3P121 Cavities in protein structure : Preservation of cavity locations in a protein from different biological species

Tunneling is a ubiquitous phenomenon. Alpha particle disintegration, the Stark effect, superconductivity in thin films, field-emission, and field-ionization are examples of electron tunneling phenomena. In the scanning tunneling microscope (STM) electron tunneling is used as an imaging modality. STM images of flat surfaces show structure at the atomic level. However, STM images of large biological species deposited onto flat surfaces are disappointing. For example, unstained virus particles imaged in the STM do not resemble their TEM counterparts.It is not clear how an STM image of a biological species is formed. Most biological species are large compared to the nominal electrode separation of ∼ 1nm that is required for electron tunneling. To form an image of a biological species, the tunneling electrodes must be separated by a distance that would normally be too large for a tunneling current to be observed.

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Protein structure and interactions

Food Colloids ◽

10.1039/9781847550842-00243 ◽

2007 ◽

pp. 243-244 ◽

Cited By ~ 1

Keyword(s):

Protein Structure

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Solid-state NMR study of protein structure. Methods based on the measurement of internuclear distances

Journal de Chimie Physique ◽

10.1051/jcp/1995921751 ◽

1995 ◽

Vol 92 ◽

pp. 1751-1760 ◽

Cited By ~ 12

Author(s):

M Auger

Keyword(s):

Protein Structure ◽

Solid State ◽

Solid State Nmr ◽

Nmr Study ◽

Internuclear Distances

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Sequence Specific Dihedral Angle Distribution: Application in Protein Structure Prediction and Evaluation

Plant Tissue Culture and Biotechnology ◽

10.3329/ptcb.v19i2.5439 ◽

1970 ◽

Vol 19 (2) ◽

pp. 217-226

Author(s):

S. M. Minhaz Ud-Dean ◽

Mahdi Muhammad Moosa

Keyword(s):

Protein Structure ◽

Dihedral Angle ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Protein Structures ◽

Angle Distribution ◽

Ramachandran Plot ◽

Specific Data ◽

Specific Distribution ◽

Structure Evaluation

Protein structure prediction and evaluation is one of the major fields of computational biology. Estimation of dihedral angle can provide information about the acceptability of both theoretically predicted and experimentally determined structures. Here we report on the sequence specific dihedral angle distribution of high resolution protein structures available in PDB and have developed Sasichandran, a tool for sequence specific dihedral angle prediction and structure evaluation. This tool will allow evaluation of a protein structure in pdb format from the sequence specific distribution of Ramachandran angles. Additionally, it will allow retrieval of the most probable Ramachandran angles for a given sequence along with the sequence specific data. Key words: Torsion angle, φ-ψ distribution, sequence specific ramachandran plot, Ramasekharan, protein structure appraisal D.O.I. 10.3329/ptcb.v19i2.5439 Plant Tissue Cult. & Biotech. 19(2): 217-226, 2009 (December)

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