Approaches to teaching fluorescence spectroscopy

Role of charged residues of the "electrostatic loop" of hSOD1 in promotion of aggregation: Implications for the mechanism of ALS-associated mutations under amyloidogenic conditions

Protein misfolding and amyloid formation are hallmarks of numerous diseases, including amyotrophic lateral sclerosis (ALS), in which hSOD1 aggregation is involved in pathogenesis. We used two point mutations in the electrostatic loop, G138E and T137R, to analyze charge distribution under destabilizing circumstances to gain more about how ALS-linked mutations affect SOD1 protein stability or net repulsive charge. We show that protein charge is important in the ALS disease process using bioinformatics and experiments. The MD simulation findings demonstrate that the mutant protein differs significantly from WT SOD1, which is consistent with the experimental evidence. The specific activity of the wild type was 1.61 and 1.48 times higher than that of the G138E and T137R mutants, respectively. Under amyloid induction conditions, the intensity of intrinsic and ANS fluorescence in both mutants reduced. Increasing the content of β-sheet structures in mutants can be attributed to aggregation propensity, which was confirmed using CD polarimetry and FTIR spectroscopy. Our findings show that two ALS-related mutations promote the formation of amyloid-like aggregates at near physiological pH under destabilizing conditions, which were detected using spectroscopic probes such as Congo red and ThT fluorescence, and also further confirmation of amyloid-like species by TEM. Overall, our results provide evidence supporting the notion that negative charge changes combined with other destabilizing factors play an important role in increasing protein aggregation by reducing repulsive negative charges.

Chemical cross-linking of a variety of green fluorescent proteins as Förster resonance energy transfer donors for Yukon orange fluorescent protein: A project-based undergraduate laboratory experience

Förster resonance energy transfer (FRET) is the basis for many techniques used in biomedical research. Due to its wide use in molecular sensing, FRET is commonly introduced in many biology, chemistry, and physics courses. While FRET is of great importance in the biophysical sciences, the complexity and difficulty of constructing FRET experiments has resulted in limited usage in undergraduate laboratory settings. Here, we present a practical undergraduate laboratory experiment for teaching FRET using a diverse set of green-emitting fluorescent proteins (FPs) as donors for a cross-linked Yukon orange FP. This laboratory experiment enables students to make the connection of basic lab procedures to real world applications and can be applied to molecular biology, biochemistry, physical chemistry, and biophysical laboratory courses. Published 2018. This article is a U.S. Government work and is in the public domain in the USA., 46(5):516-522, 2018.

An alternative allosteric pathway in thermophilic methylglyoxal synthase

Methylglyoxal synthase (MGS) is a homohexameric enzyme responsible for converting dihydroxyacetone phosphate (DHAP) to methylglyoxal and phosphate in the methylglyoxal bypass of glycolysis. Phosphate acts as an allosteric inhibitor and strong regulator for this enzyme. Previous studies on MGS from Thermus sp. GH5 (TMGS) had indicated a pathway for transmitting the signal through Pro82, Arg97 and Val101 to the active site. The necessity of these residues for heterotropic negative cooperativity between subunits of TMGS were also proposed. In this study, it has been shown that a path via a salt bridge between Arg80 and Asp100 in the narrow dimer interface provides an alternative pathway for transmission of the allosteric inhibitory signal through subunit interfaces.

Effects of γ-Irradiation on the Molecular Structures and Functions of Human Serum Albumin

In this paper, we use spectroscopic methods (fluorescence spectroscopy, UV absorption spectroscopy, and circular dichroism (CD) spectroscopy) to elucidate the effects of reactive oxygen species generated by γ-irradiation on the molecular properties of human serum albumin (HSA). The results of fluorescence spectroscopy indicated that oxidation by γ-irradiation can lead to conformational changes of HSA. Data of CD spectra suggested that with the increase of radiation dose the percentage of α-helix in HSA has decreased. The determination of protein hydrophobicity showed that the effective hydrophobicity of HSA decreased up to 62% compared to the native HSA solution due to the exposure to the γ-irradiation. Furthermore, small changes in the esterase-like activity of HSA were introduced because of oxidation. The content of bityrosine increased markedly, suggesting that the oxidized HSA was aggregated. Moreover, there was no obvious change in the molecular properties of HSA with low γ-irradiation dose. Changes happened when the irradiation dose exceeded 200 Gy.

Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology

BACKGROUND

A key challenge in interdisciplinary research is choosing the best approach from a large number of techniques derived from different disciplines and their interfaces.

RESULTS

To address this challenge in the area of Biophysics and Structural Biology, we have designed a graduate level course to teach students insightful use of experimental biophysical approaches in relationship to addressing biological questions related to biomolecular interactions and dynamics. A weekly seminar and data and literature club are used to compliment the training in class. The course contains wet-laboratory experimental demonstration and real-data analysis as well as lectures, grant proposal preparation and assessment, and student presentation components. Active student participation is mandatory in all aspects of the class. Students prepare materials for the class receiving individual and iterative feedback from course directors and local experts generating high quality classroom presentations.

CONCLUSIONS

The ultimate goal of the course is to teach students the skills needed to weigh different experimental approaches against each other in addressing a specific biological question by thinking and executing academic tasks like faculty.

The interrelationship between ligand binding and thermal unfolding of the folate binding protein. The role of self-association and pH

The present study utilized a combination of DLS (dynamic light scattering) and DSC (differential scanning calorimetry) to address thermostability of high-affinity folate binding protein (FBP), a transport protein and cellular receptor for the vitamin folate. At pH7.4 (pI=7-8) ligand binding increased concentration-dependent self-association of FBP into stable multimers of holo-FBP. DSC of 3.3μM holo-FBP showed Tm (76°C) and molar enthalpy (146kcalM(-1)) values increasing to 78°C and 163kcalM(-1) at 10μM holo-FBP, while those of apo-FBP were 55°C and 105kcalM(-1). Besides ligand binding, intermolecular forces involved in concentration-dependent multimerization thus contribute to the thermostability of holo-FBP. Hence, thermal unfolding and dissociation of holo-FBP multimers occur simultaneously consistent with a gradual decrease from octameric to monomeric holo-FBP (10μM) in DLS after a step-wise rise in temperature to 78°C≈Tm. Stable holo-FBP multimers may protect naturally occurring labile folates against decomposition or bacterial utilization. DSC established an interrelationship between diminished folate binding at pH5, especially in NaCl-free buffers, and low thermostability. Positively charged apo-FBP was almost completely unfolded and aggregated at pH5 (Tm 38°C) and holo-FBP, albeit more thermostable, was labile with aggregation tendency. Addition of 0.15M NaCl increased thermostability of apo-FBP drastically, and even more so that of holo-FBP. Electrostatic forces thus seem to contribute to a diminished thermostability at low pH. Fluorescence spectroscopy after irreversible thermal unfolding of FBP revealed a weak-affinity folate binding.

Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D(2)O and compare with experimental observations.

Structural classification of the amide I sites of a beta-hairpin with isotope label 2DIR spectroscopy

We present a theoretical study of the possibility to use isotope label two-dimensional infrared (2DIR) spectroscopy to obtain site specific structural information in trpzip2. This small beta-hairpin peptide was designed as a model system for studying protein folding in beta-sheet structures. In order to unravel the folding mechanism, the surroundings of local sites should be characterized, which in principle is possible by using 2DIR in combination with isotope labeling. This requires a classification that correlates local structures to two-dimensional spectra. To this end, we provide the first spectral simulation of the isotope label spectra of all the amide I sites in trpzip2. We find that the anti-diagonal width of the 2DIR peak associated with a labelled site is a good measure of solvent exposure and the key parameter to distinguish between solvent exposed and internal sites. The diagonal widths are not particularly sensitive to this, but they do reveal the presence of slowly interconverting turn structures.

Effects of high hydrostatic pressure on the structure of bovine alpha-lactalbumin

The effects of high hydrostatic pressure (HHP) processing (at 200 to 600 MPa, 25 to 55 degrees C, and from 5 to 15 min) on some structural properties of alpha-lactalbumin was studied in a pH range of 3.0 to 9.0. The range of HHP processes produced a variety of molten globules with differences in their surface hydrophobicity and secondary and tertiary structures. At pH values of 3 and 5, there was a decrease in the alpha-helix content concomitant with an increase in beta-strand content as the pressure increased. No changes in molecular size due to HHP-induced aggregation were detected by sodium dodecyl sulfate-PAGE. All samples showed higher thermostability as the severity of the treatment increased, indicating the formation of a less labile structure related to the HHP treatment.

Relationship between stability and bioluminescence color of firefly luciferase

Firefly luciferase catalyzes the oxidation of luciferin in the presence of ATP, Mg(2+) and molecular oxygen. The bioluminescence color of firefly luciferases is identified by the luciferase structure and assay conditions. Amongst different types of beetles, luciferase from Phrixotrix railroad worm (PhRE) with a unique additional residue (Arg353) naturally emits red bioluminescence color. By insertion of Arg356 in luciferase of Lampyris turkestanicus, corresponding to Arg353 in Phrixotrix hirtus, the color of the emitted light was changed to red. To understand the effect of this position on the bioluminescence color shift, four residues with similar sizes but different charges (Arg, Lys, Glu, and Gln) were inserted into Photinus pyralis luciferase. Comparison of mutants with native luciferase shows that mutation brought an increase in the content of secondary structure and globular compactness of (P. pylalis) luciferase. Comparative study of chemical denaturation of native and mutant luciferases by activity measurement, intrinsic and extrinsic fluorescence, circular dichroism, and DSC techniques revealed that insertion of positively charged residues (Arg, Lys) in the flexible loop (352-358) plays a significant role on the stability of (P. pyralis) luciferase and changes the light color to red.

Equilibrium and kinetic approaches for studying oligomeric protein folding

This chapter describes the approaches and considerations necessary for extension of current protein folding methods to the equilibrium and kinetic reactions of oligomeric proteins, using dimers as the primary example. Spectroscopic and transport methods to monitor folding and unfolding transitions are summarized. The data collection and analyses to determine protein stability and kinetic folding mechanisms are discussed in the context of the additional dimension of complexity that arises in higher order folding processes, compared to first order monomeric proteins. As a case study to illustrate the data analysis process, equilibrium, and kinetic data are presented for SmtB, a homodimeric DNA-binding protein from Synechococcus PCC7942.

Thermographic Phosphors for High Temperature Measurements: Principles, Current State of the Art and Recent Applications

This paper reviews the state of phosphor thermometry, focusing on developments in the past 15 years. The fundamental principles and theory are presented, and the various spectral and temporal modes, including the lifetime decay, rise time and intensity ratio, are discussed. The entire phosphor measurement system, including relative advantages to conventional methods, choice of phosphors, bonding techniques, excitation sources and emission detection, is reviewed. Special attention is given to issues that may arise at high temperatures. A number of recent developments and applications are surveyed, with examples including: measurements in engines, hypersonic wind tunnel experiments, pyrolysis studies and droplet/spray/gas temperature determination. They show the technique is flexible and successful in measuring temperatures where conventional methods may prove to be unsuitable.

Dynamics of L-tryptophan in aqueous solution by simultaneous laser induced fluorescence (LIF) and photoacoustic spectroscopy (PAS)

An experimental system for measuring simultaneously photoacoustic (PA) and fluorescence signals is described. The simultaneous measurement of laser induced fluorescence and photoacoustic signals provide a suitable method for the study of different quenching phenomena occurring in fluorescent systems. In this paper we report tryptophan solvation dynamics in water using fluorescence and photoacoustic spectra recorded simultaneously by photoacoustic and fluorescence signals as functions of concentration, indicate that quantum yield is maximum at low concentrations. Also, the energy lost in the fluorescence path of tryptophan, due to different quenching phenomena like self quenching, Resonance energy transfer (RET), solvation relaxation, etc. is clearly seen from the photoacoustic signal intensity which increases as the fluorescence intensity decreases.

Exploring the binding pocket for pyridopyrimidine ligands at the CCK1 receptor by molecular docking

Pyridopyrimidine-based analogues are among the most highly potent and selective antagonists of cholecystokinin receptor subtype-1 (CCK1R) described to date. To better understand the structural and chemical features responsible for the recognition mechanism, and to explore the binding pocket of these compounds, we performed automated molecular docking using GOLD2.2 software on some derivatives with structural diversity, and propose a putative binding conformation for each compound. The docking protocol was guided by the key role of the Asn333 residue, as revealed by site directed mutagenesis studies. The results suggest two putative binding modes located in the same pocket. Both are characterized by interaction with the main residues revealed by experiment, Asn333 and Arg336, and differ in the spatial position of the Boc-Trp moiety of these compounds. Hydrophobic contacts with residues Thr117, Phe107, Ile352 and Ile329 are also in agreement with experimental data. Despite the poor correlation obtained between the estimated binding energies and the experimental activity, the proposed models allow us to suggest a plausible explanation of the observed binding data in accordance with chemical characteristics of the compounds, and also to explain the observed diastereoselectivity of this family of antagonists towards CCK1R. The most reasonable selected binding conformations could be the starting point for future studies. Figure Superimposition of the two putative binding conformations revealed by molecular docking for pyridopyrimidine-based CCK1 antagonists.

Binding Properties of a New Anti-tumor Component (2,2′-bipyridin octylglycinato Pd(II) nitrate) with Bovine β-lactoglobulin-A and -B

An new water soluble palladium (II) complex of formula [Pd(bpy)(Oct-Gly)]NO(3), (where bpy is 2,2'-bipyridine and Oct-Gly is octylglycine) have been synthesised. The Pd(II) complex has been characterized by elemental analysis and conductivity measurements as well as spectroscopic methods such as infrared, (1)H NMR, and ultraviolet-visible. The interaction between the new Pd(II)-complex (2,2'-bipyridin octylglycinato Pd(II) nitrate), an anti-tumor component, with beta-lactoglobulin-A and -B (BLG-A and -B) was studied by fluorescence spectroscopy and far and near-UV circular dichroism (CD) spectrophotometric techniques. A strong fluorescence quenching interaction of Pd(II) complex with BLG-A and -B was observed. The quenching constant was determined using the modified Stern-Volmer equation. The calculated binding constants of Pd(II) complex with BLG-A and -B were 0.51 and 0.28 (x 10(6) M(-1)) and the corresponding average number of binding sites were 2.8 and 1.5, respectively. Far-UV CD studies showed that the Pd(II) complex can significantly change the secondary structure of BLG-A and -B via an increase in the content of alpha-helix structure, which stabilizes the secondary structure of the proteins. Near-UV CD data clearly indicate the alteration in the tertiary structure of BLG-A and -B due to the interaction with Pd(II) complex. Pd(II) complex can change and stabilize both the secondary and tertiary structures of BLG-A more than BLG-B. These conformational changes may be considered to be a deleterious effect of the designed ligand on the protein structures. The difference in the interaction properties observed for BLG-A and -B with Pd(II) complex is due to the difference in the amino acid sequences between these two variants.

A project-based biochemistry laboratory promoting the understanding and uses of fluorescence spectroscopy in the study of biomolecular structures and interactions

A laboratory project for a first semester biochemistry course is described, which integrates the traditional classroom study of the structure and function of biomolecules with the laboratory study of these molecules using fluorescence spectroscopy. Students are assigned a specific question addressing the stability/function of lipids, proteins, or nucleic acids, and asked to design an experiment to answer the question using fluorescence methodologies. Students study phase equilibria and determine the critical micelle concentration of single chain amphiphiles, the melting point of multilamellar vesicles, and the melting points and thermodynamic constants (K(eq) , ΔG(0) , ΔH(0) and ΔS(0) ) for denaturation of ds-DNA and proteins. In addition, they examine binding properties of proteins. These laboratory experiments are designed to support student learning of the major themes of structure and function in the course.

Comparison of protein surface hydrophobicity measured at various pH values using three different fluorescent probes

The influence of type of fluorescent probe on the surface hydrophobicity values determined for three native and heated proteins was assessed using uncharged [6-propionyl-2-(N, N-dimethylamino)naphthalene or PRODAN] versus anionic aliphatic (cis-parinaric acid or CPA) and aromatic (1-anilinonaphthalene-8-sulfonic acid or ANS) probes. Surface hydrophobicities of whey protein isolate, beta-lactoglobulin, and bovine serum albumin under heated (80 degrees C for 30 min) and unheated conditions and at varying pH values (3.0, 5.0, 7.0, and 9. 0) were measured using ANS, CPA, and PRODAN. ANS and CPA yielded opposing results for the effects of pH and heating on protein hydrophobicity. Hydrophobicity was lower at pH 3.0 than at other pH values for all proteins measured by PRODAN, whereas the values measured by ANS and CPA at pH 3.0 were quite high compared to those at other pH values, suggesting the influence of electrostatic interactions on anionic probe-protein binding. These results suggest that the presence or absence of a permanent charge as well as the aromatic and aliphatic nature of fluorescent probes can affect protein hydrophobicity values measured under various pH conditions.