BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Circular dichroism (CD) is an excellent tool for rapid determination of the secondary structure and folding properties of proteins that have been obtained using recombinant techniques or purified from tissues. The most widely used applications of protein CD are to determine whether an expressed, purified protein is folded, or if a mutation affects its conformation or stability. In addition, it can be used to study protein interactions. This protocol details the basic steps of obtaining and interpreting CD data, and methods for analyzing spectra to estimate the secondary structural composition of proteins. CD has the advantage that measurements may be made on multiple samples containing < or =20 microg of proteins in physiological buffers in a few hours. However, it does not give the residue-specific information that can be obtained by x-ray crystallography or NMR.

/pdf/using-circular-dichroism-spectra-to-estimate-protein-3jces2e55y.pdf

Using circular dichroism spectra to estimate protein secondary structure

http://ctrstbio.org.uic.edu/manuals/kellybba.pdf

How to study proteins by circular dichroism

The DICHROWEB web server enables on-line analyses of circular dichroism (CD) spectroscopic data, providing calculated secondary structure content and graphical analyses comparing calculated structures and experimental data. The server is located at http://www.cryst.bbk.ac.uk/cdweb and may be accessed via a password-limited user ID, available upon completion of a registration form. The server facilitates analyses using five popular algorithms and (currently) seven different reference databases by accepting data in a user-friendly manner in a wide range of formats, including those output by both commercial CD instruments and synchrotron radiation-based circular dichroism beamlines, as well as those produced by spectral processing software packages. It produces as output calculated secondary structures, a goodness-of-fit parameter for the analyses, and tabular and graphical displays of experimental, calculated and difference spectra. The web pages associated with the server provide information on CD spectroscopic methods and terms, literature references and aids for interpreting the analysis results.

/pdf/dichroweb-an-online-server-for-protein-secondary-structure-hd7qh9hbof.pdf

DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data.

Circular dichroism (CD) spectroscopy has been a valuable method for the analysis of protein secondary structures for many years. With the advent of synchrotron radiation circular dichroism (SRCD) and improvements in instrumentation for conventional CD, lower wavelength data are obtainable and the information content of the spectra increased. In addition, new computation and bioinformatics methods have been developed and new reference databases have been created, which greatly improve and facilitate the analyses of CD spectra. This article discusses recent developments in the analysis of protein secondary structures, including features of the DICHROWEB analysis webserver.

http://people.cryst.bbk.ac.uk/~ubcg25a/biopolymers_DW.pdf

Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases

A user-friendly website for the analysis of protein secondary structures from Circular Dichroism (CD) and Synchrotron Radiation Circular Dichroism (SRCD) spectra has been created.

/pdf/dichroweb-an-interactive-website-for-the-analysis-of-protein-3en72cff4f.pdf

DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra.

The Peptaibol Database is a sequence and structure resource for the unusual class of peptides known as peptaibols. These peptides exhibit antibiotic and membrane channel-forming activities. The database includes sequence, biological source and bibliographical data for the naturally occurring peptaibols. Information is also collated for the growing number of peptaibol 3D structures determined by either crystallography or NMR spectroscopy. The database can be obtained as a whole or can be queried by name, group, sequence motif, biological origin and/or literature reference. The Peptaibol Database can be freely accessed at http://www.cryst.bbk.ac.uk/peptaibol.

http://people.cryst.bbk.ac.uk/~ubcg25a/NAR_pep.pdf

The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols.

Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically-defined spectroscopic signatures derived from proteins with known three-dimensional structures. Many proteins identified as being “Intrinsically Disordered Proteins” have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as “other”, “random coil”, “unordered”, or “disordered”. However the “other” category can also include polyproline II (PPII)-type structures, whose spectral properties have not been well-distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII-type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid-containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.2558

Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: Applications in secondary structure analyses

Lee Whitmore

Papers

DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data.

Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases

DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra.

The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols.

Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: Applications in secondary structure analyses