DEFINING alpha-HELIX GEOMETRY BY C-alpha ATOM TRACE vs (phi-psi) TORSION ANGLES: A COMPARATIVE ANALYSIS

A regular secondary structure is described by a well defined set of values for the backbone dihedral angles (phi,psi and omega) in a polypeptide chain. However in real protein structures small local variations give rise to distortions from the ideal structures, which can lead to considerable variation in higher order organization. Protein structure analysis and accurate assignment of various structural elements, especially their terminii, are important first step in protein structure prediction and design. Various algorithms are available for assigning secondary structure elements in proteins but some lacunae still exist. In this study, results of a recently developed in-house program ASSP have been compared with those from STRIDE, in identification of alpha-helical regions in both globular and membrane proteins. It is found that, while a combination of hydrogen bond patterns and backbone torsional angles (phi-psi) are generally used to define secondary structure elements, the geometry of the C-alpha atom trace by itself is sufficient to define the parameters of helical structures in proteins. It is also possible to differentiate the various helical structures by their C-alpha trace and identify the deviations occurring both at mid-positions as well as at the terminii of alpha-helices, which often lead to occurrence of 3(10) and pi-helical fragments in both globular and membrane proteins.

Top Yukawa coupling measurement with indefinite CP Higgs in e(+)e(-) -> t(t)over-bar Phi

We consider the issue of the top quark Yukawa coupling measurement in a model-independent and general case with the inclusion of CP violation in the coupling. Arguably the best process to study this coupling is the associated production of the Higgs boson along with a t (t) over bar pair in a machine like the International Linear Collider (ILC). While detailed analyses of the sensitivity of the measurement-assuming a Standard Model (SM)-like coupling is available in the context of the ILC-conclude that the coupling could be pinned down to about a 10% level with modest luminosity, our investigations show that the scenario could be different in the case of a more general coupling. The modified Lorentz structure resulting in a changed functional dependence of the cross section on the coupling, along with the difference in the cross section itself leads to considerable deviation in the sensitivity. Our studies of the ILC with center-of-mass energies of 500 GeV, 800 GeV, and 1000 GeV show that moderate CP mixing in the Higgs sector could change the sensitivity to about 20%, while it could be worsened to 75% in cases which could accommodate more dramatic changes in the coupling. Detailed considerations of the decay distributions point to a need for a relook at the analysis strategy followed for the case of the SM, such as for a model-independent analysis of the top quark Yukawa coupling measurement. This study strongly suggests that a joint analysis of the CP properties and the Yukawa coupling measurement would be the way forward at the ILC and that caution must be exercised in the measurement of the Yukawa couplings and the conclusions drawn from it.