%0 Journal Article %J Nucleic Acids Research %D 2011 %T BSDB: the biomolecule stretching database. %A Sikora, Mateusz %A Joanna I. Sulkowska %A Witkowski, Bartlomiej S %A Cieplak, Marek %K Biomechanical Phenomena %K Databases, Protein %K Models, Chemical %K Molecular Dynamics Simulation %K Protein Structure, Secondary %K Proteins %X We describe the Biomolecule Stretching Data Base that has been recently set up at http://www.ifpan.edu.pl/BSDB/. It provides information about mechanostability of proteins. Its core is based on simulations of stretching of 17 134 proteins within a structure-based model. The primary information is about the heights of the maximal force peaks, the force-displacement patterns, and the sequencing of the contact-rupturing events. We also summarize the possible types of the mechanical clamps, i.e. the motifs which are responsible for a protein's resistance to stretching. %B Nucleic Acids Research %V 39 %P D443-50 %8 2011 Jan %G eng %N Database issue %R 10.1093/nar/gkq851 %0 Journal Article %J Journal of the American Chemical Society %D 2010 %T Untying knots in proteins. %A Joanna I. Sulkowska %A Sułkowski, Piotr %A Szymczak, Piotr %A Cieplak, Marek %K Amino Acids %K Protein Conformation %K Proteins %X A shoelace can be readily untied by pulling its ends rather than its loops. Attempting to untie a native knot in a protein can also succeed or fail depending on where one pulls. However, thermal fluctuations induced by the surrounding water affect conformations stochastically and may add to the uncertainty of the outcome. When the protein is pulled by the termini, the knot can only get tightened, and any attempt at untying results in failure. We show that, by pulling specific amino acids, one may easily retract a terminal segment of the backbone from the knotting loop and untangle the knot. At still other amino acids, the outcome of pulling can go either way. We study the dependence of the untying probability on the way the protein is grasped, the pulling speed, and the temperature. Elucidation of the mechanisms underlying this dependence is critical for a successful experimental realization of protein knot untying. %B Journal of the American Chemical Society %V 132 %P 13954-6 %8 2010 Oct 13 %G eng %N 40 %R 10.1021/ja102441z %0 Journal Article %J PLoS Comput Biol %D 2009 %T Mechanical strength of 17,134 model proteins and cysteine slipknots. %A Sikora, Mateusz %A Joanna I. Sulkowska %A Cieplak, Marek %K Amino Acids %K Cysteine %K elasticity %K Humans %K Models, Molecular %K Molecular Dynamics Simulation %K Protein Folding %K Proteins %K Tensile Strength %X A new theoretical survey of proteins' resistance to constant speed stretching is performed for a set of 17,134 proteins as described by a structure-based model. The proteins selected have no gaps in their structure determination and consist of no more than 250 amino acids. Our previous studies have dealt with 7510 proteins of no more than 150 amino acids. The proteins are ranked according to the strength of the resistance. Most of the predicted top-strength proteins have not yet been studied experimentally. Architectures and folds which are likely to yield large forces are identified. New types of potent force clamps are discovered. They involve disulphide bridges and, in particular, cysteine slipknots. An effective energy parameter of the model is estimated by comparing the theoretical data on characteristic forces to the corresponding experimental values combined with an extrapolation of the theoretical data to the experimental pulling speeds. These studies provide guidance for future experiments on single molecule manipulation and should lead to selection of proteins for applications. A new class of proteins, involving cysteine slipknots, is identified as one that is expected to lead to the strongest force clamps known. This class is characterized through molecular dynamics simulations. %B PLoS Comput Biol %V 5 %P e1000547 %8 2009 Oct %G eng %N 10 %R 10.1371/journal.pcbi.1000547 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2009 %T On the remarkable mechanostability of scaffoldins and the mechanical clamp motif. %A Valbuena, Alejandro %A Oroz, Javier %A Hervás, Rubén %A Vera, Andrés Manuel %A Rodríguez, David %A Menéndez, Margarita %A Joanna I. Sulkowska %A Cieplak, Marek %A Carrión-Vázquez, Mariano %K Amino Acid Motifs %K Biotechnology %K Cellulose %K Clostridium thermocellum %K Computer Simulation %K Databases, Protein %K Kinetics %K Microscopy, Atomic Force %K Nanotechnology %K Protein Conformation %K Protein Engineering %K Protein Folding %K Protein Structure, Secondary %K Proteins %K Stress, Mechanical %X Protein mechanostability is a fundamental biological property that can only be measured by single-molecule manipulation techniques. Such studies have unveiled a variety of highly mechanostable modules (mainly of the Ig-like, beta-sandwich type) in modular proteins subjected to mechanical stress from the cytoskeleton and the metazoan cell-cell interface. Their mechanostability is often attributed to a "mechanical clamp" of secondary structure (a patch of backbone hydrogen bonds) fastening their ends. Here we investigate the nanomechanics of scaffoldins, an important family of scaffolding proteins that assembles a variety of cellulases into the so-called cellulosome, a microbial extracellular nanomachine for cellulose adhesion and degradation. These proteins anchor the microbial cell to cellulose substrates, which makes their connecting region likely to be subjected to mechanical stress. By using single-molecule force spectroscopy based on atomic force microscopy, polyprotein engineering, and computer simulations, here we show that the cohesin I modules from the connecting region of cellulosome scaffoldins are the most robust mechanical proteins studied experimentally or predicted from the entire Protein Data Bank. The mechanostability of the cohesin modules studied correlates well with their mechanical kinetic stability but not with their thermal stability, and it is well predicted by computer simulations, even coarse-grained. This extraordinary mechanical stability is attributed to 2 mechanical clamps in tandem. Our findings provide the current upper limit of protein mechanostability and establish shear mechanical clamps as a general structural/functional motif widespread in proteins putatively subjected to mechanical stress. These data have important implications for the scaffoldin physiology and for protein design in biotechnology and nanotechnology. %B Proceedings of the National Academy of Sciences of the United States of America %V 106 %P 13791-6 %8 2009 Aug 18 %G eng %N 33 %R 10.1073/pnas.0813093106 %0 Journal Article %J ACTA PHYSICA POLONICA A %D 2009 %T Tests of the Structure-Based Models of Proteins %A Cieplak, Marek %A Joanna I. Sulkowska %X The structure-based models of proteins are deØned through the condition that their ground state coincides with the native structure of the proteins. There are many variants of such models and they yield different properties. Optimal variants can be selected by making comparisons to experimental data on single-molecule stretching. Here, we discuss the 15 best performing variants and focus on Øne tuning the selection process by adjusting the velocity of stretching to match the experimental conditions. The very best variant is found to correspond to the 10-12 potential in the native contacts with the energies modulated by the Miyazawa{Jernigan statistical potential and variable length parameters. The second best model incorporates the Lennard{Jones potential with uniform amplitudes. We then make a detailed comparison of the two models in which theoretical surveys of stretching properties of 7510 proteins were made previously. %B ACTA PHYSICA POLONICA A %V 115 %G eng %N 2 %& 441 %0 Journal Article %J Proteins %D 2008 %T Predicting the order in which contacts are broken during single molecule protein stretching experiments. %A Joanna I. Sulkowska %A Kloczkowski, Andrzej %A Sen, Taner Z %A Cieplak, Marek %A Jernigan, Robert L %K Green Fluorescent Proteins %K Models, Chemical %K Protein Denaturation %K Proteins %K Tensile Strength %X We combine two methods to enable the prediction of the order in which contacts are broken under external stretching forces in single molecule experiments. These two methods are Gō-like models and elastic network models. The Gō-like models have shown remarkable success in representing many aspects of protein behavior, including the reproduction of experimental data obtained from atomic force microscopy. The simple elastic network models are often used successfully to predict the fluctuations of residues around their mean positions, comparing favorably with the experimentally measured crystallographic B-factors. The behavior of biomolecules under external forces has been demonstrated to depend principally on their elastic properties and the overall shape of their structure. We have studied in detail the muscle protein titin and green fluorescent protein and tested for ten other proteins. First, we stretch the proteins computationally by performing stochastic dynamics simulations with the Gō-like model. We obtain the force-displacement curves and unfolding scenarios of possible mechanical unfolding. We then use the elastic network model to calculate temperature factors (B-factors) and compare the slowest modes of motion for the stretched proteins and compare them with the predicted order of breaking contacts between residues in the Gō-like model. Our results show that a simple Gaussian network model is able to predict contacts that break in the next time stage of stretching. Additionally, we have found that the contact disruption is strictly correlated with the highest force exerted by the backbone on these residues. Our prediction of bond-breaking agrees well with the unfolding scenario obtained with the Gō-like model. We anticipate that this method will be a useful new tool for interpreting stretching experiments. %B Proteins %V 71 %P 45-60 %8 2008 Apr %G eng %N 1 %R 10.1002/prot.21652 %0 Journal Article %J Biophys J %D 2008 %T Selection of optimal variants of Gō-like models of proteins through studies of stretching. %A Joanna I. Sulkowska %A Cieplak, Marek %K Analysis of Variance %K Biomechanical Phenomena %K Models, Molecular %K Protein Conformation %K Protein Folding %K Proteins %K Reproducibility of Results %K Temperature %K Thermodynamics %X The Gō-like models of proteins are constructed based on the knowledge of the native conformation. However, there are many possible choices of a Hamiltonian for which the ground state coincides with the native state. Here, we propose to use experimental data on protein stretching to determine what choices are most adequate physically. This criterion is motivated by the fact that stretching processes usually start with the native structure, in the vicinity of which the Gō-like models should work the best. Our selection procedure is applied to 62 different versions of the Gō model and is based on 28 proteins. We consider different potentials, contact maps, local stiffness energies, and energy scales--uniform and nonuniform. In the latter case, the strength of the nonuniformity was governed either by specificity or by properties related to positioning of the side groups. Among them is the simplest variant: uniform couplings with no i, i + 2 contacts. This choice also leads to good folding properties in most cases. We elucidate relationship between the local stiffness described by a potential which involves local chirality and the one which involves dihedral and bond angles. The latter stiffness improves folding but there is little difference between them when it comes to stretching. %B Biophys J %V 95 %P 3174-91 %8 2008 Oct %G eng %N 7 %R 10.1529/biophysj.107.127233 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2008 %T Stabilizing effect of knots on proteins. %A Joanna I. Sulkowska %A Sulkowski, Piotr %A Szymczak, P %A Cieplak, Marek %K Computer Simulation %K Disulfides %K Hot Temperature %K Humans %K Models, Chemical %K Ornithine Carbamoyltransferase %K Protein Folding %K Protein Structure, Secondary %K Stress, Mechanical %X Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot. %B Proceedings of the National Academy of Sciences of the United States of America %V 105 %P 19714-9 %8 2008 Dec 16 %G eng %N 50 %R 10.1073/pnas.0805468105 %0 Journal Article %J Biophys J %D 2008 %T Stretching to understand proteins - a survey of the protein data bank. %A Joanna I. Sulkowska %A Cieplak, Marek %K Computer Simulation %K Databases, Protein %K elasticity %K Models, Chemical %K Models, Molecular %K Proteins %K Sequence Analysis, Protein %K Stress, Mechanical %K Structure-Activity Relationship %X We make a survey of resistance of 7510 proteins to mechanical stretching at constant speed as studied within a coarse-grained molecular dynamics model. We correlate the maximum force of resistance with the native structure, predict proteins which should be especially strong, and identify the nature of their force clamps. %B Biophys J %V 94 %P 6-13 %8 2008 Jan 1 %G eng %N 1 %R 10.1529/biophysj.107.105973 %0 Journal Article %J Phys Rev Lett %D 2008 %T Tightening of knots in proteins. %A Joanna I. Sulkowska %A Sułkowski, Piotr %A Szymczak, P %A Cieplak, Marek %K Algorithms %K Diffusion %K Models, Molecular %K Protein Conformation %K Solvents %K Stochastic Processes %K Temperature %X We perform theoretical studies of stretching of 20 proteins with knots within a coarse-grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns, whereas in homopolymers they diffuse around and eventually slide off. The waiting times of the jumps are increasingly stochastic as the temperature is raised. Knots typically do not return to their native locations when a protein is released after stretching. %B Phys Rev Lett %V 100 %P 058106 %8 2008 Feb 8 %G eng %N 5 %0 Journal Article %J Journal of Physics: Condensed Matter %D 2007 %T Mechanical stretching of proteins—a theoretical survey of the Protein Data Bank %A Joanna I. Sulkowska %A Cieplak, Marek %X The mechanical stretching of single proteins has been studied experimentally for about 50 proteins, yielding a variety of force patterns and peak forces. Here we perform a theoretical survey of proteins of known native structure and map out the landscape of possible dynamical behaviours under stretching at constant speed. We consider 7510 proteins comprising not more than 150 amino acids and 239 longer proteins. The model used is constructed based on the native geometry. It is solved by methods of molecular dynamics and validated by comparing the theoretical predictions to experimental results. We characterize the distribution of peak forces and investigate correlations with the system size and with the structure classification as characterized by the CATH scheme. Despite the presence of such correlations, proteins with the same CATH index may belong to different classes of dynamical behaviour. We identify proteins with the biggest forces and show that they belong to few topology classes. We determine which protein segments act as mechanical clamps and show that, in most cases, they correspond to long stretches of parallel β-strands, but other mechanisms are also possible. %B Journal of Physics: Condensed Matter %V 19 %G eng %N 283201 %R 10.1088/0953-8984/19/28/283201 %0 Journal Article %J J Chem Phys %D 2005 %T Thermal unfolding of proteins. %A Cieplak, Marek %A Joanna I. Sulkowska %K Chemistry, Physical %K Computer Simulation %K Connectin %K Kinetics %K Models, Molecular %K Molecular Conformation %K Muscle Proteins %K Protein Conformation %K Protein Denaturation %K Protein Folding %K Protein Kinases %K Protein Structure, Secondary %K Proteins %K Temperature %K Time Factors %X Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature, contacts break at separate time scales and unfolding proceeds approximately in a way reverse to folding. Features in these scenarios agree with experiments and atomic simulations on titin. %B J Chem Phys %V 123 %P 194908 %8 2005 Nov 15 %G eng %N 19 %R 10.1063/1.2121668