Conformational change in the activation of lipase: an analysis in terms of low-frequency normal modes

Effects of alcohol concentration and temperature on the dynamics and stability of mutant Staphylococcal lipase

The stability and activity of lipase in organic media are important parameters in determining how quickly biocatalysis proceeds. This study aimed to examine the effects of two commonly used alcohols in industrial applications, methanol (MtOH) and ethanol (EtOH) on the conformational stability and catalytic activity of G210C lipase, a laboratory-evolved mutant of Staphylococcus epidermidis AT2 lipase. Simulation studies were performed using an open-form predicted structure under 30, 40 and 50% of MtOH and EtOH at 25 °C and 45 °C. The overall enzyme structure becomes more flexible with increasing concentration of MtOH and exhibited the highest flexibility in 40% EtOH. In EtOH, the movement of the lid was found to be temperature-dependent with a noticeable shift in the lid position at 45 °C. Lid opening was evidenced at 50% of MtOH and EtOH which was supported by the increase in SASA of hydrophobic residues of the lid and catalytic triad. The active site remained mostly intact. An open-closed lid transition was observed when the structure was re-simulated in water. Experimental evaluation of the lipase stability showed that the half-life reduced when the enzyme was treated with 40% (v/v) and 50% (v/v) of EtOH and MtOH respectively. The finding implies that a high concentration of alcohol and elevated temperature can induce the lid opening of lipase which could be essential for the activation of the enzyme, provided that the catalytic performance in the active site is not compromised.Communicated by Ramaswamy H. Sarma.

Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

The recently proposed Hamiltonian adaptive resolution scheme (H-AdResS) allows the performance of molecular simulations in an open boundary framework. It allows changing, on the fly, the resolution of specific subsets of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the molecular mechanics/coarse-grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Toward this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.

Combination of site-directed mutagenesis and yeast surface display enhances Rhizomucor miehei lipase esterification activity in organic solvent

To increase the activity of Rhizomucor miehei lipase (RML) in organic solvent, multiple sequence alignments and rational site-directed mutagenesis were used to create RML variants. The obtained proteins were surface-displayed on Pichia pastoris by fusion to Flo1p as an anchor protein. The synthetic activity of four variants showed from 1.1- to 5-fold the activity of native lipase in an esterification reaction in heptane with alcohol and caproic acid as substrates. The increase in esterification activity may be attributed to the four mutations changing the flexibility of RML or facilitating the reaction. In conclusion, this method demonstrated that multiple sequence alignments and rational site-directed mutagenesis combined with yeast display technology is a faster and more effective means of obtaining high-efficiency esterification lipase variants compared with previous similar methods.

Dynamic influence of the two membrane-proximal immunoglobulin-like domains upon the peptide-binding platform domain in class I and class II major histocompatibility complexes: normal mode analysis

Major histocompatibility complexes (MHCs) mainly fall into class I and class II. The two classes have similar structures, with two membrane-proximal immunoglobulin-like domains and a peptide-binding platform domain, though their organizations are different. We simulated the dynamics of a whole and partial model deficient in either of the two membrane-proximal domains for class I and class II using normal mode analysis. Our study showed that the influence of the two membrane-proximal domains upon the dynamics of the platform domain were decisively different between class II and class I. Both membrane-proximal domains (the alpha2 and beta2 domains) of class II MHC, especially the alpha2 domain, influenced the most important pocket that accommodates a large hydrophobic anchor side chain of the N-terminal side of the bound peptide, though the pocket was not in the alpha2 domain neighborhood. By contrast, the two membrane-proximal domains (the alpha3 and beta2m domains) of class I MHC had little influence upon the most important pocket that accommodates the N-terminal residue of the bound peptide. These results suggest that the two membrane-proximal domains of class II MHC have a greater influence upon peptide-binding than those of class I MHC.

Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase

BACKGROUND

The characteristic of most lipases is the interfacial activation at a lipid interface or in non-polar solvents. Interfacial activation is linked to a large conformational change of a lid, from a closed to an open conformation which makes the active site accessible for substrates. While for many lipases crystal structures of the closed and open conformation have been determined, the pathway of the conformational transition and possible bottlenecks are unknown. Therefore, molecular dynamics simulations of a closed homology model and an open crystal structure of Burkholderia cepacia lipase in water and toluene were performed to investigate the influence of solvents on structure, dynamics, and the conformational transition of the lid.

RESULTS

The conformational transition of B. cepacia lipase was dependent on the solvent. In simulations of closed B. cepacia lipase in water no conformational transition was observed, while in three independent simulations of the closed lipase in toluene the lid gradually opened during the first 10-15 ns. The pathway of conformational transition was accessible and a barrier was identified, where a helix prevented the lid from opening to the completely open conformation. The open structure in toluene was stabilized by the formation of hydrogen bonds.In simulations of open lipase in water, the lid closed slowly during 30 ns nearly reaching its position in the closed crystal structure, while a further lid opening compared to the crystal structure was observed in toluene. While the helical structure of the lid was intact during opening in toluene, it partially unfolded upon closing in water. The closing of the lid in water was also observed, when with eight intermediate structures between the closed and the open conformation as derived from the simulations in toluene were taken as starting structures. A hydrophobic beta-hairpin was moving away from the lid in all simulations in water, which was not observed in simulations in toluene. The conformational transition of the lid was not correlated to the motions of the beta-hairpin structure.

CONCLUSION

Conformational transitions between the experimentally observed closed and open conformation of the lid were observed by multiple molecular dynamics simulations of B. cepacia lipase. Transitions in both directions occurred without applying restraints or external forces. The opening and closing were driven by the solvent and independent of a bound substrate molecule.

A dynamics study of the A-chain of ricin by terahertz vibrational calculation and normal modes analysis

We studied the terahertz (THz) spectroscopy and low frequency normal modes of both apo- and holo- (adenosine monophosphate (AMP)-bound) ricin-A-chain (RTA) as a means to understand the dynamical changes that RTA undergoes upon substrate binding. The calculated THz spectra of apo- and holo-RTAs demonstrated a general intensity suppression upon substrate binding, which is attributed to the reduced number of collective motion in THz region. In normal mode analysis of RTA we find a shearing motion that is shared by both the apo- and holo-RTAs, whereas a breathing motion, and an upward hinge rising and an alpha-G bending characteristic motion are dampened significantly upon AMP binding, suggesting these motions are involved in the necessary flexibility of the active site. In contrast, we find a normal mode motion that separates domains I and II of RTA at the interface that is more common in the holo-protein. We hypothesized that the flexibility of the entrance of RTA can facilitate the entry of rRNA and allow the substrate to adjust its conformation and orientation prior to depurination. This process suggests an rRNA binding pathway which is supplemental the current RTA depurination mechanism.

Terahertz spectroscopy of bacteriorhodopsin and rhodopsin: similarities and differences

We studied the low-frequency terahertz spectroscopy of two photoactive protein systems, rhodopsin and bacteriorhodopsin, as a means to characterize collective low-frequency motions in helical transmembrane proteins. From this work, we found that the nature of the vibrational motions activated by terahertz radiation is surprisingly similar between these two structurally similar proteins. Specifically, at the lowest frequencies probed, the cytoplasmic loop regions of the proteins are highly active; and at the higher terahertz frequencies studied, the extracellular loop regions of the protein systems become vibrationally activated. In the case of bacteriorhodopsin, the calculated terahertz spectra are compared with the experimental terahertz signature. This work illustrates the importance of terahertz spectroscopy to identify vibrational degrees of freedom which correlate to known conformational changes in these proteins.

Role of the Lid Hydrophobicity Pattern in Pancreatic Lipase Activity

Pancreatic lipase is a soluble globular protein that must undergo structural modifications before it can hydrolyze oil droplets coated with bile salts. The binding of colipase and movement of the lipase lid open access to the active site. Mechanisms triggering lid mobility are unclear. The *KNILSQIVDIDGI* fragment of the lid of the human pancreatic lipase is predicted by molecular modeling to be a tilted peptide. Tilted peptides are hydrophobicity motifs involved in membrane fusion and more globally in perturbations of hydrophobic/hydrophilic interfaces. Analysis of this lid fragment predicts no clear consensus of secondary structure that suggests that its structure is not strongly sequence determined and could vary with environment. Point mutations were designed to modify the hydrophobicity profile of the [240-252] fragment and their consequences on the lipase-mediated catalysis were tested. Two mutants, in which the tilted peptide motif was lost, also have poor activity on bile salt-coated oil droplets and cannot be reactivated by colipase. Conversely, one mutant in which a different tilted peptide is created retains colipase dependence. These results suggest that the tilted hydrophobicity pattern of the [240-252] fragment is neither important for colipase binding to lipase, nor for interfacial binding but is important to trigger the maximal catalytic efficiency of lipase in the presence of bile salt.

Mechanistic study of proton transfer and hysteresis in catalytic antibody 16E7 by site-directed mutagenesis and homology modeling

Antibody 16E7 catalyzes the carbon protonation of enol ether 2 to hemiacetal 3, and the carbon deprotonation of benzisoxazole 7 to phenol 8. This antibody shows an extreme case of hysteresis, requiring several hours to reach full activity. Antibody 16E7 was expressed as recombinant chimeric Fab in Escherichia coli. A model for the three-dimensional structure was produced by homology modeling and used for a docking procedure to obtain models for antibody-ligand complexes. Site-direct mutagenesis of GluL39, identified as a possible catalytic residue by the model, to either glutamine or alanine abolished catalysis, showing that both the protonation reaction of enol ether 2 and the deprotonation of benzisoxazole 7 are promoted by the same residue. The model furthermore suggested that substrate access to the catalytic site might be hindered by a flexible HCDR3 loop held in closed position by a hydrogen bond between SerH99 and GluL39, which could explain the observed hysteresis effect. In agreement with this model, mutagenesis of SerH99 to alanine, or deletion of this residue, was found to reduce hysteresis by approximately 50%.

Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant

Trypsin and chymotrypsin are both serine proteases with high sequence and structural similarities, but with different substrate specificity. Previous experiments have demonstrated the critical role of the two loops outside the binding pocket in controlling the specificity of the two enzymes. To understand the mechanism of such a control of specificity by distant loops, we have used the Gaussian network model to study the dynamic properties of trypsin and chymotrypsin and the roles played by the two loops. A clustering method was introduced to analyze the correlated motions of residues. We have found that trypsin and chymotrypsin have distinct dynamic signatures in the two loop regions, which are in turn highly correlated with motions of certain residues in the binding pockets. Interestingly, replacing the two loops of trypsin with those of chymotrypsin changes the motion style of trypsin to chymotrypsin-like, whereas the same experimental replacement was shown necessary to make trypsin have chymotrypsin's enzyme specificity and activity. These results suggest that the cooperative motions of the two loops and the substrate-binding sites contribute to the activity and substrate specificity of trypsin and chymotrypsin.

Specificity in lipases: a computational study of transesterification of sucrose

Computational conformational searches of putative transition states of the reaction of sucrose with vinyl laurate catalyzed by lipases from Candida antarctica B and Thermomyces lanuginosus have been carried out. The dielectric of the media have been varied to understand the role of protein plasticity in modulating the observed regioselective transesterification. The binding pocket of lipase from Candida adapts to the conformational variability of the various substates of the substrates by small, local adjustments within the binding pocket. In contrast, the more constrained pocket of the lipase from Thermomyces adapts by adjusting through concerted global motions between subdomains. This leads to the identification of one large pocket in Candida that accommodates both the sucrose and the lauroyl moieties of the transition state, whereas in Thermomyces the binding pocket is smaller, leading to the localization of the two moieties in two distinct pockets; this partly rationalizes the broader specificity of the former relative to the latter. Mutations have been suggested to exploit the differences towards changing the observed selectivities.

MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids

Analysis of vibrational motions and thermal fluctuational dynamics is a widely used approach for studying structural, dynamic and functional properties of proteins and nucleic acids. Development of a freely accessible web server for computation of vibrational and thermal fluctuational dynamics of biomolecules is thus useful for facilitating the relevant studies. We have developed a computer program for computing vibrational normal modes and thermal fluctuational properties of proteins and nucleic acids and applied it in several studies. In our program, vibrational normal modes are computed by using modified AMBER molecular mechanics force fields, and thermal fluctuational properties are computed by means of a self-consistent harmonic approximation method. A web version of our program, MoViES (Molecular Vibrations Evaluation Server), was set up to facilitate the use of our program to study vibrational dynamics of proteins and nucleic acids. This software was tested on selected proteins, which show that the computed normal modes and thermal fluctuational bond disruption probabilities are consistent with experimental findings and other normal mode computations. MoViES can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl.

Interaction between the antigen and antibody is controlled by the constant domains: normal mode dynamics of the HEL-HyHEL-10 complex

The antigen binding fragment (Fab) of a monoclonal antibody (HyHEL-10) consists of variable domains (Fv) and constant domains (CL-CH1). Normal modes have been calculated from the three-dimensional structures of hen egg lysozyme (HEL) with Fab, those of HEL with Fv, and so on. Only a small structural change was found between HEL-Fab and HEL-Fv complexes. However, HEL-Fv had a one order of magnitude lower dissociation constant than HEL-Fab. The Calpha fluctuations of HEL-Fab differed from those of HEL-Fv with normal mode calculation, and the dynamics can be thought to be related to the protein-protein interactions. CL-CH1 may have influence not only around local interfaces between CL-CH1 and Fv, but also around the interacting regions between HEL and Fv, which are longitudinally distant. Eighteen water molecules were found in HEL-Fv around the interface between HEL and Fv compared with one water molecule in HEL-Fab. These solvent molecules may occupy the holes and channels, which may occur due to imperfect complementarity of the complex. Therefore, the suppression of atomic vibration around the interface between Fv and HEL can be thought to be related to favorable and compact interface formation by complete desolvation. It is suggested that the ability to control the antigen-antibody affinity is obtained from modifying the CL-CH1. The second upper loop in the constant domain of the light chain (UL2-CL), which is a conserved gene in several light chains, showed the most remarkable fluctuation changes. UL2-CL could play an important role and could be attractive for modification in protein engineering.

Correlation between normal modes in the 20-200 cm-1 frequency range and localized torsion motions related to certain collective motions in proteins

In certain biologically relevant collective motions, such as protein domain motions and sub-domain motions, large amplitude movements are localized in one or a few flexible regions consisting of a small number of residues. This paper explores the possible use of normal mode analysis in probing localized vibrational torsion motions in these flexible regions that may be related to certain collective motions. The normal modes of 10 structures of five proteins in different conformation (TRP repressor, calmodulin, calbindin D(9k), HIV-1 protease and troponin C), known to have shear or hinge domain or sub-domain motion, respectively, are analyzed. Our study identifies, for each structure, unique normal modes in the 20-200 cm-1 frequency range, whose corresponding motions are primarily concentrated in the region where large amplitude torsion movements of a known domain or sub-domain motion occur. This suggests possible correlation between normal modes at 20-200 cm-1 frequency range and initial fluctuational motions leading to localized collective motions in proteins, and thus the potential application of normal mode analysis in facilitating the study of biologically important localized motions in biomolecules.

Elastic models of conformational transitions in macromolecules

We develop a computationally efficient and physically realistic method to simulate the transition of a macromolecule between two conformations. Our method is based on a coarse-grained elastic network model in which contact interactions between spatially proximal parts of the macromolecule are modelled with Gaussian/harmonic potentials. To delimit the interactions in such models, we introduce a cutoff to the permitted number of nearest neighbors. This generates stiffness (Hessian) matrices that are both sparse and quite uniform, hence, allowing for efficient computations. Several toy models are tested using our method to mimic simple classes of macromolecular motions such as stretching, hinge bending, shear, compression, ligand binding and nucleic acid structural transitions. Simulation results demonstrate that the method developed here reliably generates sequences of feasible intermediate conformations of macromolecules, since our method observes steric constraints and produces monotonic changes to virtual bond angles and torsion angles. A final application is made to the opening process of the protein lactoferrin.

Dynamic characteristics of a peptide-binding groove of human HLA-A2 class I MHC molecules: normal mode analysis of the antigen peptide-class I MHC complex

Class I major histocompatibility complex (MHC) binds antigen peptides with various sequences. We performed a normal mode analysis of HLA-A2 MHC that binds three peptides with different affinity. HLA-A2 MHC has a peptide-binding groove composed of two alpha-helices (residue 49-84, residue 140-179). Some residues in the center of the groove showed an increase in fluctuations and some residue pairs between two helix groups showed a negative change in correlations by removing the antigen peptide. The extent of the fluctuation and correlation changes correlated well with the experimental ranking of the three peptides in binding affinity. Some definite anti-correlative motions were found between two helix groups in low frequency modes (<50 cm(-1)) by removing the antigen peptide. We propose that the above anti-correlative motions play an important role to bind the antigen peptide, especially in obtaining a "dynamic fit."

Efficient generation of feasible pathways for protein conformational transitions

We develop a computationally efficient method to simulate the transition of a protein between two conformations. Our method is based on a coarse-grained elastic network model in which distances between spatially proximal amino acids are interpolated between the values specified by the two end conformations. The computational speed of this method depends strongly on the choice of cutoff distance used to define interactions as measured by the density of entries of the constant linking/contact matrix. To circumvent this problem we introduce the concept of using a cutoff based on a maximum number of nearest neighbors. This generates linking matrices that are both sparse and uniform, hence allowing for efficient computations that are independent of the arbitrariness of cutoff distance choices. Simulation results demonstrate that the method developed here reliably generates feasible intermediate conformations, because our method observes steric constraints and produces monotonic changes in virtual bond and torsion angles. Applications are readily made to large proteins, and we demonstrate our method on lactate dehydrogenase, citrate synthase, and lactoferrin. We also illustrate how this framework can be used to complement experimental techniques that partially observe protein motions.

Conformational change of proteins arising from normal mode calculations

A normal mode analysis of 20 proteins in 'open' or 'closed' forms was performed using simple potential and protein models. The quality of the results was found to depend upon the form of the protein studied, normal modes obtained with the open form of a given protein comparing better with the conformational change than those obtained with the closed form. Moreover, when the motion of the protein is a highly collective one, then, in all cases considered, there is a single low-frequency normal mode whose direction compares well with the conformational change. When it is not, in most cases there is still a single low-frequency normal mode giving a good description of the pattern of the atomic displacements, as they are observed experimentally during the conformational change. Hence a lot of information on the nature of the conformational change of a protein is often found in a single low-frequency normal mode of its open form. Since this information can be obtained through the normal mode analysis of a model as simple as that used in the present study, it is likely that the property captured by such an analysis is for the most part a property of the shape of the protein itself. One of the points that has to be clarified now is whether or not amino acid sequences have been selected in order to allow proteins to follow a single normal mode direction, as least at the very beginning of their conformational change.