166 research outputs found
Molecular modeling of an antigenic complex between a viral peptide and a class I major histocompatibility glycoprotein
Computer simulation of the
conformations of short antigenic peptides (&lo
residues) either free or bound to their receptor,
the major histocompatibility complex (MHC)-
encoded glycoprotein H-2 Ld, was employed to
explain experimentally determined differences
in the antigenic activities within a set of related
peptides. Starting for each sequence from the
most probable conformations disclosed by a
pattern-recognition technique, several energyminimized
structures were subjected to molecular
dynamics simulations (MD) either in vacuo
or solvated by water molecules. Notably, antigenic
potencies were found to correlate to the
peptides propensity to form and maintain an
overall a-helical conformation through regular
i,i + 4 hydrogen bonds. Accordingly, less active
or inactive peptides showed a strong tendency
to form i,i+3 hydrogen bonds at their Nterminal
end. Experimental data documented
that the C-terminal residue is critical for interaction
of the peptide with H-2 Ld. This finding
could be satisfactorily explained by a 3-D
Q.S.A.R. analysis postulating interactions between
ligand and receptor by hydrophobic
forces. A 3-D model is proposed for the complex
between a high-affinity nonapeptide and the H-
2 Ld receptor. First, the H-2 Ld molecule was
built from X-ray coordinates of two homologous
proteins: HLA-A2 and HLA-Aw68, energyminimized
and studied by MD simulations. With
HLA-A2 as template, the only realistic simulation
was achieved for a solvated model with minor
deviations of the MD mean structure from
the X-ray conformation. Water simulation of the
H-2 Ld protein in complex with the antigenic
nonapeptide was then achieved with the template-
derived optimal parameters. The bound
peptide retains mainly its a-helical conformation
and binds to hydrophobic residues of H-2
Ld that correspond to highly polymorphic positions
of MHC proteins. The orientation of the
nonapeptide in the binding cleft is in accordance
with the experimentally determined distribution
of its MHC receptor-binding residues
(agretope residues). Thus, computer simulation was successfully employed to explain functional
data and predicts a-helical conformation
for the bound peptid
Fragment-free approach to protein folding using conditional neural fields
Motivation: One of the major bottlenecks with ab initio protein folding is an effective conformation sampling algorithm that can generate native-like conformations quickly. The popular fragment assembly method generates conformations by restricting the local conformations of a protein to short structural fragments in the PDB. This method may limit conformations to a subspace to which the native fold does not belong because (i) a protein with really new fold may contain some structural fragments not in the PDB and (ii) the discrete nature of fragments may prevent them from building a native-like fold. Previously we have developed a conditional random fields (CRF) method for fragment-free protein folding that can sample conformations in a continuous space and demonstrated that this CRF method compares favorably to the popular fragment assembly method. However, the CRF method is still limited by its capability of generating conformations compatible with a sequence
Designing succinct structural alphabets
Motivation: The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more likely substructures. We call them the ‘structural alphabet’ for this segment. Classical approaches such as ROSETTA used sequence profile and secondary structure information, to predict structural fragments. In contrast, we utilize more structural information, such as solvent accessibility and contact capacity, for finding structural fragments
Identification of essential and non-essential single-stranded DNA-binding proteins in a model archaeal organism
Single-stranded DNA-binding proteins (SSBs) play vital roles in all aspects of DNA metabolism in all three domains of life and are characterized by the presence of one or more OB fold ssDNA-binding domains. Here, using the genetically tractable euryarchaeon Haloferax volcanii as a model, we present the first genetic analysis of SSB function in the archaea. We show that genes encoding the OB fold and zinc finger-containing RpaA1 and RpaB1 proteins are individually non-essential for cell viability but share an essential function, whereas the gene encoding the triple OB fold RpaC protein is essential. Loss of RpaC function can however be rescued by elevated expression of RpaB, indicative of functional overlap between the two classes of haloarchaeal SSB. Deletion analysis is used to demonstrate important roles for individual OB folds in RpaC and to show that conserved N- and C-terminal domains are required for efficient repair of DNA damage. Consistent with a role for RpaC in DNA repair, elevated expression of this protein leads to enhanced resistance to DNA damage. Taken together, our results offer important insights into archaeal SSB function and establish the haloarchaea as a valuable model for further studies
Assigning a function to a conserved archaeal metallo-β-lactamase from Haloferax volcanii
The metallo-β-lactamase family of enzymes comprises a large group of proteins with diverse functions in the metabolism of the cell. Among others, this superfamily contains proteins which are involved in DNA and RNA metabolism, acting as nucleases in e.g. repair and maturation. Many proteins have been annotated in prokaryotic genomes as being potential metallo-β-lactamases, but very often the function has not been proven. The protein HVO_2763 from Haloferax volcanii is such a potential metallo-β-lactamase. HVO_2763 has sequence similarity to the metallo-β-lactamase tRNase Z, a tRNA 3′ processing endonuclease. Here, we report the characterisation of this metallo-β-lactamase HVO_2763 in the halophilic archaeon Haloferax volcanii. Using different in vitro assays with the recombinant HVO_2763, we could show that the protein does not have tRNA 3′ processing or exonuclease activity. According to transcriptome analyses of the HVO_2763 deletion strain, expression of proteins involved in membrane transport is downregulated in the mutant. Therefore, HVO_2763 might be involved directly or indirectly in membrane transport
Applications of Green's functions to acoustic ducts and cavities with rigid boundaries
The present work is concerned with descriptions of acoustic wave behaviour in the presence of rigid boundaries. The unifying theme of this work is the application of Green’s function techniques to a selection of duct and cavity problems in acoustics. Although the central theme of this thesis is theoretical, experiments are also performed to test the validity of the theory. The thesis covers two basic areas: the diffraction of sound in cylindrical pipes fitted with flanges and orifice plates; and the inverse acoustics of rigid rectangular cavities.
The diffraction of sound from flanged cylindrical waveguides is a classical problem in acoustics. Chapter 2 deals with the initial work on this subject. In this chapter, non—dissipative, inviscid, linear wave theory is compared with experiment and some of the mathematical formulations of this problem by previous authors are unified. A central problem with the ‘classical’ theory is the prediction of velocity singularities at sharp edges.
In Chapter 3, the diffraction of sound is considered in a cylindrical duct with a thin orifice plate blockage, in the presence of a mean flow. Viscosity in the fluid produces vorticity, the strength of which may be determined by the requirement that the fluid velocity at the orifice rim be finite. Theoretical analysis is performed based on this principle. Numerical calculations are made for various physical parameters and an experiment is performed to test the predictions of the theory.
Chapter 4 deals with inverse wave problems in a rigid rectangular, two dimensional cavity. The primary emphasis of this chapter is on reconstructing a spatially incoherent random source within a rigid rectangular cavity by pressure measurements on the cavity walls. The related problem of reconstructing a deterministic point source under these conditions is also addressed. Two other formalisms are derived. Again, they are both set in a rigid rectangular cavity. The first of these is a method for iteratively reconstructing a source profile. The second formalism concerns the problem of reconstructing a rigid scatterer under the restriction of the first Born approximation
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