[...]... from Bacillus subtilis (Schindelin et al., 1993); (b) 2PTL: an immunoglobulin light chain-binding domain of protein L, (Wikström et al., 1995); (c) 1NYF: SH3 domain from fyn proto-oncogene tyrosine kinase (Morton et al., 1996); (d) 2AIT: α-amylase inhibitor tendamistat, (Kline et al., 1988); (e) 1FNF: fragment of human fibronectin encompassing type-III (Leahy et al., 1992) Coordinates are from the Brookhaven... 1HDN: histidine-containing phosphocarrier protein, (van Nuland et al., 1994); (b) 1PBA: activation domain from porcine procarboxypeptidase B, (Vendrell et al., 1991); (c) 1PGB: B1 immunoglobulin-binding domain of streptococcal protein G (Gallagher et al., 1994); (d) 1UBQ: human erythrocytes ubiquitin, (Vijay-Kumar et al., 1987); (e) 1URN: RNA-binding domain of the U1A spliceosomal protein complexed... protein with further correctly folded protein molecules (c) catalyzes further misfolding (d, e) In soluble proteins, hydrophilic sidechains (that of aspartic acid, glutamic acid, lysine, arginine, asparagine, glutamine) have a higher preference for a location at the surface Hydrophobic sidechains (that of alanine, valine, leucine, isoleucine, phenylalanine, tryptophan) are preferentially located inside... acyl-coenzyme A binding protein (b) hemoglobin A (d) myoglobin (e) viral capsid protein domain (g) fumarate reductase respiratory complex 1.1 Structure of the native state (a) cold shock protein (c) SH3 domain 7 (b) domain of protein L (d) tendamistat (e) fibronectin fragment Fig 1.7 Examples of proteins with mainly sheet-shaped secondary structure (a) 1CSP: major cold shock protein (CSPB) from Bacillus... microsecond (10–6 s) small angle X-ray scattering spectral domain optical coherence tomography scanning ion conductance microscope scanning near-field optical microscope scanning probe microscope single-stranded DNA scanning transmission electron microscope scanning thermal microscope scanning tunneling microscope transmission electron microscope triglycine sulfate total internal reflection trinitrotoluene... References 215 Index 247 Symbols arrow indicating a process or a coordinate axis arrow pointing to a label or indicating a distance Å angström (10–10 m; 0.1 nm) AC alternating current ADC analog-to-digital converter AFM atomic force microscope ATP adenosine triphosphate BESSY (Berlin Electron Synchrotron Storage Ring) bp base pair BSA bovine serum albumin BSE bovine spongiform encephalopathy... structure and rate of folding is so important because it tells us a lot about the mechanism of protein folding and helps to solve the so-called folding paradox (see Nölting et al., 2003; Nölting, 2005) Inter-residue contacts were calculated at a cut-off distance of 4 Å, and no contacts of hydrogen atoms were included in the calculations Coordinates of the proteins and the β-hairpin were taken from the... A typical protein contains 50– 1000 amino acid residues An interesting exception is titin, a protein found in skeletal muscle, containing about 27,000 residues in a single chain The next level, the secondary structure, refers to certain common repeating structures of the backbone of the polypeptide chain There are three main types of secondary structure: helix, sheet, and turns That which cannot be... the resolution of folding transition states, see, e.g., Nölting, 2005 The structure of the folding transition Fig 1.9a Inter-residue contact map for the main folding transition state of the monomeric protein src SH3 domain (Nölting and Andert, 2000) The sizes and fillings of the circles indicate the magnitudes of structural consolidation, measured by the so-called Φ-value (Nölting, 2005) The diagonal... proteins provide evidence for a nucleation-condensation mechanism of folding in which structure growth starts with the formation of a diffuse folding nucleus which catalyzes further structure formation (Nölting, 2005; Chap 11) Fig 1.9b Inter-residue contact map for the main folding transition state of chymotrypsin inhibitor 2 (CI2) (Nölting and Andert, 2000) The sizes and fillings of the circles indicate . 30 D-13187 Berlin Germany nolting@pitb.de Library of Congress Control Number: 2005929410 ISBN-10 3-5 4 0-2 7703-X 2nd Edition Springer Berlin Heidelberg New York ISBN-13 97 8-3 -5 4 0-2 770 3-3 2nd Edition. alt="" Methods in Modern Biophysics Bengt Nölting Methods in Modern Biophysics Second Edition With 267 Figures 123 Dr. Bengt Nölting Prussian Private Institute of Technology at Berlin Am Schlosspark. amino acids see Nölting, 2005. A typical protein contains 50–1000 amino acid residues. An interesting exception is titin, a protein found in skeletal muscle, containing about 27,000 residues in