Trends in template/fragment-free protein structure prediction

Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward

Packing helices in proteins by global optimization of a potential energy function

An efficient method has been developed for packing α-helices in proteins. It treats α-helices as rigid bodies and uses a simplified Lennard–Jones potential with Miyazawa–Jernigan contact-energy parameters to describe the interactions between the α-helical elements in this coarse-grained system. Global conformational searches to generate packing arrangements rapidly are carried out with a Monte Carlo-with-minimization type of approach. The results for 42 proteins show that the approach reproduces native-like folds of α-helical proteins as low-energy local minima of this highly simplified potential function

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests

Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of α and α+β proteins [60–70 residues with C(α) rms deviation (rmsd) <6 Å]. However, for α+β proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two α and three α+β, with sizes of 53–235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue α+β protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-Å C(α) rmsd. So far this protein is the largest α+β protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly α-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 Å rmsd, except the 32 C-terminal residues, most of which form a β-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction

Folding Simulations of the A and B Domains of Protein G

We study wild type and mutants of the A and B domain of protein G using all-atom Go-models. Our data substantiate the usefulness of such simulation for probing the folding mechanism of proteins and demonstrate that multi-funnel versions of such models allow also to probe more complicated funnel landscapes. In our case, such models reproduce the experimentally observed distributions of the GA98 and GB98 mutants which differ only by one residue but fold into different structures. They also reveal details on the folding mechanism in these two proteins

Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics

International audienceHeat-shock proteins 70 (Hsp70s) are key molecular chaperones, which assist in the folding and refolding/disaggregation of proteins. Hsp70s, which consist of a nucleotide-binding domain (NBD, consisting of NBD-I and NBD-II subdomains) and a substrate-binding domain [SBD, further split into the beta-sheet (SBD-beta) and alpha-helical (SBD-alpha) subdomains], occur in two major conformations having (a) a closed SBD, in which the SBD and NBD domains do not interact, and (b) an open SBD, in which SBD-alpha interacts with NBD-I and SBD-beta interacts with the top parts of NBD-I and NBD-II. In the SBD-closed conformation, SBD is bound to a substrate protein, with release occurring after transition to the open conformation. While the transition from the closed to the open conformation is triggered efficiently by binding of adenosine triphosphate (ATP) to the NBD, it also occurs, although less frequently, in the absence of ATP. The reverse transition occurs after ATP hydrolysis. Here, we report canonical and multiplexed replica exchange simulations of the conformational dynamics of Hsp70s using a coarse-grained molecular dynamics approach with the UNRES force field. The simulations were run in the following three modes: (i) with the two halves of the NBD unrestrained relative to each other, (ii) with the two halves of the NBD restrained in an "open" geometry as in the SBD-closed form of DnaK (2KHO), and (iii) with the two halves of NBD restrained in a "closed" geometry as in known experimental structures of ATP-bound NBD forms of Hsp70. Open conformations, in which the SBD interacted strongly with the NBD, formed spontaneously during all simulations; the number of transitions was largest in simulations carried out with the "closed" NBD domain, and smallest in those carried out with the "open" NBD domain; this observation is in agreement with the experimentally observed influence of ATP-binding on the transition of Hsp70s from the SBD-closed to the SBD-open form. Two kinds of open conformations were observed: one in which SBD-alpha interacts with NBD-I and SBD-beta interacts with the top parts of NBD-I and NBD-II (as observed in the structures of nucleotide exchange factors), and another one in which this interaction pattern is swapped. A third type of motion, in which SBD-alpha binds to NBD without dissociating from SBD-beta, was also observed. It was found that the first stage of interdomain communication (approach of SBD-beta, to NBD) is coupled with the rotation of the long axes of NBD-I and NBD-II toward each other. To the best of our knowledge, this is the first successful simulation of the full transition of an Hsp70 from the SBD-closed to the SBD-open conformation