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Journal of Chemical Information and... Apr 2017Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its...
Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.
Topics: Molecular Dynamics Simulation; Muramidase; Principal Component Analysis; Protein Conformation
PubMed: 28301154
DOI: 10.1021/acs.jcim.6b00646 -
FEMS Microbiology Letters Dec 1992Autolysis of Enterococcus hirae ATCC 9790 is the result of the action of endogenous enzymes that hydrolyze bonds in the protective and shape-maintaining cell wall... (Review)
Review
The autolytic ('suicidase') system of Enterococcus hirae: from lysine depletion autolysis to biochemical and molecular studies of the two muramidases of Enterococcus hirae ATCC 9790.
Autolysis of Enterococcus hirae ATCC 9790 is the result of the action of endogenous enzymes that hydrolyze bonds in the protective and shape-maintaining cell wall peptidoglycan. It is thought that these potentially suicidal enzymes play a positive role(s) in wall growth and division and are expressed as autolysins when cell wall assembly and/or repair are inhibited. E. hirae possesses two potentially autolytic enzymes, both of which are muramidases. Although they hydrolyze the same bond as hen egg-white lysozyme, both are high-molecular-mass, complex enzymes. Muramidase-1 is synthesized as a zymogen, requiring protease activation. It is a glucoenzyme that is also multiply nucleotidylated with an unusual nucleotide, 5-mercaptouridine monophosphate. Muramidase-2 is almost certainly a product of a separate gene. The deduced amino acid sequence of a cloned gene for extracellular muramidase-2 showed several unusual features. It appears to be a two-, or perhaps three-domain protein with a putative glycosidase-active site near the N-terminal end and six 45-amino-acid-long repeats at the C-terminal end which are presumed to be involved with high-affinity binding to the insoluble peptidoglycan substrate. Muramidase-2 binds penicillin with low affinity. The presence of several amino acid groupings characteristic of serine-active site beta-lactam-interactive proteins is consistent with the possible presence of a penicillin-binding, third domain. Indirect evidence consistent with a role(s) for these enzymes in cell wall growth and division has been obtained. However, proof of such role(s) awaits modern genetic, molecular, and biochemical analyses.
Topics: Amino Acid Sequence; Autolysis; Binding Sites; Enterococcus; Genes, Bacterial; Molecular Sequence Data; Muramidase; N-Acetylmuramoyl-L-alanine Amidase
PubMed: 1362171
DOI: 10.1111/j.1574-6968.1992.tb14050.x -
Protein Science : a Publication of the... Oct 2018A simple "diffusion-to-capture" model is used to estimate the upper limit to the growth rate of macromolecular crystals under conditions when the rate limiting process...
A simple "diffusion-to-capture" model is used to estimate the upper limit to the growth rate of macromolecular crystals under conditions when the rate limiting process is the mass transfer of sample from solution to the crystal. Under diffusion-limited crystal growth conditions, this model predicts that the cross-sectional area of a crystal will increase linearly with time; this prediction is validated by monitoring the growth rate of lysozyme crystals. A consequence of this analysis is that when crystal growth is diffusion-limited, micron-sized crystals can be produced in ~1 s, which would be compatible with the turnover time of many enzymes. Consequently, the ability to record diffraction patterns from sub-micron sized crystals by X-ray Free Electron Lasers and micro-electron diffraction technologies opens the possibility of trapping intermediate enzyme states by crystallization.
Topics: Crystallization; Humans; Macromolecular Substances; Muramidase
PubMed: 30056633
DOI: 10.1002/pro.3491 -
Angewandte Chemie (International Ed. in... May 2021Nanochaperones have been designed and used for regulating the (re)folding of proteins, treating protein misfolding-related diseases, and, more recently, in drug...
Nanochaperones have been designed and used for regulating the (re)folding of proteins, treating protein misfolding-related diseases, and, more recently, in drug delivery. Despite various successes, a complete understanding of the working mechanisms remains elusive, which represents a challenge for the realization of their full potential. Here, we thoroughly investigated the functioning of differently charged nanochaperones that regulate the refolding of thermally denatured lysozyme. We found that the balance between the capture and release of lysozyme clients that are controlled by nanochaperones plays a key role in regulating refolding. More importantly, the findings could be applied to other enzymes with various physicochemical properties. On the basis of these results, we could recover the activity of enzymes with high efficiency either after 20 days of storage at 40 °C or heating at high temperatures for 30-60 min. Our results provide important new design strategies for nanochaperone systems to improve their properties and expand their applications.
Topics: Molecular Chaperones; Muramidase; Particle Size; Protein Denaturation; Protein Folding; Temperature
PubMed: 33595165
DOI: 10.1002/anie.202101462 -
Molecules (Basel, Switzerland) Dec 2021Lysozyme is a key effector molecule of the innate immune system in both vertebrate and invertebrate. It is classified into six types, one of which is the goose-type...
Lysozyme is a key effector molecule of the innate immune system in both vertebrate and invertebrate. It is classified into six types, one of which is the goose-type (g-type). To date, no study on g-type lysozyme in crustacean has been documented. Here, we report the identification and characterization of a g-type lysozyme (named LysG1) from the shrimp inhabiting a deep-sea hydrothermal vent in Manus Basin. LysG1 possesses conserved structural features of g-type lysozymes. The recombinant LysG1 (rLysG1) exhibited no muramidase activity and killed selectively Gram-negative bacteria in a manner that depended on temperature, pH, and metal ions. rLysG1 bound target bacteria via interaction with bacterial cell wall components, notably lipopolysaccharide (LPS), and induced cellular membrane permeabilization, which eventually caused cell lysis. The endotoxin-binding capacity enabled rLysG1 to alleviate the inflammatory response induced by LPS. Mutation analysis showed that the bacterial binding and killing activities of rLysG1 required the integrity of the conserved α3 and 4 helixes of the protein. Together, these results provide the first insight into the activity and working mechanism of g-type lysozyme in crustacean and deep-sea organisms.
Topics: Animals; Arthropod Proteins; Crustacea; Gram-Negative Bacteria; Hydrothermal Vents; Muramidase
PubMed: 34946706
DOI: 10.3390/molecules26247624 -
Journal of Molecular Graphics &... 2001In vacuo proteins provide a simple laboratory to explore the roles of sequence, temperature, charge state, and initial configuration in protein folding. Moreover, by the... (Review)
Review
In vacuo proteins provide a simple laboratory to explore the roles of sequence, temperature, charge state, and initial configuration in protein folding. Moreover, by the very absence of solvent, the study of anhydrous proteins in vacuo will also help us to understand specific environmental effects. From the experimental viewpoint, these systems are now beginning to be characterized at low resolution. Molecular dynamics (MD) simulations, in combination with tools for protein shape analysis, can complement experiments and provide further insights on the folding-unfolding transitions of these proteins. We review some aspects of this issue by using the results from a detailed MD study of hen egg-white lysozyme. For lysozyme ions, unfolding can be triggered by Coulombic repulsion. In neutral lysozyme, unfolding can be induced by centrifugal forces and also by weakening the monomer-monomer interaction. In both cases, the resulting unfolded transients can be used as initial configurations for relaxation dynamics. All trajectories are analyzed in terms of global molecular shape features of the backbone, including its anisometry and chain entanglement complexity. This strategy allows us to quantify separately the degree of polymer collapse and the evolution of large-scale folding features. Using these last two notions, we discuss some basic questions regarding the nature of the accessible paths associated with unfolding from, and refolding into, compact conformers.
Topics: Animals; Computer Simulation; Mathematics; Models, Molecular; Muramidase; Protein Denaturation; Protein Folding; Protein Structure, Tertiary; Vacuum
PubMed: 11381520
DOI: 10.1016/s1093-3263(00)00130-3 -
The Journal of Physical Chemistry. B Dec 2013We present a quantum mechanics/molecular mechanics (QM/MM) method to evaluate the partial charges of amino acid residues for use in MM potentials based on their protein...
We present a quantum mechanics/molecular mechanics (QM/MM) method to evaluate the partial charges of amino acid residues for use in MM potentials based on their protein environment. For each residue of interest, the nearby residues are included in the QM system while the rest of the protein is treated at the MM level of theory. After a short structural optimization, the partial charges of the central residue are fit to the electrostatic potential using the restrained electrostatic potential (RESP) method. The resulting charges and electrostatic potential account for the individual environment of the residue, although they lack the transferable nature of library partial charges. To evaluate the quality of the QM/MM RESP charges, thermodynamic integration is used to measure the pKa shift of the aspartic acid residues in three different proteins, turkey egg lysozyme, beta-cryptogein, and Thioredoxin. Compared to the AMBER ff99SB library values, the QM/MM RESP charges show better agreement between the calculated and experimental pK(a) values for almost all of the residues considered.
Topics: Animals; Egg White; Models, Molecular; Muramidase; Quantum Theory; Static Electricity; Thermodynamics; Thioredoxins; Turkeys
PubMed: 24176005
DOI: 10.1021/jp409568h -
The Journal of Physical Chemistry. B Dec 2018In this work, we investigated the kinetics of binding of hen egg-white lysozyme with tri- N-acetylglucosamine in aqueous solutions, at two values of pH, 3.2 and 11, as a...
In this work, we investigated the kinetics of binding of hen egg-white lysozyme with tri- N-acetylglucosamine in aqueous solutions, at two values of pH, 3.2 and 11, as a function of ionic strength, by a stopped-flow method with tryptophyl fluorescence observation of the transients. We analyzed registered reaction progress curves by employing numerical integration of appropriate chemical master equations. We discriminated between several binding models and established that the process observed in experiments follows a two-step mechanism, composed of four elementary stages: diffusional formation of an encounter complex, dissociation of the encounter complex, conformational transition of the encounter complex to the final complex, and the reverse transformation, i.e., from the final complex to the encounter complex. We evaluated rate constants of these elementary stages and determined their dependencies on solution ionic strength. Regardless of solution pH, rate constants of both forward and reverse conformational transitions increase with an increasing ionic strength. This suggests that ionic screening of intramolecular electrostatic interactions may act to lower the activation barrier for conformational transition in proteins.
Topics: Hydrogen-Ion Concentration; Ions; Kinetics; Muramidase; Protein Conformation; Trisaccharides
PubMed: 30477301
DOI: 10.1021/acs.jpcb.8b07525 -
Current Protein & Peptide Science Dec 2007Amyloid fibrils are highly ordered protein assemblies known to contribute to the pathology of a variety of genetic and aging-associated diseases. More recently, these... (Review)
Review
Amyloid fibrils are highly ordered protein assemblies known to contribute to the pathology of a variety of genetic and aging-associated diseases. More recently, these fibrils have been shown to be useful as structural scaffolds in both natural biological systems and nanotechnology applications. The intense interest in amyloid fibrils has led to the investigation of well-characterized proteins, such as hen egg white lysozyme (HEWL), as model systems to examine structural and mechanistic principles that may be generally applicable to all amyloid fibrils. The purpose of this review is to critically examine the fibril-formation literature of proteins in the lysozyme family with respect to the known structure and folding properties of these proteins. The goal is to identify similarities and differences within the family, examine general misfolding / aggregation principles, and identify key areas of importance for future work on the fibril formation of these proteins.
Topics: Amino Acid Sequence; Amyloid; Animals; Humans; Models, Molecular; Molecular Sequence Data; Muramidase; Protein Folding; Protein Structure, Secondary; Thermodynamics
PubMed: 18220842
DOI: 10.2174/138920307783018659 -
Biophysical Journal Mar 2017Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for...
Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for possible new therapies; however, the control mechanisms are under debate. Calculations have indicated protein vibrations enable structural change. However, previous measurements found these vibrations only weakly depend on the functional state. By using the novel technique of anisotropic terahertz microscopy, we find that there is a dramatic change to the vibrational directionality with inhibitor binding to lysozyme, whereas the vibrational energy distribution, as measured by neutron inelastic scattering, is only slightly altered. The anisotropic terahertz measurements provide unique access to the directionality of the intramolecular vibrations, and immediately resolve the inconsistency between calculations and previous measurements, which were only sensitive to the energy distribution. The biological importance of the vibrational directions versus the energy distribution is revealed by our calculations comparing wild-type lysozyme with a higher catalytic rate double deletion mutant. The vibrational energy distribution is identical, but the more efficient mutant shows an obvious reorientation of motions. These results show that it is essential to characterize the directionality of motion to understand and control protein dynamics to optimize or inhibit function.
Topics: Entropy; Molecular Dynamics Simulation; Movement; Muramidase; Protein Conformation; Vibration
PubMed: 28297652
DOI: 10.1016/j.bpj.2016.12.049