Due to the inherent complexity of the associated problems, investigations of the basic principles of protein folding and evolution are usually restricted to simplified protein models.Our group has developed methods and programs for exact and complete solving of problems typical for studies using HP-like 3D lattice protein models.Addressed tasks ...
Two groups of studies recently proved to provide insights into such intrinsic, structure-induced effects: elastic network models that permit us to visualize the cooperative changes in conformation that are most readily accessible near native state conditions, and information-theoretic approaches that elucidate the most efficient pathways of sign...
Creator:
Bahar, Ivet (University of Pittsburgh)
Created:
2008-01-15
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Motor proteins, such as kinesins and dyneins, are responsible for several fundamental transport functions inside the cell. Disruptions of these underlying mechanisms are linked to many neurodegenerative diseases such as Alzheimer's, Paraplegia and Amyotrophic Lateral Sclerosis (ALS). Impaired functionality of motor proteins, possibly caused due ...
Creator:
Bhaban, Shreyas (University of Minnesota, Twin Cities)
Created:
2015-11-20
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Many small single-domain proteins undergo cooperative, switch-likefolding/unfolding transitions with very low populations of intermediate,i.e., partially folded, conformations. The phenomenon of cooperative foldingis not readily accounted for by common notions about driving forces for folding. I will discuss how common protein chain models with ...
Creator:
Chan, Hue-Sun (University of Toronto)
Created:
2008-01-17
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
This talk (and a related poster) describes Lie-group-theoretic techniques that can be applied in the analysis and modeling of protein conformations. Three topics are covered: (1) Conformational transitions between two known end states; (2) proper normalization of helix-helix crossing angle data in the PDB; (3) models of the conformational entrop...
Creator:
Chirikjian, Gregory S. (Johns Hopkins University)
Created:
2008-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
The geometrical problem of protein folding, especially in its later stages, is composed of two types of freedom, the full torsional flexibility of loops connecting nearly rigid structural pieces (helices, beta-sheets etc), and the relative placing of such pieces. We present a method for sampling the feasible conformations of protein loops, based...
Creator:
Coutsias, Evangelos A. (University of New Mexico)
Created:
2008-01-15
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Some proteins contain locally knotted structures. Many algorithms have been developed in order to detect local knotting in protein conformations. In some cases these algorithms are used to rule out computationally generated structures containing local knots as knotted proteins are rare. However, there are several types of proteins which contain ...
Creator:
Darcy, Isabel K. (The University of Iowa)
Created:
2008-01-11
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Sequence-structure relationships in proteins are highly asymmetric sincemany sequences fold into relatively few structures. What is the number ofsequences that fold into a particular protein structure? Is it possible toswitch between stable protein folds by point mutations? To address thesequestions we compute a directed graph of sequences and s...
Creator:
Elber, Ron (The University of Texas at Austin)
Created:
2008-01-15
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Synechococcus elongatus, a single celled cyanobacterium, has a remarkably precise and robust circadian clock which has been reconstituted in vitro with just three proteins. Its simplicity makes it an ideal system for understanding dynamical functions that can arise from the kinetics of multiple phosphorylations. Recent experiments and theoretica...
Creator:
Fisher, Daniel S. (Stanford University)
Created:
2008-03-04
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Coarse master equations and diffusion models provide powerful tools to study the equilibrium and non-equilibrium properties of molecular systems. Maximum likelihood and Bayesian approaches have been used successfully to construct such models from the observed dynamics projected onto discrete and continuous low-dimensional sub-spaces. By using a ...
Creator:
Hummer, Gerhard (National Institutes of Health (NIH))
Created:
2008-01-17
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Are protein motions limited because of a higher level of cooperativity than indicated by usual potentials?Recently derived four-body coarse-grained potentials show improved performance in threading over pairwise potentials. Their apparently increased extent of cooperativity is consistent with the high level of control of motions manifested in th...
Creator:
Jernigan, Robert L. (Iowa State University)
Created:
2008-01-15
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
As the number of proteins for whicha high resolution structure is known grow, it is importantto classify them. A classification of protein structure wouldbe useful for example to derive structural signatures for the protein functions. Classification requires a measure of protein structure similarity: while there are tools available to align and ...
Creator:
Koehl, Patrice (University of California, Davis)
Created:
2008-01-11
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Efficient exploration of the configuration space of a protein is essential for its structure prediction. In this talk we will consider two recent Monte Carlo developments for such a task: (i) equi-energy (EE) sampler and (ii) fragment regrowth via energy-guided sequential sampling (FRESS). The EE sampler provides accurate estimation of the densi...
Creator:
Kou, Samuel (Harvard University)
Created:
2008-01-16
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Proteins are large macromolecules constituted by chains of amino acid residues to accomplish many biological tasks required by living organisms: catalyzing reactions, DNA replication and repair, and moving molecules around. Imagining how these protein molecules are formed (i.e. folded) into three-dimensional structures lead biologists to believe...
Creator:
Millett, Kenneth (University of California, Santa Barbara)
Created:
2019-06-19
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Recent progress in obtaining docked protein complexes will be discussed.The combination of exhaustive search, clustering and localized globaloptimization can reliably find energy minima to highly nonconvex biomolecularenergy functions. Using an energy function that adds desolvation andscreened electrostatics to classical molecular mechanics pote...
Creator:
Mitchell, Julie C. (University of Wisconsin, Madison)
Created:
2008-01-17
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Globally the energy landscape of a folding protein resembles a partially rough funnel. The local roughness of the funnel reflects transient trapping of the protein configurations in local free energy minima. The overall funnel shape of the landscape, superimposed on this roughness, arises because the interactions present in the native structure ...
Creator:
Onuchic, José Nelson (University of California, San Diego)
Created:
2008-01-17
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Classical studies show that for many proteins, the information required for specifying the tertiary structure is contained in the amino acid sequence. However, the potential complexity of this information is truly enormous, a problem that makes defining the rules for protein folding difficult through either computational or experimental methods....
Creator:
Ranganathan, Rama (UT Southwestern Medical Center)
Created:
2008-03-03
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Protein design opens new ways to probe the determinants of folding, to facilitate the study of proteins, and to arrive at novel molecules, materials and nanostructures. Recent theoretical methods for identifying the properties of amino acid sequences consistent with a desired structure and function will be discussed. Such methods address the str...
Creator:
Saven, Jeffery G. (University of Pennsylvania)
Created:
2008-01-14
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
Solved protein structures from PDB depict a static picture, but proteins are flexible. We are interested in understanding how they move near the native conformation, or between two given conformations, without resorting to heavy-duty molecular dynamics techniques. Geometric simulations focus on motions of constrained structures behaving much lik...
Creator:
Streinu, Ileana (Smith College)
Created:
2008-01-11
Contributed By:
University of Minnesota, Institute for Mathematics and its Applications.
