Identifying molecular mechanisms of catechol o-methyltransferase activity and regulation

Catechol O-methyltransferase (COMT) is a regioselective enzyme that functions by metabolizing catecholamines such as neurotransmitters and hormones via methylation at a single hydroxyl of the catechol moiety. Two cofactors are necessary in order to catalyze the reaction: S-adenosyl-L-methionine (SAM) and a divalent metal cation. Through computational docking studies, we show that a reason metal cations may be necessary for catalysis is due to its role in aligning the donating methyl group of SAM with the nucleophile of the substrate. It is intriguing that an enzyme whose sole function is to degrade catecholamines contains highly conserved residues responsible for regioselective behavior at the catechol moiety, a function in which site-specific chemistry seems unnecessary. Our barrier height calculations for two different COMT ligands suggest that deprotonating the meta- hydroxyl leads to higher rates of methylation and consequently there is evolutionary pressure for selecting residues that can dock the ligand in an ideal conformation for efficient catalysis. Our group previously identified three major haplotypes of COMT, where two single nucleotide polymorphisms (SNPs) produce synonymous changes and an additional SNP that creates a low enzymatic activity variant (Val108Met). Here we show that the allelic variant encoding for the low activity protein shows the highest translational efficiency among the haplotypes, suggesting evolutionary selection of an RNA-structure destabilizing allele to compensate for the low activity mutation present within its protein structure. We provide a mechanism whereby destabilizing alleles may facilitate translation initiation via computational modeling of each mRNA haplotype. One of several biological factors that COMT influences is pain perception because of its role in degrading the neurotransmitters. Peripherally injected serotonin has been clinically shown to induce a hyperalgesic effect. Here we report that serotonin-induced hyperalgesia may be induced by inhibition of COMT. Our kinetic assays reveal serotonin as a non-competitive inhibitor with respect to catechol substrates. From computational modeling, we observe serotonin actively competing with the methyl donor S-adenosyl-L-methionine at the active site. Binding of COMT to serotonin inhibits the methyl donor from entering the active site, thus preventing methylation of COMT substrates

Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity

A cell's interior is comprised of macromolecules that can occupy up to 40% of its available volume. Such crowded environments can influence the stability of proteins and their rates of reaction. Using discrete molecular dynamics simulations, we investigate how both the size and number of neighboring crowding reagents affect the thermodynamic and folding properties of structurally diverse proteins. We find that crowding induces higher compaction of proteins. We also find that folding becomes less cooperative with the introduction of crowders into the system. The crowders may induce alternative non-native protein conformations, thus creating barriers for protein folding in highly crowded media

Regioselectivity of catechol O-methyltransferase confers enhancement of catalytic activity

Catechol O-methyltransferase (COMT) metabolizes catechol moieties by methylating a single hydroxyl group at the meta- or para- hydroxyl position. Hydrophobic amino acids near the active site of COMT influence the regioselectivity of this reaction. Our sequence analysis highlights their importance by showing that these residues are highly conserved throughout evolution. Reaction barriers calculated in the gas phase reveal a lower barrier during methylation at the meta- position, suggesting that the observed meta-regioselectivity of COMT can be attributed to the substrate itself, and that COMT has evolved residues to orient the substrate in a manner that increases the rate of catalysis

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions

Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

Until now it has been impractical to observe protein folding in silico for proteins larger than 50 residues. Limitations of both force field accuracy and computational efficiency make the folding problem very challenging. Here we employ discrete molecular dynamics (DMD) simulations with an all-atom force field to fold fast-folding proteins. We extend the DMD force field by introducing long-range electrostatic interactions to model salt-bridges and a sequence-dependent semi-empirical potential accounting for natural tendencies of certain amino acid sequences to form specific secondary structures. We enhance the computational performance by parallelizing the DMD algorithm. Using a small number of commodity computers, we achieve sampling quality and folding accuracy comparable to the explicit-solvent simulations performed on high-end hardware. We demonstrate that DMD can be used to observe equilibrium folding of villin headpiece and WW domain, study two-state folding kinetics and sample near-native states in ab initio folding of proteins of ~100 residues

Effectiveness of an Inpatient Movement Disorders Program for Patients with Atypical Parkinsonism

This paper investigated the effectiveness of an inpatient movement disorders program for patients with atypical parkinsonism, who typically respond poorly to pharmacologic intervention and are challenging to rehabilitate as outpatients. Ninety-one patients with atypical parkinsonism participated in an inpatient movement disorders program. Patients received physical, occupational, and speech therapy for 3 hours/day, 5 to 7 days/week, and pharmacologic adjustments based on daily observation and data. Differences between admission and discharge scores were analyzed for the functional independence measure (FIM), timed up and go test (TUG), two-minute walk test (TMW), Berg balance scale (BBS) and finger tapping test (FT), and all showed significant improvement on discharge (P > .001). Clinically significant improvements in total FIM score were evident in 74% of the patients. Results were similar for ten patients whose medications were not adjusted. Patients with atypical parkinsonism benefit from an inpatient interdisciplinary movement disorders program to improve functional status

Computational neuroscience: a frontier of the 21st century

The human brain is a biological organ, weighing about three pounds or 1.4 kg, that determines our behaviors, thoughts, emotions and consciousness. Although comprising only 2% of the total body weight, the brain consumes about 20% of the oxygen entering the body. With the expensive energy demand, the brain enables us to perceive and act upon the external world, as well as reflect on our internal thoughts and feelings. The brain is actually never at ‘rest’. Brain activities continue around the clock, ranging from functions enabling human–environment interactions to housekeeping during sleep, including processes such as synaptic homeostasis and memory formation. Whereas one could argue that sciences in the last century were dominated by physics and molecular biology, in the current century one of our major challenges is to elucidate how the brain works. A full understanding of brain functions and malfunctions is likely the most demanding task we will ever have

Computational neuroscience: a frontier of the 21st century

The human brain is a biological organ, weighing about three pounds or 1.4 kg, that determines our behaviors, thoughts, emotions and consciousness. Although comprising only 2% of the total body weight, the brain consumes about 20% of the oxygen entering the body. With the expensive energy demand, the brain enables us to perceive and act upon the external world, as well as reflect on our internal thoughts and feelings. The brain is actually never at ‘rest’. Brain activities continue around the clock, ranging from functions enabling human–environment interactions to housekeeping during sleep, including processes such as synaptic homeostasis and memory formation. Whereas one could argue that sciences in the last century were dominated by physics and molecular biology, in the current century one of our major challenges is to elucidate how the brain works. A full understanding of brain functions and malfunctions is likely the most demanding task we will ever have

Irreversible Adsorption from Dilute Polymer Solutions

We study irreversible polymer adsorption from dilute solutions theoretically. Universal features of the resultant non-equilibrium layers are predicted. Two cases are considered, distinguished by the value of the local monomer-surface sticking rate Q: chemisorption (very small Q) and physisorption (large Q). Early stages of layer formation entail single chain adsorption. While single chain physisorption times tau_ads are typically microsecs, for chemisorbing chains of N units we find experimentally accessible times tau_ads = Q^{-1} N^{3/5}, ranging from secs to hrs. We establish 3 chemisorption universality classes, determined by a critical contact exponent: zipping, accelerated zipping and homogeneous collapse. For dilute solutions, the mechanism is accelerated zipping: zipping propagates outwards from the first attachment, accelerated by occasional formation of large loops which nucleate further zipping. This leads to a transient distribution omega(s) \sim s^{-7/5} of loop lengths s up to a size s_max \approx (Q t)^{5/3} after time t. By tau_ads the entire chain is adsorbed. The outcome of the single chain adsorption episode is a monolayer of fully collapsed chains. Having only a few vacant sites to adsorb onto, late arriving chains form a diffuse outer layer. In a simple picture we find for both chemisorption and physisorption a final loop distribution Omega(s) \sim s^{-11/5} and density profile c(z) \sim z^{-4/3} whose forms are the same as for equilibrium layers. In contrast to equilibrium layers, however, the statistical properties of a given chain depend on its adsorption time; the outer layer contains many classes of chain, each characterized by different fraction of adsorbed monomers f. Consistent with strong physisorption experiments, we find the f values follow a distribution P(f) \sim f^{-4/5}.Comment: 18 pages, submitted to Eur. Phys. J. E, expanded discussion sectio