TY - JOUR A1 - Tolan, Dean R. A1 - Schuler, Benjamin A1 - Beernink, Peter T. A1 - Jaenicke, Rainer T1 - Thermodynamic analysis of the dissociation of the aldolase tetramer substituted at one or both of the subunit interfaces N2 - The fructose-1,6-bis(phosphate) aldolase isologous tetramer tightly associates through two different subunit interfaces defined by its 222 symmetry. Both single- and double-interfacial mutant aldolases have a destabilized quaternary structure, but there is little effect on the catalytic activity. These enzymes are however thermolabile. This study demonstrates the temperature-dependent dissociation of the mutant enzymes and determines the dissociation free energies of both mutant and native aldolase. Subunit dissociation is measured by sedimentation equilibrium in the analytical ultracentrifuge. At 25C the tetramerdimer dissociation constants for each single-mutant enzyme are similar, about 10 -6 M. For the double-mutant enzyme, sedimentation velocity experiments on sucrose density gradients support a tetramermonomer equilibrium. Furthermore, sedimentation equilibrium experiments determined a dissociation constant of 10- 15 M3 for the double-mutant enzyme. By the same methods the upper limit for the dissociation constant of wild-type aldolase A is approximately 10-28 M3, which indicates an extremely stable tetramer. The thermodynamic values describing monomer-tetramer and dimer-tetramer equilibria are analyzed with regard to possible cooperative interaction between the two subunit interfaces. Y1 - 2003 UR - http://www.reference-global.com/doi/abs/10.1515/BC.2003.162 ER - TY - JOUR A1 - Schuler, Benjamin A1 - Seckler, Robert T1 - P22 tailspike folding mutants revisited : effects on thermodynamic stability of the isolated beta-helix domain Y1 - 1998 ER - TY - JOUR A1 - Schuler, Benjamin A1 - Rachel, Reinhard A1 - Seckler, Robert T1 - Formation of fibrous aggregates from a non-native intermediate : the isolated P22 tailspike -helix domain Y1 - 1999 ER - TY - GEN A1 - Schuler, Benjamin A1 - Lipman, Everett A. A1 - Steinbach, Peter J. A1 - Kumke, Michael Uwe A1 - Eaton, William A. T1 - Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence N2 - To determine whether Förster resonance energy transfer (FRET) measurements can provide quantitative distance information in single-molecule fluorescence experiments on polypeptides, we measured FRET efficiency distributions for donor and acceptor dyes attached to the ends of freely diffusing polyproline molecules of various lengths. The observed mean FRET efficiencies agree with those determined from ensemble lifetime measurements but differ considerably from the values expected from Förster theory, with polyproline treated as a rigid rod. At donor–acceptor distances much less than the Förster radius R0, the observed efficiencies are lower than predicted, whereas at distances comparable to and greater than R0, they are much higher. Two possible contributions to the former are incomplete orientational averaging during the donor lifetime and, because of the large size of the dyes, breakdown of the point-dipole approximation assumed in Förster theory. End-to-end distance distributions and correlation times obtained from Langevin molecular dynamics simulations suggest that the differences for the longer polyproline peptides can be explained by chain bending, which considerably shortens the donor–acceptor distances. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 008 KW - Förster resonance energy transfer KW - molecular dynamics KW - polypeptide KW - FRET Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-12229 ER - TY - JOUR A1 - Schuler, Benjamin A1 - Lipman, Everett A. A1 - Steinbach, P. J. A1 - Kumke, Michael Uwe A1 - Eaton, W. A. T1 - Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence N2 - To determine whether Forster resonance energy transfer (FRET) measurements can provide quantitative distance information in single-molecule fluorescence experiments on polypeptides, we measured FRET efficiency distributions for donor and acceptor dyes attached to the ends of freely diffusing polyproline molecules of various lengths. The observed mean FRET efficiencies agree with those determined from ensemble lifetime measurements but differ considerably from the values expected from Forster theory, with polyproline treated as a rigid rod. At donor-acceptor distances much less than the Forster radius R-o, the observed efficiencies are lower than predicted, whereas at distances comparable to and greater than R-0, they are much higher. Two possible contributions to the former are incomplete orientational averaging during the donor lifetime and, because of the large size of the dyes, breakdown of the point-dipole approximation assumed in Forster theory. End-to-end distance distributions and correlation times obtained from Langevin molecular dynamics simulations suggest that the differences for the longer polyproline peptides can be explained by chain bending, which considerably shortens the donor-acceptor distances Y1 - 2005 SN - 0027-8424 ER - TY - JOUR A1 - Schuler, Benjamin A1 - Fürst, Frank A1 - Osterroth, Frank A1 - Steinbacher, Stefan A1 - Huber, Robert A1 - Seckler, Robert T1 - Plasticity and steric strain in a parallel beta-helix: Rational mutations in P22 tailspike protein N2 - By means of genetic screens, a great number of mutations that affect the folding and stability of the tailspike protein from Salmonella phage P22 have been identified. Temperature-sensitive folding (tsf) mutations decrease folding yields at high temperature, but hardly affect thermal stability of the native trimeric structure when assembled at low temperature. Global suppressor (su) mutations mitigate this phenotype. Virtually all of these mutations are located in the central domain of tailspike, a large parallel beta-helix. We modified tailspike by rational single amino acid replacements at three sites in order to investigate the influence of mutations of two types: (1) mutations expected to cause a tsf phenotype by increasing the side-chain volume of a core residue, and (2) mutations in a similar structural context as two of the four known su mutations, which have been suggested to stabilize folding intermediates and the native structure by the release of backbone strain, an effect well known for residues that are primarily evolved for function and not for stability or folding of the protein. Analysis of folding yields, refolding kinetics and thermal denaturation kinetics in vitro show that the tsf phenotype can indeed be produced rationally by increasing the volume of side chains in the beta-helix core. The high-resolution crystal structure of mutant T326F proves that structural rearrangements only take place in the remarkably plastic lumen of the beta-helix, leaving the arrangement of the hydrogen-bonded backbone and thus the surface of the protein unaffected. This supports the notion that changes in the stability of an intermediate, in which the beta-helix domain is largely formed, are the essential mechanism by which tsf mutations affect tailspike folding. A rational design of su mutants, on the other hand, appears to be more difficult. The exchange of two residues in the active site expected to lead to a drastic release of steric strain neither enhanced the folding properties nor the stability of tailspike. Apparently, side-chain interactions in these cases overcompensate for backbone strain, illustrating the extreme optimization of the tailspike protein for conformational stability. The result exemplifies the view arising from the statistical analysis of the distribution of backbone dihedral angles in known three-dimensional protein structures that the adoption of straight phi/psi angles other than the most favorable ones is often caused by side-chain interactions. Y1 - 2000 UR - http://www3.interscience.wiley.com/cgi-bin/abstract/71001984/START ER - TY - JOUR A1 - Rhoades, E. A1 - Cohen, M. A1 - Gussakovsky, E. A1 - Schuler, Benjamin A1 - Haran, G. T1 - Single molecule protein folding Y1 - 2004 SN - 0006-3495 ER - TY - JOUR A1 - Nettels, Daniel A1 - Müller-Späth, Sonja A1 - Küster, Frank A1 - Hofmann, Hagen A1 - Haenni, Domminik A1 - Rüegger, Stefan A1 - Reymond, Luc A1 - Hoffmann, Armin S. A1 - Kubelka, Jan A1 - Heinz, Benjamin A1 - Gast, Klaus A1 - Best, Robert B. A1 - Schuler, Benjamin T1 - Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins N2 - We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With singlemolecule FRET, this question can be addressed even under nearnative conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperaturedependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse. Y1 - 2009 UR - http://www.pnas.org/content/106/49/20740.full.pdf+html SN - 0027-8424 ER - TY - JOUR A1 - Miller, Stefan A1 - Schuler, Benjamin A1 - Seckler, Robert T1 - Phages P22 tailspike protein: Removal of head-binding domain unmasks efects of folding mutations on native- state thermal stability Y1 - 1998 ER - TY - JOUR A1 - Miller, Stefan A1 - Schuler, Benjamin A1 - Seckler, Robert T1 - A reversibly unfolding fragment of P22 tailspike protein with native structure : the isolated beta-helix domain Y1 - 1998 ER -