-
[show abstract]
[hide abstract]
ABSTRACT: Protein-protein interactions play critical roles in biology, and computational design of interactions could be useful in a range of applications. We describe in detail a general approach to de novo design of protein interactions based on computed, energetically optimized interaction hotspots, which was recently used to produce high-affinity binders of influenza hemagglutinin. We present several alternative approaches to identify and build the key hotspot interactions within both core secondary structural elements and variable loop regions and evaluate the method's performance in natural-interface recapitulation. We show that the method generates binding surfaces that are more conformationally restricted than previous design methods, reducing opportunities for off-target interactions.
Journal of Molecular Biology 09/2011; 413(5):1047-62. · 4.00 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Many globular and natively disordered proteins can convert into amyloid fibrils. These fibrils are associated with numerous pathologies as well as with normal cellular functions, and frequently form during protein denaturation. Inhibitors of pathological amyloid fibril formation could be useful in the development of therapeutics, provided that the inhibitors were specific enough to avoid interfering with normal processes. Here we show that computer-aided, structure-based design can yield highly specific peptide inhibitors of amyloid formation. Using known atomic structures of segments of amyloid fibrils as templates, we have designed and characterized an all-D-amino-acid inhibitor of the fibril formation of the tau protein associated with Alzheimer's disease, and a non-natural L-amino-acid inhibitor of an amyloid fibril that enhances sexual transmission of human immunodeficiency virus. Our results indicate that peptides from structure-based designs can disrupt the fibril formation of full-length proteins, including those, such as tau protein, that lack fully ordered native structures. Because the inhibiting peptides have been designed on structures of dual-β-sheet 'steric zippers', the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers.
Nature 06/2011; 475(7354):96-100. · 36.28 Impact Factor
-
John Karanicolas,
Jacob E Corn,
Irwin Chen,
Lukasz A Joachimiak,
Orly Dym,
Sun H Peck,
Shira Albeck,
Tamar Unger,
Wenxin Hu,
Gaohua Liu,
Scott Delbecq,
Gaetano T Montelione,
Clint P Spiegel,
David R Liu,
David Baker
[show abstract]
[hide abstract]
ABSTRACT: The de novo design of protein-protein interfaces is a stringent test of our understanding of the principles underlying protein-protein interactions and would enable unique approaches to biological and medical challenges. Here we describe a motif-based method to computationally design protein-protein complexes with native-like interface composition and interaction density. Using this method we designed a pair of proteins, Prb and Pdar, that heterodimerize with a Kd of 130 nM, 1000-fold tighter than any previously designed de novo protein-protein complex. Directed evolution identified two point mutations that improve affinity to 180 pM. Crystal structures of an affinity-matured complex reveal binding is entirely through the designed interface residues. Surprisingly, in the in vitro evolved complex one of the partners is rotated 180° relative to the original design model, yet still maintains the central computationally designed hotspot interaction and preserves the character of many peripheral interactions. This work demonstrates that high-affinity protein interfaces can be created by designing complementary interaction surfaces on two noninteracting partners and underscores remaining challenges.
Molecular cell 03/2011; 42(2):250-60. · 14.61 Impact Factor
-
Andrew Leaver-Fay,
Michael Tyka,
Steven M Lewis,
Oliver F Lange,
James Thompson,
Ron Jacak,
Kristian Kaufman,
P Douglas Renfrew,
Colin A Smith,
Will Sheffler, [......],
Zoran Popović,
James J Havranek, John Karanicolas,
Rhiju Das,
Jens Meiler,
Tanja Kortemme,
Jeffrey J Gray,
Brian Kuhlman,
David Baker,
Philip Bradley
[show abstract]
[hide abstract]
ABSTRACT: We have recently completed a full re-architecturing of the ROSETTA molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy-to-use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as ROSETTA3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.
Methods in enzymology 01/2011; 487:545-74. · 1.90 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We present fragment assembly of RNA with full-atom refinement (FARFAR), a Rosetta framework for predicting and designing noncanonical motifs that define RNA tertiary structure. In a test set of thirty-two 6-20-nucleotide motifs, FARFAR recapitulated 50% of the experimental structures at near-atomic accuracy. Sequence redesign calculations recovered native bases at 65% of residues engaged in noncanonical interactions, and we experimentally validated mutations predicted to stabilize a signal recognition particle domain.
Nature Methods 02/2010; 7(4):291-4. · 19.28 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The computer-based design of protein-protein interactions is a rigorous test of our understanding of molecular recognition and an attractive approach for creating novel tools for cell and molecular research. Considerable attention has been placed on redesigning the affinity and specificity of naturally occurring interactions. Several studies have shown that reducing the desolvation costs for binding while preserving shape complimentarity and hydrogen bonding is an effective strategy for improving binding affinities. In favorable cases specificity has been designed by focusing only on interactions with the target protein, while in cases with closely related off-target proteins it has been necessary to explicitly disfavor unwanted binding partners. The rational design of protein-protein interactions from scratch is still an unsolved problem, but recent developments in flexible backbone design and energy functions hold promise for the future.
Current Opinion in Structural Biology 08/2009; 19(4):458-63. · 9.42 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Based on the crystal structure of the cross-beta spine formed by the peptide NNQQNY, we have developed a computational approach for identifying those segments of amyloidogenic proteins that themselves can form amyloid-like fibrils. The approach builds on experiments showing that hexapeptides are sufficient for forming amyloid-like fibrils. Each six-residue peptide of a protein of interest is mapped onto an ensemble of templates, or 3D profile, generated from the crystal structure of the peptide NNQQNY by small displacements of one of the two intermeshed beta-sheets relative to the other. The energy of each mapping of a sequence to the profile is evaluated by using ROSETTADESIGN, and the lowest energy match for a given peptide to the template library is taken as the putative prediction. If the energy of the putative prediction is lower than a threshold value, a prediction of fibril formation is made. This method can reach an accuracy of approximately 80% with a P value of approximately 10(-12) when a conservative energy threshold is used to separate peptides that form fibrils from those that do not. We see enrichment for positive predictions in a set of fibril-forming segments of amyloid proteins, and we illustrate the method with applications to proteins of interest in amyloid research.
Proceedings of the National Academy of Sciences 04/2006; 103(11):4074-8. · 9.68 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We describe the Multiscale Modeling Tools for Structural Biology (MMTSB) Tool Set (https://mmtsb.scripps.edu/software/mmtsbToolSet.html), which is a novel set of utilities and programming libraries that provide new enhanced sampling and multiscale modeling techniques for the simulation of proteins and nucleic acids. The tool set interfaces with the existing molecular modeling packages CHARMM and Amber for classical all-atom simulations, and with MONSSTER for lattice-based low-resolution conformational sampling. In addition, it adds new functionality for the integration and translation between both levels of detail. The replica exchange method is implemented to allow enhanced sampling of both the all-atom and low-resolution models. The tool set aims at applications in structural biology that involve protein or nucleic acid structure prediction, refinement, and/or extended conformational sampling. With structure prediction applications in mind, the tool set also implements a facility that allows the control and application of modeling tasks on a large set of conformations in what we have termed ensemble computing. Ensemble computing encompasses loosely coupled, parallel computation on high-end parallel computers, clustered computational grids and desktop grid environments. This paper describes the design and implementation of the MMTSB Tool Set and illustrates its utility with three typical examples--scoring of a set of predicted protein conformations in order to identify the most native-like structures, ab initio folding of peptides in implicit solvent with the replica exchange method, and the prediction of a missing fragment in a larger protein structure.
Journal of Molecular Graphics and Modelling 06/2004; 22(5):377-95. · 2.18 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Because of the association of beta-sheet formation with the initiation and propagation of amyloid diseases, model systems have been sought to further our understanding of this process. WW domains have been proposed as one such model system. Whereas the folding of the WW domains from human Yes-associated protein (YAP) and Pin have been shown to obey single-exponential kinetics, the folding of the WW domain from formin-binding protein (FBP) 28 has been shown to proceed via biphasic kinetics. From an analysis of free-energy landscapes from atomic-level molecular dynamics simulations, the biphasic folding kinetics observed in the FBP WW domain may be traced to the ability of this WW domain to adopt two slightly different forms of packing in its hydrophobic core. This conformational change is propagated along the peptide backbone and affects the position of a tryptophan residue shown in other WW domains to play a key role in binding. The WW domains of Pin and YAP do not support more than one type of packing each, leading to monophasic folding kinetics. The ability of the FBP WW domain to assume two different types of packing may, in turn, explain the capacity of this WW domain to bind two classes of ligand, a property that is not shared by other WW domains. These findings lead to the hypothesis that lability with respect to conformations separated by an observable barrier as a requirement for function is incompatible with the ability of a protein to fold via single-exponential kinetics.
Proceedings of the National Academy of Sciences 04/2004; 101(10):3432-7. · 9.68 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The use of simple theoretical models has provided a considerable contribution to our present understanding of the means by which proteins adopt their native fold from the plethora of available unfolded states. A common assumption in building computationally tractable models has been the neglect of stabilizing non-native interactions in the class of models described as "Gō-like." The focus of this study is the characterization of the folding of a number of proteins via a Gō-like model, which aims to map a maximal amount of information reflecting the protein sequence onto a "minimalist" skeleton. This model is shown to contain sufficient information to reproduce the folding transition states of a number of proteins, including topologically analogous proteins that fold via different transition states. Remarkably, these models also demonstrate consistency with the general features of folding transition states thought to be stabilized by non-native interactions. This suggests that native interactions are the primary determinant of most protein folding transition states, and that non-native interactions lead only to local structural perturbations. A prediction is also included for an asymmetrical folding transition state of bacteriophage lambda protein W, which has yet to be subjected to experimental characterization.
Journal of Molecular Biology 12/2003; 334(2):309-25. · 4.00 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: A class of models that represents a protein chain as a sequence of "folded" and "unfolded" residues has recently been used to correlate rates and mechanisms of protein folding with the protein native structure. In order to better understand the conditions under which these "Ising-like" models apply, we compare results from this model to those obtained from an off-lattice model which uses the same potential function. We find that Ising-like models by construction impose folding via a highly sequential nucleation-condensation mechanism, which in turn leads to more rugged energy landscapes, fewer "pathways" to the native state, and in the specific case examined here, the cold shock protein A from Escherichia coli, a qualitative difference in the most likely order of events in folding.
Proteins Structure Function and Bioinformatics 12/2003; 53(3):740-7. · 3.39 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The mechanism of formation of beta-sheets is of great importance because of the significant role of such structures in the initiation and propagation of amyloid diseases. In this study we examine the folding of a series of three-stranded antiparallel beta-sheets known as WW domains. Whereas other WW domains have been shown to fold with single-exponential kinetics, the WW domain from murine formin-binding protein 28 has recently been shown to fold with biphasic kinetics. By using a combination of kinetics and thermodynamics to characterize a simple model for this protein, the origins of the biphasic kinetics is found to lie in the fact that most of the protein is able to fold without requiring one of the beta-hairpins to be correctly registered. The correct register of this hairpin is enforced by a surface-exposed hydrophobic contact, which is not present in other WW domains. This finding suggests the use of judiciously chosen surface-exposed hydrophobic pairs as a protein design strategy for enforcing the desired strand registry.
Proceedings of the National Academy of Sciences 05/2003; 100(7):3954-9. · 9.68 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Topology has been shown to be an important determinant of many features of protein folding; however, the delineation of sequence effects on folding remains obscure. Furthermore, differentiation between the two influences proves difficult due to their intimate relationship. To investigate the effect of sequence in the absence of significant topological differences, we examined the folding mechanisms of segment B1 peptostreptococcal protein L and segment B1 of streptococcal protein G. These proteins share the same highly symmetrical topology. Despite this symmetry, neither protein folds through a symmetrical transition state. We analyzed the origins of this difference using theoretical models. We found that the strength of the interactions present in the N-terminal hairpin of protein L causes this hairpin to form ahead of the C-terminal hairpin. The difference in chain entropy associated with the formation of the hairpins of protein G proves sufficient to beget initiation of folding at the shorter C-terminal hairpin. Our findings suggest that the mechanism of folding may be understood by examination of the free energy associated with the formation of partially folded microstates.
Protein Science 11/2002; 11(10):2351-61. · 2.80 Impact Factor
