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1.
Results Chem ; 52023 Jan.
Article in English | MEDLINE | ID: mdl-37485304

ABSTRACT

Vapor-phase molecular simulation studies of aromatic compounds with five or more fluorine atoms on the ring reveal emission spectra characterized by S0 → πσ* and πσ*→S0 transitions. In this study, the absorption, excitation, and solvent-dependent emission spectra of fluorinated benzenes, including pentaflurophenyalanine (F5Phe), which is a potential marker for biochemical research, were collected and compared to the results of the simulation. Time-dependent self-consistent field (TD-SCF) density functional theory (DFT) calculations were performed to examine the nature of excited states and relevant photo-physical processes. The results show that pentafluorobenzene (PFB) and hexafluorobenzene (HFB) show behavior consistent with the vapor phase simulation studies, that tracts well with benzenes substituted with fewer fluorine atoms. For example, 1,2,3-trifluorobenzene (123TFB) and 1,2,3,4-tetrafluorobenzene (1234TFB) show emission spectra with varying intensities of tails and shoulders. Those features are attributed to πσ*→S0 transitions where the πσ* state has been stabilized in the presence of solvents like water, acetonitrile, and isopropanol, which are different from their simulated behavior in the gas phase. The emission in water solvent especially shows a significant increase in the emission intensity at 310 nm, which is common for all studied samples. The emission spectrum of F5Phe closely reflects that of PFB, which arises from the interplay of both ππ *→S0 and πσ*→S0 transitions. Also, it is observed that the interaction between adjacent σ* orbitals of C-F bond for 123-TFB, 1234-TFB, 12345-PFB, and 123456-HFB contributes to further narrowing the energy gap between S0 and S1 states with a significant red shift on the emission spectra compared to their isomers.

2.
Vib Spectrosc ; 96: 93-100, 2018 May.
Article in English | MEDLINE | ID: mdl-30369718

ABSTRACT

Estrogens are a group of steroid compounds found in the human body that are eventually discharged and ultimately end up in sewer effluents. Since these compounds can potentially affect the endocrine system its detection and quantification in sewer water is important. In this study, estrogens such as estrone (E1), estradiol (E2), estriol (E3), and ethynylestradiol (EE2) were discriminated and quantitated using Raman spectroscopy. Simulated Raman spectra were correlated with experimental data to identify unique marker peaks, which proved to be useful in differentiating each estrogen molecules. Among these marker peaks are Raman modes arising from hydroxyl groups of the estrogen molecules in the spectral region 3200-3700 cm-1. Other Raman modes unique to each of the estrogen samples were also identified, including peaks at 1722 cm-1 for E1 and 2109 cm-1 for EE2, which corresponds to their distinctive structures each containing a different set of functional groups. To quantify the components of estrogen mixtures, the intensities of each identifying Raman bands, at 581 cm-1 for E1, 546 cm-1 for E2, 762 cm-1 for E3 and 597 cm-1 for EE2, were compared and normalized against the intensity of a common peak at 783 cm-1. Quantitative analysis yielded most results within an acceptable 20% error.

3.
Methods Mol Biol ; 1824: 1-16, 2018.
Article in English | MEDLINE | ID: mdl-30039398

ABSTRACT

This chapter includes information about the structure in equilibrium of the bioactive molecule hIAPP22-29 (NFGAILSS). The experimental structure was derived using X-ray and its 2D NOESY NMR experiments in d 6-DMSO and d-HFIP solvents. This molecule contains eight of the ten amino acids of the 20-29 region of the human islet amyloid polypeptide (hIAPP) often referred as the "amyloidogenic core." Amyloid deposits are well-known to cause as many as 20 pathological neurodegenerative disorders such as Alzheimer, Parkinson, Huntington, and Creutzfeldt-Jakob. The experimental structure was relaxed using molecular dynamics (MD) in simulation boxes consisting in DMSO and HFIP; the latter not provided by the applied software. The calculations were performed in GPUs and supercomputers, and some basic scripting is described for reference. The simulations confirmed the inter- and intramolecular forces that led to an "amyloidogenic core" observed from NOE experiments. The results showed that in DMSO and HFIP environment, Phe is not in spatial proximity with Leu or Ile, and this is consistent with an amyloidogenic core. However, in an amphipathic environment such as the model lipid bilayers, this communication is possible and may influence peptide amyloidogenic properties. The knowledge gained through this study may contribute to the rational drug design of novel peptides or organic molecules acting by modifying preventing amyloidogenic properties of the hIAPP peptide.


Subject(s)
Dimethyl Sulfoxide/chemistry , Islet Amyloid Polypeptide/chemistry , Magnetic Resonance Spectroscopy/methods , Molecular Dynamics Simulation , Peptide Fragments/chemistry , Humans , Protein Structure, Secondary
4.
Methods Mol Biol ; 1824: 17-31, 2018.
Article in English | MEDLINE | ID: mdl-30039399

ABSTRACT

Human islet amyloid polypeptide (hIAPP) is a 37-residue hormone that is co-stored and co-secreted with insulin. In type 2 diabetes, the polypeptide misfolds to form amyloid plaques in the pancreas. The self-assembly of hIAPP has been linked to the loss of insulin production and ß-cell death. Recent investigations have revealed that soluble oligomers of hIAPP are the cytotoxic species responsible for ß-cell death and not insoluble amyloid fibrils. Compounds that prevent the self-assembly of hIAPP or drive self-assembly to the state of innocuous insoluble amyloid may be of potential therapeutic value. In this report we summarize key methods employed in our efforts to identify peptide-based modulators of amylin self-assembly that utilize π-electronic effects or electrostatic charge repulsion. These peptide-based modulators may serve as lead compounds for the development of more drug-like molecules and demonstrate that tuning π-electron density and employing charged amyloid disrupting elements are viable approaches toward the design of potential amyloid inhibitors.


Subject(s)
Islet Amyloid Polypeptide/chemistry , Protein Aggregates , Protein Aggregation, Pathological , Static Electricity , Humans
5.
J Raman Spectrosc ; 48(10): 1282-1288, 2017 Oct.
Article in English | MEDLINE | ID: mdl-29225410

ABSTRACT

Two α-cyanohydroxycinnamic acid positional isomers, α-cyano-4-hydroxycinnamic acid (CHCA4) and α-cyano-3-hydroxycinnamic acid (CHCA3), were characterized using Raman spectroscopy. We analyzed the implications of the collected Raman spectral shifts, and verified them through other spectroscopic techniques, to arrive at plausible three dimensional structures of CHCA3 and CHCA4. The positions of these groups were mapped by systematically analyzing the orientation and type of interactions functional groups make in each CHCA isomer. We determined whether or not the carboxylic moieties are forming dimeric links and ascertained the existence of ring-ring π-stacking interactions. We also assessed the nature of the hydrogen bonding between -CN and -OH groups. The results were then taken together to model plausible three dimensional structures for each compound. The data revealed a structure for CHCA4 that matches the published x-ray crystallographic structure. We then applied the same spectral analysis to CHCA3 to reveal its plausible three dimensional structure. The structural details revealed may account for the functional properties of the two α-cyanohydroxycinnamic acid positional isomers.

6.
J Phys Chem B ; 121(43): 10036-10045, 2017 11 02.
Article in English | MEDLINE | ID: mdl-28990791

ABSTRACT

Triosephosphate isomerase (TIM) catalyzes the interconversion between dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (GAP), via an enediol(ate) intermediate. Determination of substrate population distribution in the TIM/substrate reaction mixture at equilibrium and characterization of the substrate-enzyme interactions in the Michaelis complex are ongoing efforts toward the understanding of the TIM reaction mechanism. By using isotope-edited difference Fourier transform infrared studies with unlabeled and 13C-labeled substrates at specific carbon(s), we are able to show that in the reaction mixture at equilibrium the keto DHAP is the dominant species and the populations of aldehyde GAP and enediol(ate) are very low, consistent with the results from previous X-ray structural and 13C NMR studies. Furthermore, within the DHAP side of the Michaelis complex, there is a set of conformational substates that can be characterized by the different C2═O stretch frequencies. The C2═O frequency differences reflect the different degree of the C2═O bond polarization due to hydrogen bonding from active site residues. The C2═O bond polarization has been considered as an important component for substrate activation within the Michaelis complex. We have found that in the enzyme-substrate reaction mixture with TIM from different organisms the number of substates and their population distribution within the DHAP side of the Michaelis complex may be different. These discoveries provide a rare opportunity to probe the interconversion dynamics of these DHAP substates and form the bases for the future studies to determine if the TIM-catalyzed reaction follows a simple linear reaction pathway, as previously believed, or follows parallel reaction pathways, as suggested in another enzyme system that also shows a set of substates in the Michaelis complex.


Subject(s)
Spectroscopy, Fourier Transform Infrared , Triose-Phosphate Isomerase/chemistry , Triose-Phosphate Isomerase/metabolism , Catalytic Domain , Dihydroxyacetone/chemistry , Glyceraldehyde 3-Phosphate/chemistry , Molecular Structure , Solutions , Substrate Specificity
7.
Bioconjug Chem ; 28(2): 666-677, 2017 02 15.
Article in English | MEDLINE | ID: mdl-28071890

ABSTRACT

Human islet amyloid polypeptide (hIAPP), also known as amylin, is a 37 residue peptide hormone that is stored and co-secreted with insulin. hIAPP plays a pivotal role in type 2 diabetes and is the major component of amyloid deposits found in the pancreas of patients afflicted with the disease. The self-assembly of hIAPP and the formation of amyloid is linked to the death of insulin producing ß-cells. Recent findings suggest that soluble hIAPP oligomers are the cytotoxic species responsible for ß-cell loss whereas amyloid fibrils themselves may indeed be innocuous. Potential avenues of therapeutic intervention include the development of compounds that prevent hIAPP self-assembly as well as those that reduce or eliminate lag time and rapidly accelerate the formation of amyloid fibrils. Both of these approaches minimize temporal exposure to soluble cytotoxic hIAPP oligomers. Toward this end our laboratory has pursued an electrostatic repulsion approach to the development of potential inhibitors and modulators of hIAPP self-assembly. Peptide conjugates were constructed in which benzene carboxylic acids of varying charge were employed as electrostatic disrupting elements and appended to the N-terminal of the hIAPP22-29 (NFGAILSS) self-recognition sequence. The self-assembly kinetics of conjugates were characterized by turbidity measurements and the structure of aggregates probed by Raman and CD spectroscopy while the morphology was assessed using transmission electron microscopy. Several benzene carboxylic acid peptide conjugates failed to self-assemble and some were found to inhibit the aggregation of full-length amylin while others served to enhance the rate of amyloid formation and/or increase the yield of amyloid produced. Studies reveal that the geometric display of free carboxylates on the benzene ring of the conjugates plays an important role in the activity of conjugates. In addition, a number of free benzene carboxylic acids were found to modulate amylin self-assembly on their own. The results of these investigations confirm the viability of the electrostatic repulsion approach to the modulation of amyloid formation and may aid the design and development of potential therapeutic agents.


Subject(s)
Amyloid/antagonists & inhibitors , Benzene/pharmacology , Islet Amyloid Polypeptide/metabolism , Peptides/pharmacology , Protein Aggregates/drug effects , Amino Acid Sequence , Amyloid/metabolism , Amyloid/ultrastructure , Benzene/chemistry , Carboxylic Acids/chemistry , Carboxylic Acids/pharmacology , Humans , Islet Amyloid Polypeptide/chemistry , Islet Amyloid Polypeptide/ultrastructure , Models, Molecular , Peptides/chemistry
8.
Biochemistry ; 55(27): 3803-14, 2016 Jul 12.
Article in English | MEDLINE | ID: mdl-27319381

ABSTRACT

Laser-induced temperature-jump relaxation spectroscopy was used to study the active site mobile-loop dynamics found in the binding of the NADH nucleotide cofactor and oxamate substrate mimic to lactate dehydrogenase in Bacillus stearothermophilus thermophilic bacteria (bsLDH). The kinetic data can be best described by a model in which NADH can bind only to the open-loop apoenzyme, oxamate can bind only to the bsLDH·NADH binary complex in the open-loop conformation, and oxamate binding is followed by closing of the active site loop preventing oxamate unbinding. The open and closed states of the loop are in dynamic equilibrium and interconvert on the submillisecond time scale. This interconversion strongly accelerates with an increase in temperature because of significant enthalpy barriers. Binding of NADH to bsLDH results in minor changes of the loop dynamics and does not shift the open-closed equilibrium, but binding of the oxamate substrate mimic shifts this equilibrium to the closed state. At high excess oxamate concentrations where all active sites are nearly saturated with the substrate mimic, all active site mobile loops are mainly closed. The observed active-loop dynamics for bsLDH is very similar to that previously observed for pig heart LDH.


Subject(s)
Geobacillus stearothermophilus/enzymology , L-Lactate Dehydrogenase/chemistry , L-Lactate Dehydrogenase/metabolism , NAD/metabolism , Animals , Binding Sites , Catalytic Domain , Kinetics , Protein Binding , Protein Conformation , Substrate Specificity , Swine , Thermodynamics
9.
J Mol Struct ; 1094: 203-209, 2015 Aug 15.
Article in English | MEDLINE | ID: mdl-25937671

ABSTRACT

In the present study, a comparative Raman vibrational analysis of alpha-cyano-4-hydroxycinnamic acid (4CHCA) and its derivative, alpha-cyano-3-hydroxycinnamic acid (3CHCA), was performed. The Raman spectra of the 4CHCA and 3CHCA in solid form were obtained and analyzed to determine differences between the two structurally similar derivatives. For comparison, the CHCA derivatives cyanocinnamic acid (CCA) and coumaric acid (CA) were also studied. The plausible vibrational assignments were made and matched with those obtained theoretically using density functional theory (DFT) based method employing a 6-31 g basis set. The computational wavenumbers obtained were in good agreement with the observed experimental results. This was the first reported Raman study of CCA, 3CHCA and 4CHCA.

10.
Arch Biochem Biophys ; 567: 46-58, 2015 Feb 01.
Article in English | MEDLINE | ID: mdl-25524740

ABSTRACT

A comprehensive investigation of peptides derived from the 22-29 region of human islet amyloid polypeptide (hIAPP) that contain phenylalanine analogs at position 23 with a variety of electron donating and withdrawing groups, along with heteroaromatic surrogates, has been employed to interrogate how π-electron distribution effects amyloid formation. Kinetic aggregation studies using turbidity measurements indicate that electron rich aromatic ring systems consistently abolish the amyloidogenic propensity of hIAPP(22-29). Electron poor systems modulate the rate of aggregation. Raman and Fourier transform infrared spectroscopy confirm the parallel ß-sheet secondary structure of aggregates derived from peptides containing electron poor phenylalanine analogs and provide direct evidence of ring stacking. Transmission electron microscopy confirms the presence of amyloid fibrils. The effect of aryl substituent geometry on peptide self-assembly reveals that the electronic nature of substituents and not their steric profile is responsible for failure of the electron donating group peptides to aggregate. Non-aggregating hIAPP(22-29) peptides were found to inhibit the self-assembly of full-length hIAPP(1-37). The most potent inhibitory peptides contain phenylalanine with the p-amino and p-formamido functionalities. These novel peptides may serve as leads for the development of future aggregation inhibitors. A potential mechanism for inhibition of amylin self-assembly by electron rich (-29) peptides is proposed.


Subject(s)
Electrons , Islet Amyloid Polypeptide/chemistry , Peptide Fragments/chemistry , Protein Aggregation, Pathological , Amino Acid Sequence , Humans
11.
Biochemistry ; 52(11): 1886-92, 2013 Mar 19.
Article in English | MEDLINE | ID: mdl-23428201

ABSTRACT

Large scale dynamics within the Michaelis complex mimic of Bacillus stearothermophilus thermophilic lactate dehydrogenase, bsLDH·NADH·oxamate, were studied with site specific resolution by laser-induced temperature jump relaxation spectroscopy with a time resolution of 20 ns. NADH emission and Trp emission from the wild type and a series of single-tryptophan bsLDH mutants, with the tryptophan positions different distances from the active site, were used as reporters of evolving structure in response to the rapid change in temperature. Several distinct dynamical events were observed on the millisecond to microsecond time scale involving motion of atoms spread over the protein, some occurring concomitantly or nearly concomitantly with structural changes at the active site. This suggests that a large portion of the protein-substrate complex moves in a rather concerted fashion to bring about catalysis. The catalytically important surface loop undergoes two distinct movements, both needed for a competent enzyme. Our results also suggest that what is called "loop motion" is not just localized to the loop and active site residues. Rather, it involves the motion of atoms spread over the protein, even some quite distal from the active site. How these results bear on the catalytic mechanism of bsLDH is discussed.


Subject(s)
Geobacillus stearothermophilus/enzymology , L-Lactate Dehydrogenase/genetics , L-Lactate Dehydrogenase/metabolism , Tryptophan/genetics , Catalytic Domain , Geobacillus stearothermophilus/genetics , Geobacillus stearothermophilus/metabolism , Kinetics , L-Lactate Dehydrogenase/chemistry , Models, Molecular , NAD/chemistry , NAD/metabolism , Oxamic Acid/chemistry , Oxamic Acid/metabolism , Point Mutation , Protein Conformation , Temperature , Tryptophan/chemistry , Tryptophan/metabolism
12.
Proteins ; 81(4): 690-703, 2013 Apr.
Article in English | MEDLINE | ID: mdl-23229921

ABSTRACT

The role aromatic amino acids play in the formation of amyloid is a subject of controversy. In an effort to clarify the contribution of aromaticity to the self-assembly of human islet amyloid polypeptide (hIAPP)22-29 , peptide analogs containing electron donating groups (EDGs) or electron withdrawing groups (EWGs) as substituents on the aromatic ring of Phe-23 at the para position have been synthesized and characterized using turbidity measurements in conjunction with Raman and fluorescence spectroscopy. Results indicate the incorporation of EDGs on the aromatic ring of Phe-23 virtually abolish the ability of hIAPP22-29 to form amyloid. Peptides containing EWGs were still capable of forming aggregates. These aggregates were found to be rich in ß-sheet secondary structure. Transmission electron microscopy images of the aggregates confirm the presence of amyloid fibrils. The observed difference in amyloidogenic propensity between peptides containing EDGs and those with EWGs appears not to be based on differences in peptide hydrophobicity. Fluorescence and Raman spectroscopic investigations reveal that the environment surrounding the aromatic ring becomes more hydrophobic and ordered upon aggregation. Furthermore, Raman measurements of peptide analogs containing EWGs, conclusively demonstrate a distinct downshift in the CC ring mode (ca. 1600 cm(-1) ) upon aggregation that has previously been shown to be indicative of π-stacking. While previous work has demonstrated that π-stacking is not an absolute requirement for fibrillization, our findings indicate that Phe-23 also contributes to fibril formation through π-stacking interactions and that it is not only the hydrophobic nature of this residue that is relevant in the self-assembly of hIAPP22-29 . © Proteins 2013. © 2012 Wiley Periodicals, Inc.


Subject(s)
Amyloid/chemistry , Electrons , Islet Amyloid Polypeptide/chemistry , Phenylalanine/chemistry , Amyloid/metabolism , Amyloid/ultrastructure , Humans , Hydrophobic and Hydrophilic Interactions , Islet Amyloid Polypeptide/metabolism , Islet Amyloid Polypeptide/ultrastructure , Phenylalanine/metabolism , Protein Structure, Secondary
13.
J Phys Chem B ; 115(23): 7670-8, 2011 Jun 16.
Article in English | MEDLINE | ID: mdl-21568287

ABSTRACT

A series of isotope edited IR measurements, both static as well as temperature jump relaxation spectroscopy, are performed on lactate dehydrogenase (LDH) to determine the ensemble of structures available to its Michaelis complex. There clearly has been a substantial reduction in the number of states available to the pyruvate substrate (as modeled by the substrate mimic, oxamate) and NADH when bound to protein compared to dissolved in solution, as determined by the bandwidths and positions of the critical C(2)═O band of the bound substrate mimic and the C(4)-H stretch of the NADH reduced nicotinamide group. Moreover, it is found that a strong ionic bond (characterized by a signature IR band discovered in this study) is formed between the carboxyl group of bound pyruvate with (presumably) Arg171, forming a strong "anchor" within the protein matrix. However, conformational heterogeneity within the Michaelis complex is found that has an impact on both catalytic efficiency and thermodynamics of the enzyme.


Subject(s)
L-Lactate Dehydrogenase , Vibration , Catalytic Domain , Crystallography, X-Ray , L-Lactate Dehydrogenase/chemistry , L-Lactate Dehydrogenase/metabolism , Models, Molecular , NAD/chemistry , NAD/metabolism , Protein Conformation , Pyruvic Acid/chemistry , Pyruvic Acid/metabolism , Spectroscopy, Fourier Transform Infrared
14.
Appl Spectrosc ; 63(7): 767-74, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19589214

ABSTRACT

The spectral properties of the SH2 and active site-directed sequences of the bivalent Src kinase inhibitor Ac-EELL(F5)Phe-(GABA)3-pYEEIE-amide (1) have been determined. Ac-pYEEIE-amide (2) and AcEELL(F5)Phe-amide (3), as well as the amino acids phosphotyrosine (pTyr) and pentafluorophenylalanine (F5)Phe, have been characterized by electronic absorption, fluorescence, and vibrational spectroscopy. Specific and unique marker bands that originate from the phosphate group of pTyr and the fluorinated aromatic ring of (F5)Phe have been identified, with the latter showing some solvent dependence. Peptide 2 was found to have excitation and emission wavelengths emanating from pTyr at 268 and 295 nm, respectively, whereas peptide 3 displayed excitation and emission peaks attributable to (F5)Phe at 274 and 315 nm, respectively. Fourier transform infrared (FT-IR) analysis of the amino acid pTyr identified distinct marker bands at approximately 930, 1090, and 1330 cm(-1) that could be attributed to the phosphate group. These markers were also observed in the IR spectrum of peptide 2. Likewise, peptide 3 displayed a characteristic C-F stretching mode at 961 cm(-1) due to the presence of (F5)Phe, including two C-F reporting ring modes at 1509 and 1527 cm(-1). Identifying and monitoring spectroscopic changes in these marker bands may afford a means to observe the molecular interactions that occur when peptides 1-3 bind to the Src kinase.


Subject(s)
Peptides/chemistry , Protein Kinase Inhibitors/chemistry , Spectroscopy, Fourier Transform Infrared/methods , src Homology Domains , src-Family Kinases/antagonists & inhibitors , Catalytic Domain , Computer Simulation , Models, Chemical , Peptides/pharmacology , Phenylalanine/chemistry , Phosphotyrosine/chemistry , Protein Kinase Inhibitors/pharmacology , Solvents/chemistry , src-Family Kinases/chemistry , src-Family Kinases/metabolism
15.
Biochemistry ; 48(12): 2777-87, 2009 Mar 31.
Article in English | MEDLINE | ID: mdl-19267450

ABSTRACT

The correlation of the UVRR nuW3 mode with the tryptophan chi(2,1) dihedral angle [Maruyama and Takeuchi (1995) J. Raman Spectrosc. 26, 319; Miura et al. (1989) J. Raman Spectrosc. 20, 667; Takeuchi (2003) Biopolymers 72, 305] has been extended to a full, 360 degrees rotation. The 3-fold periodicity of the relationship (cos 3chi(2,1)) over 360 degrees results in up to six dihedral angles for a given nuW3. Consideration of a Newman plot of dihedral angles for proteinaceous tryptophans taken from the Protein Data Bank shows that sterically hindered ranges of dihedral angle reduce the possible chi(2,1) to one or two. However, not all proteinaceous tryptophans follow the nuW3-chi(2,1) relationship. Hydrogen bonding at the indole amine, weaker, electrostatic cation-pi and anion-quadrapole interactions, and environmental hydrophobicity are examined as possible contributing factors to noncompliance with the relationship. This evaluation suggests that cumulative weak electrostatic and nonpolar interactions, contributing to steric hindrance, characterize the environment of tryptophans that obey the nuW3-chi(2,1) relationship, matching that of the crystalline tryptophan derivatives used to formulate the relationship. In the absence of methods to quantify these weak interactions, measurement of the full width half-maximum bandwidth (fwhm) of the W3 band is suggested as a primary screen for evaluating the applicability of the nuW3-chi(2,1) relationship.


Subject(s)
Tryptophan/chemistry , Databases, Protein , Hydrophobic and Hydrophilic Interactions , Models, Molecular , Spectrum Analysis, Raman
16.
Biochemistry ; 46(35): 10055-62, 2007 Sep 04.
Article in English | MEDLINE | ID: mdl-17696453

ABSTRACT

During cell volume regulation, intracellular concentration changes occur in both inorganic and organic osmolytes in order to balance the extracellular osmotic stress and maintain cell volume homeostasis. Generally, salt and urea increase the Km's of enzymes and trimethylamine N-oxide (TMAO) counteracts these effects by decreasing Km's. The hypothesis to account for these effects is that urea and salt shift the native state ensemble of the enzyme toward conformers that are substrate-binding incompetent (BI), while TMAO shifts the ensemble toward binding competent (BC) species. Km's are often complex assemblies of rate constants involving several elementary steps in catalysis, so to better understand osmolyte effects we have focused on a single elementary event, substrate binding. We test the conformational shift hypothesis by evaluating the effects of salt, urea, and TMAO on the mechanism of binding glycerol 3-phosphate, a substrate analogue, to yeast triosephosphate isomerase. Temperature-jump kinetic measurements promote a mechanism consistent with osmolyte-induced shifts in the [BI]/[BC] ratio of enzyme conformers. Importantly, salt significantly affects the binding constant through its effect on the activity coefficients of substrate, enzyme, and enzyme-substrate complex, and it is likely that TMAO and urea affect activity coefficients as well. Results indicate that the conformational shift hypothesis alone does not account for the effects of osmolytes on Km's.


Subject(s)
Cell Size/drug effects , Glycerophosphates/metabolism , Methylamines/pharmacology , Models, Molecular , Sodium Chloride/pharmacology , Triose-Phosphate Isomerase/metabolism , Urea/pharmacology , Algorithms , Dose-Response Relationship, Drug , Enzyme Activation/drug effects , Glycerophosphates/chemistry , Kinetics , Methylamines/metabolism , Models, Chemical , Osmosis/drug effects , Protein Binding/drug effects , Protein Denaturation/drug effects , Protein Folding , Sodium Chloride/metabolism , Substrate Specificity/drug effects , Thermodynamics , Triose-Phosphate Isomerase/drug effects , Urea/metabolism
17.
Biochemistry ; 42(10): 2941-51, 2003 Mar 18.
Article in English | MEDLINE | ID: mdl-12627960

ABSTRACT

As for many enzymes, the enzymatic pathway of triosephosphate isomerase (TIM) includes the partially rate determining motion of an active site loop (loop 6, residues 166-176), which must remain closed during chemistry but must open just before product release. The motion of this loop was monitored using laser induced temperature-jump relaxation spectroscopy at nanosecond to millisecond time resolution. Trp168 in the hinge of the mobile loop served as a fluorophore reporter in a mutant of the yeast enzyme. The opening rate was studied as a function of the concentration of glycerol 3-phosphate, a substrate surrogate. Monoexponential kinetics were observed; assuming a simple two-step ligand release mechanism involving an encounter complex intermediate, the time scales of loop opening and closing were derived. The opening rate of the loop at 25 degrees C was determined to be 2500 +/- 1000 s(-1), in remarkable agreement with solution and solid state NMR measurements. The closing rate at the same temperature was 46,700 +/- 1800 s(-1). The rates were also studied as a function of the sample temperature following the jump. Enthalpies of activation of the loop motion, DeltaH(close) and DeltaH(open), were estimated to be 13.8 and 14.1 kcal/mol, respectively. The enthalpy of dissociation estimated from the kinetic studies is in reasonable agreement with steady-state values. Moreover, the enthalpy was dissected, for the first time, into components associated with ion binding and with protein conformational change. The enthalpy of the release reaction appeared to have a substantial contribution from the dissociation of the ligand from the encounter complex, found to be endothermic at 6 kcal/mol. In contrast, the population ratio of the open to closed loop conformations is found to favor the closed conformation but to be substantially less temperature dependent than the release step. Preliminary data of other ligands show that G3P behavior resembles that of the substrate but differs from 2-phosphoglycolate, a tight binding inhibitor, and phosphate. This study represents one of the first detailed comparisons between NMR and fluorescence based probes of protein motion and results in good agreement between the methods. The data in aggregate support a model in which the rate of the loop opening for TIM is dependent on the ligand and results in opening rates in the presence of the product that are comparable to enzymatic throughput, kcat.


Subject(s)
Saccharomyces cerevisiae Proteins/chemistry , Thermodynamics , Triose-Phosphate Isomerase/chemistry , Binding Sites/genetics , Enzyme Activation/genetics , Enzyme Inhibitors/chemistry , Glycerophosphates/chemistry , Hot Temperature , Kinetics , Ligands , Models, Chemical , Motion , Mutation , Protein Conformation , Saccharomyces cerevisiae Proteins/genetics , Spectrometry, Fluorescence/methods , Spectrum Analysis/methods , Substrate Specificity/genetics , Triose-Phosphate Isomerase/antagonists & inhibitors , Triose-Phosphate Isomerase/genetics
18.
Biopolymers ; 67(1): 26-40, 2002.
Article in English | MEDLINE | ID: mdl-11842411

ABSTRACT

The spectroscopic and solution properties of a series of amidated acids (delivery agents), which promote the gastrointestinal absorption of USP heparin and other drugs that show poor oral bioavailability, are investigated using Raman and NMR spectroscopy. The results show evidence for self-association at low concentrations of delivery agents that increases as the concentration of the delivery agent is increased. The self-associate is characterized by ring-ring stacking interactions, and the best geometrical arrangement for the stacking is the parallel-shifted arrangement of the rings. In addition, the amide group participates in the formation of intermolecular hydrogen bonds in the self-associate. Unlike the rigid ring, the tails of these delivery agents remain relatively flexible in the self-associate. It is suggested that the limited solubility of the delivery agents at physiological pH arises from a percentage of protonated carboxyls. Their presence promotes the formation of intermolecular hydrophobic and ring stacking interactions, which are otherwise weakened by an ionized carboxyl group.


Subject(s)
Acids/chemistry , Amides/chemistry , Acids/pharmacology , Administration, Oral , Amides/pharmacology , Animals , Drug Delivery Systems , Humans , Intestinal Absorption , Macromolecular Substances , Magnetic Resonance Spectroscopy , Spectrum Analysis, Raman
19.
Biopolymers ; 67(1): 41-8, 2002.
Article in English | MEDLINE | ID: mdl-11842412

ABSTRACT

Raman and NMR studies are performed to characterize the solution structures of complexes between heparin and a group of amidated acids, which act as delivery agents that facilitate the gastrointestinal absorption of orally administered heparin. At concentrations typically employed for the oral drug delivery of heparin, the contact points between heparin complexed with the delivery agents include points near the OH groups of heparin. The results suggest that heparin interacts rather nonspecifically with the amidated acids as monomers and with self-associated complexes of the delivery agents. It is also found that the carboxyl groups of at least one of the bioactive delivery agents easily protonates when it forms complexes with itself or heparin. This attribute may be one reason why this class of compounds is effective in the oral delivery of heparin.


Subject(s)
Acids/chemistry , Amides/chemistry , Anticoagulants/chemistry , Heparin/chemistry , Acids/metabolism , Amides/metabolism , Anticoagulants/metabolism , Heparin/metabolism , In Vitro Techniques , Ions , Macromolecular Substances , Magnetic Resonance Spectroscopy , Protons , Solutions , Spectrum Analysis, Raman , Structure-Activity Relationship , Vibration
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