue with Berkovich retraction in non-Archimedean geometry by using "hybrid" technique. We also study their symmetries explicitly which can be regarded as crystallographic groups. In particular, a conjecture of Kontsevich-Soibelman is solved at an enhanced level for finite quotients of abelian varieties in any dimension.Comment: 30 pages, v2: added an appendix which discusses a certain limiting process of CY metrics to non-Archimedean CY metric and corrected some typos, v3: corrected some typos and minor mathematical error

Protein folding: could hydrophobic collapse be coupled with hydrogen-bond formation?

AbstractA judicious examination of an exhaustive PDB sample of soluble globular proteins of moderate size (N<102) reveals a commensurable relationship between hydrophobic surface burial and number of backbone hydrogen bonds. An analysis of 50 000 conformations along the longest all-atom MD trajectory allows us to infer that not only the hydrophobic collapse is concurrent with the formation of backbone amide-carbonyl hydrogen bonds, they are also dynamically coupled processes. In statistical terms, hydrophobic clustering of the side chains is inevitably conducive to backbone burial and the latter process becomes thermodynamically too costly and kinetically unfeasible without amide-carbonyl hydrogen-bond formation. Furthermore, the desolvation of most hydrogen bonds is exhaustive along the pathway, implying that such bonds guide the collapse process

A new look at an old view of denaturant induced protein unfolding

We re-examine a site-binding approach independently proposed by Schellman (Schellman, J.A. (1958) Compt. rend. Lab. Carlsberg Ser. Chim. 30, 439-449) and Aune and Tanford (Aune, K.C. and Tanford, D. (1969) Biochemistry, 8, 4586-4590) for explicitly including the denaturant concentration within the protein unfolding equilibrium. We extend and formalize the approach through development of a multi-dimensional analytical model in which the folding reaction coordinate is defined by the number of denaturant molecules bound to sites located on either the initially folded, or unfolded, states of the protein. We use the developed method to re-examine the mechanistic determinants underlying the sigmoidal shape of the unfolding transition. A natural feature of our method is that it presents a landscape picture of the denaturant induced protein unfolding reaction

Interaction of β-lactoglobulin with chaperonin GroEL

Sakai, Kazuko, Hoshino, Masaru and Goto, Yuji "Interaction of β-lactoglobulin with chaperonin GroEL", Proceedings of the Indian National Science Academy, 68, 4A, 341-347, Indian National Science Academy, 200