191 research outputs found
Four small puzzles that Rosetta doesn't solve
A complete macromolecule modeling package must be able to solve the simplest
structure prediction problems. Despite recent successes in high resolution
structure modeling and design, the Rosetta software suite fares poorly on
deceptively small protein and RNA puzzles, some as small as four residues. To
illustrate these problems, this manuscript presents extensive Rosetta results
for four well-defined test cases: the 20-residue mini-protein Trp cage, an even
smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease
inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies,
several lines of evidence indicate that conformational sampling is not the
major bottleneck in modeling these small systems. Instead, approximations and
omissions in the Rosetta all-atom energy function currently preclude
discriminating experimentally observed conformations from de novo models at
atomic resolution. These molecular "puzzles" should serve as useful model
systems for developers wishing to make foundational improvements to this
powerful modeling suite.Comment: Published in PLoS One as a manuscript for the RosettaCon 2010 Special
Collectio
Secondary-Structure Design of Proteins by a Backbone Torsion Energy
We propose a new backbone-torsion-energy term in the force field for protein
systems. This torsion-energy term is represented by a double Fourier series in
two variables, the backbone dihedral angles phi and psi. It gives a natural
representation of the torsion energy in the Ramachandran space in the sense
that any two-dimensional energy surface periodic in both phi and psi can be
expanded by the double Fourier series. We can then easily control
secondary-structure-forming tendencies by modifying the torsion-energy surface.
For instance, we can increase/decrease the alpha-helix-forming-tendencies by
lowering/raising the torsion-energy surface in the alpha-helix region and
likewise increase/decrease the beta-sheet-forming tendencies by
lowering/raising the surface in the beta-sheet region in the Ramachandran
space. We applied our approach to AMBER parm94 and AMBER parm96 force fields
and demonstrated that our modifications of the torsion-energy terms resulted in
the expected changes of secondary-structure-forming-tendencies by performing
folding simulations of alpha-helical and beta-hairpin peptides.Comment: 13 pages, (Revtex4), 5 figure
Ultrafast Structural Dynamics of BlsA, a Photoreceptor from the Pathogenic Bacterium Acinetobacter baumannii
Acinetobacter baumannii is an important human pathogen that can form biofilms and persist under harsh environmental conditions. Biofilm formation and virulence are modulated by blue light, which is thought to be regulated by a BLUF protein, BlsA. To understand the molecular mechanism of light sensing, we have used steady-state and ultrafast vibrational spectroscopy to compare the photoactivation mechanism of BlsA to the BLUF photosensor AppA from Rhodobacter sphaeroides. Although similar photocycles are observed, vibrational data together with homology modeling identify significant differences in the β5 strand in BlsA caused by photoactivation, which are proposed to be directly linked to downstream signaling
Molecular determinants of binding to the Plasmodium subtilisin-like protease 1.
PfSUB1, a subtilisin-like protease of the human malaria parasite Plasmodium falciparum, is known to play important roles during the life cycle of the parasite and has emerged as a promising antimalarial drug target. In order to provide a detailed understanding of the origin of binding determinants of PfSUB1 substrates, we performed molecular dynamics simulations in combination with MM-GBSA free energy calculations using a homology model of PfSUB1 in complex with different substrate peptides. Key interactions, as well as residues that potentially make a major contribution to the binding free energy, are identified at the prime and nonprime side of the scissile bond and comprise peptide residues P4 to P2'. This finding stresses the requirement for peptide substrates to interact with both prime and nonprime side residues of the PfSUB1 binding site. Analyzing the energetic contributions of individual amino acids within the peptide-PfSUB1 complexes indicated that van der Waals interactions and the nonpolar part of solvation energy dictate the binding strength of the peptides and that the most favorable interactions are formed by peptide residues P4 and P1. Hot spot residues identified in PfSUB1 are dispersed over the entire binding site, but clustered areas of hot spots also exist and suggest that either the S4-S2 or the S1-S2' binding site should be exploited in efforts to design small molecule inhibitors. The results are discussed with respect to which binding determinants are specific to PfSUB1 and, therefore, might allow binding selectivity to be obtained
Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations
The comparative dynamics and inhibitor binding free energies of group-1 and group-2 pathogenic influenza A subtype neuraminidase (NA) enzymes are of fundamental biological interest and relevant to structure-based drug design studies for antiviral compounds. In this work, we present seven generalized Born molecular dynamics simulations of avian (N1)- and human (N9)-type NAs in order to probe the comparative flexibility of the two subtypes, both with and without the inhibitor oseltamivir bound. The enhanced sampling obtained through the implicit solvent treatment suggests several provocative insights into the dynamics of the two subtypes, including that the group-2 enzymes may exhibit similar motion in the 430-binding site regions but different 150-loop motion. End-point free energy calculations elucidate the contributions to inhibitor binding free energies and suggest that entropic considerations cannot be neglected when comparing across the subtypes. We anticipate the findings presented here will have broad implications for the development of novel antiviral compounds against both seasonal and pandemic influenza strains
Carbohydrate Recognition by an Architecturally Complex α-N-Acetylglucosaminidase from Clostridium perfringens
CpGH89 is a large multimodular enzyme produced by the human and animal pathogen Clostridium perfringens. The catalytic activity of this exo-α-d-N-acetylglucosaminidase is directed towards a rare carbohydrate motif, N-acetyl-β-d-glucosamine-α-1,4-d-galactose, which is displayed on the class III mucins deep within the gastric mucosa. In addition to the family 89 glycoside hydrolase catalytic module this enzyme has six modules that share sequence similarity to the family 32 carbohydrate-binding modules (CBM32s), suggesting the enzyme has considerable capacity to adhere to carbohydrates. Here we suggest that two of the modules, CBM32-1 and CBM32-6, are not functional as carbohydrate-binding modules (CBMs) and demonstrate that three of the CBMs, CBM32-3, CBM32-4, and CBM32-5, are indeed capable of binding carbohydrates. CBM32-3 and CBM32-4 have a novel binding specificity for N-acetyl-β-d-glucosamine-α-1,4-d-galactose, which thus complements the specificity of the catalytic module. The X-ray crystal structure of CBM32-4 in complex with this disaccharide reveals a mode of recognition that is based primarily on accommodation of the unique bent shape of this sugar. In contrast, as revealed by a series of X-ray crystal structures and quantitative binding studies, CBM32-5 displays the structural and functional features of galactose binding that is commonly associated with CBM family 32. The functional CBM32s that CpGH89 contains suggest the possibility for multivalent binding events and the partitioning of this enzyme to highly specific regions within the gastrointestinal tract
First Measurement of Electroproduction off Nuclei in the Current and Target Fragmentation Regions
We report results of hyperon production in semi-inclusive
deep-inelastic scattering off deuterium, carbon, iron, and lead targets
obtained with the CLAS detector and the Continuous Electron Beam Accelerator
Facility 5.014~GeV electron beam. These results represent the first
measurements of the multiplicity ratio and transverse momentum
broadening as a function of the energy fraction~() in the current and target
fragmentation regions. The multiplicity ratio exhibits a strong suppression at
high~~and~an enhancement at~low~. The measured transverse momentum
broadening is an order of magnitude greater than that seen for light mesons.
This indicates that the propagating entity interacts very strongly with the
nuclear medium, which suggests that propagation of diquark configurations in
the nuclear medium takes place at least part of the time, even at high~. The
trends of these results are qualitatively described by the Giessen
Boltzmann-Uehling-Uhlenbeck transport model, particularly for the multiplicity
ratios. These observations will potentially open a new era of studies of the
structure of the nucleon as well as of strange baryons.Comment: 14 pages, 6 figure
Observation of azimuth-dependent suppression of hadron pairs in electron scattering off nuclei
We present the first measurement of di-hadron angular correlations in
electron-nucleus scattering. The data were taken with the CLAS detector and a
5.0 GeV electron beam incident on deuterium, carbon, iron, and lead targets.
Relative to deuterium, the nuclear yields of charged-pion pairs show a strong
suppression for azimuthally opposite pairs, no suppression for azimuthally
nearby pairs, and an enhancement of pairs with large invariant mass. These
effects grow with increased nuclear size. The data are qualitatively described
by the GiBUU model, which suggests that hadrons form near the nuclear surface
and undergo multiple-scattering in nuclei. These results show that angular
correlation studies can open a new way to elucidate how hadrons form and
interact inside nucleiComment: 6 pages, 4 figure
Observation of Azimuth-Dependent Suppression of Hadron Pairs in Electron Scattering Off Nuclei
We present the first measurement of dihadron angular correlations in electron-nucleus scattering. The data were taken with the CLAS detector and a 5.0 GeV electron beam incident on deuterium, carbon, iron, and lead targets. Relative to deuterium, the nuclear yields of charged-pion pairs show a strong suppression for azimuthally opposite pairs, no suppression for azimuthally nearby pairs, and an enhancement of pairs with large invariant mass. These effects grow with increased nuclear size. The data are qualitatively described by the gibuu model, which suggests that hadrons form near the nuclear surface and undergo multiple scattering in nuclei. These results show that angular correlation studies can open a new way to elucidate how hadrons form and interact inside nuclei
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