Impact of point mutations on the structure and thermal stability of ribonuclease T1 in aqueous solution probed by Fourier transform infrared spectroscopy

The effect of aspirin-HSA complexation on the protein secondary structure

This study was designed to determine the secondary structure of human serum albumin (HSA) in the presence of aspirin in H2O and D2O solutions at physiological pH, using aspirin concentrations of 0.0001-5 mM with final protein concentration of 2% w/v. UV-vis spectra and Fourier transform infrared (FTIR) difference spectroscopy with its self-deconvolution, second derivative resolution enhancement, and curve-fitting procedures were applied to characterize the drug binding mode, the binding constant, and the protein secondary structure in the aspirin-HSA complexes. Spectroscopic evidence showed that no aspirin-protein interaction occurs at very low drug concentration (0.0001 mM), whereas at higher drug contents (0.001-0.1 mM) the aspirin anion binding (H-bonding) is mainly through the ε-amino NH3+ group with overall binding constant of K = 1.4 × 104 M-1. At high drug concentrations (1-5 mM), acetylation of Lys-199 was observed. Aspirin binding results in protein secondary structural changes from that of the α-helix 55% (free HSA) to 49%, β-sheet 22% (free HSA) to 31%, β-anti 12% (free HSA) to 4% and turn 11% (free HSA) to 16% in the aspirin-HSA complexes..Key words: aspirin, protein, drug, binding mode, binding constant secondary structure, FTIR spectroscopy.

Interaction of RNase A with VO3- and VO2+ ions. Metal ion binding mode and protein secondary structure

Some of vanadyl complexes have shown potential to inhibit RNase activity by acting as transition state analogue, while at the same time not inhibiting DNase. To gain an insight into the interaction of protein with vanadate (VO3-) and vanadyl (VO2+) ions, the present study was designed to examine the binding of ribonuclase A (RNase A) with NaVO3 and VOSO4 in aqueous solution at physiological pH with metal ion concentrations of 0.001 mM to 1 mM, and protein concentration of 2% w/v. Absorption spectra and Fourier transform infrared (FTIR) spectroscopy with self-deconvolution and second derivative resolution enhancement were used to determine the cation binding mode, association constant and the protein secondary structure in the presence of vanadate and vanadyl ions in aqueous solution. Spectroscopic results show that an indirect metal ion interaction occurs with the polypeptide C = O, C-N (via H2O) with overall binding constants of K(VO3-) = 3.93x10(2) M(-1) and K(VO2+) = 4.20x10(3) M(-1). At high metal ion concentrations, major protein secondary structural changes occur from that of the alpha-helix 29% (free enzyme) to 23-24%; beta-sheet (pleated and anti) 50% (free enzyme) to 64-66% and turn 21% (free enzyme) to 10-12% in the metal-RNase complexes. The observed structural changes indicate a partial protein unfolding in the presence of high metal ion concentration.

Two-dimensional IR correlation spectroscopy: sequential events in the unfolding process of the lambda cro-V55C repressor protein

A question often posed in protein folding/unfolding studies is whether the process is fully cooperative or whether it contains sequential elements. To address this question, one needs tools capable of resolving different events. It seems that, at least in certain cases, two-dimensional (2D) IR correlation spectroscopy can provide answers to this question. To illustrate this point, we have turned to the Cro-V55C dimer of the lambda Cro repressor, a protein known to undergo thermal unfolding in two discrete steps through a stable equilibrium intermediate. The secondary structure of this intermediate is compatible with that of a partially unfolded protein and involves a reorganization of the N terminus, whereas the antiparallel beta-ribbon formed by the C-terminal part of each subunit remains largely intact. To establish whether the unfolding process involves sequential events, we have performed a 2D correlation analysis of IR spectra recorded over the temperature range of 20-95 degrees C. The 2D IR correlation analysis indeed provides evidence for a sequential formation of the stable intermediate, which is created in three (closely related) steps. A first step entails the unfolding of the short N-terminal beta-strand, followed by the unfolding of the alpha-helices in a second step, and the third step comprises the reorganization of the remaining beta-sheet and of some unordered segments in the protein. The complete unfolding of the stable intermediate at higher temperatures also undergoes sequential events that ultimately end with the breaking of the H bonds between the two beta-strands at the dimer interface.

Interaction of cisplatin drug with RNase A

cis-Pt(NH3)2Cl2 (cisplatin) is an antitumor drug with many severe toxic side effects including enzymatic structural changes associated with its mechanism of action. This study is designed to examine the interaction of cisplatin drug with ribonuclease A (RNase A) in aqueous solution at physiological pH, using drug concentration of 0.0001 mM to 0.1 mM with final protein concentration of 2% w/v. Absorption spectra and Fourier transform infrared (FTIR) spectroscopy with its self-deconvolution, second derivative resolution enhancement and curve-fitting procedures were used to characterize the drug binding mode, association constant and the protein secondary structure in the cisplatin-RNase complexes. Spectroscopic results show that at low drug concentration (0.0001 mM), no interaction occurs between cisplatin and RNase, while at higher drug concentrations, cisplatin binds indirectly to the polypeptide C=O, C-N (via H2O or NH3 group) and directly to the S-H donor atom with overall binding constant 5.66 x 10(3)M(-1). At high drug concentration, major protein secondary structural changes occur from that of the alpha-helix 29% (free enzyme) to 20% and beta-sheet 39% (free enzyme) to 45% in the cisplatin-RNase complexes. The observed structural changes indicate a partial protein unfolding in the presence of cisplatin at high drug concentration.

New structural insights into the refolding of ribonuclease T1 as seen by time-resolved Fourier-transform infrared spectroscopy

To get new structural insights into different phases of the renaturation of ribonuclease T1 (RNase T1), the refolding of the thermally unfolded protein was initiated by rapid temperature jumps and detected by time-resolved Fourier-transform infrared spectroscopy. The characteristic spectral changes monitoring the formation of secondary structure and tertiary contacts were followed on a time scale of 10(-3) to 10(3) seconds permitting the characterization of medium and slow folding reactions. Additionally, structural information on the folding events that occurred within the experimental dead time was indirectly accessed by comparative analysis of kinetic and steady-state refolding data. At slightly destabilizing refolding temperatures of 45 degrees C, which is close to the unfolding transition region, no specific secondary or tertiary structure is formed within 180 ms. After this delay all infrared markers bands diagnostic for individual structural elements indicate a strongly cooperative and relatively fast folding, which is not complicated by the accumulation of intermediates. At strongly native folding temperatures of 20 degrees C, a folding species of RNase T1 is detected within the dead time, which already possesses significant amounts of antiparallel beta-sheets, turn structures, and to some degree tertiary contacts. The early formed secondary structure is supposed to comprise the core region of the five-stranded beta-sheet. Despite these nativelike characteristics the subsequent refolding events are strongly heterogeneous and slow. The refolding under strongly native conditions is completed by an extremely slow formation or rearrangement of a locally restricted beta-sheet region accompanied by the further consolidation of turns and denser backbone packing. It is proposed that these late events comprise the final packing of strand 1 (residues 40-42) of the five-stranded beta-sheet against the rest of this beta-sheet system within an otherwise nativelike environment. This conclusion was supported by the comparison of refolding of RNase T1 and its variant W59Y RNase T1 that enabled the assignment of these very late events to the trans-->cis isomerization reaction of the prolyl peptide bond preceding Pro-39.

Novel matrix descriptor for secondary structure segments in proteins: demonstration of predictability from circular dichroism spectra

An extension to standard protein secondary structure predictions using optical spectra that encompasses the number and average lengths of segments of uniform secondary structure in the sequence is demonstrated. The connectivity and numbers of segments can be described by a matrix descriptor [sij] (i, j representing segment types such as helix and beta-sheet strands). Independent knowledge of the fractional concentration of each secondary structure type and of the total number of residues in the protein then with [sij] yields the average segment length of each type. The physical background for prediction of this extended structural descriptor from spectral data is summarized, rules for its generation from reference X-ray structures are defined, and formal variants of its form are discussed. Using a novel neural network approach to analyze a training set of electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) spectra for 23 proteins, matrix descriptors encompassing helix, sheet, and other forms are predicted. The results show that the matrix descriptor can be predicted to an accuracy comparable to that of conventionally predicted average fractional secondary structures. In this respect the ECD predictions of [sij] were significantly more accurate than the VCD ones, which may result from the longer range length dependence of the ECD bandshape and intensity. Summary results for a parallel analysis using Fourier transform infrared spectra indicate somewhat lower reliability than those for VCD.

The Effect of Cholesterol on the Solution Structure of Proteins of Photosystem II. Protein Secondary Structure and Photosynthetic Oxygen Evolution

Cholesterol induces large perturbations in the physical properties of membranes, especially in the structural organization of the phospholipid bilayers and the aggregation and solubility of proteins at physiological temperatures. This study was designed to examine the interaction of cholesterol with lipid and proteins of chloroplasts photosystem II (PSII) submembrane fractions in air dried film at pH 6-7 with cholesterol concentrations of 0.01 to 20 mM. Fourier transform infrared difference spectroscopy with its self-deconvolution and second derivative methods as well as curve-fitting procedures are used, in order to determine the cholesterol binding mode, the protein conformational changes, and the structural properties of cholesterol-protein complexes. Correlations between the effect of cholesterol on the protein secondary structure and the rate of oxygen evolution in PSII are also established. Spectroscopic evidence showed that at low cholesterol concentration (0.01 and 0.1 mM), minor chol-protein and chol-lipid interactions (through hydrogen bonding) occur with no major perturbations of the protein secondary structure. As cholesterol concentration increases (5 and 10 and 20 mM), major alterations of the protein secondary structure are observed from that of the alpha-helix 47% (uncomplexed protein) to 43-39% (complexes) and the beta-sheet structure 18% (uncomplexed protein) to 22-26% (complexes). Those changes coincide with a partial decrease in the rate of the oxygen evolution (8-33%) is observed in the presence of cholesterol at high concentration. Copyright 1999 Academic Press.

Two-dimensional mid-IR and near-IR correlation spectra of ribonuclease A: using overtones and combination modes to monitor changes in secondary structure

We introduce near-IR spectroscopy as an ancillary tool for monitoring structural changes of proteins in aqueous solution using ribonuclease A (RNase A) as a model protein. The thermal unfolding of RNase A results in clear spectral changes in the near-IR and the mid-IR regions. In the near-IR the most pronounced changes are observed in the spectral region between 4820 and 4940 cm-1. The strong N-H combination band found at 4867 cm-1 in the spectrum of native RNase A shifts to 4878 cm-1 upon thermal unfolding. Hydrogen-deuterium exchange experiments that validate the N-H character of this mode can also be used to estimate the number of unexchanged amide protons after exposure to D2O. The transition profiles and temperatures derived from the temperature dependence of the N-H combination mode were found to be practically identical with those derived from the temperature dependence of the C = O amide I band in the mid-IR region, demonstrating that the near-IR region can be used as a conformation-sensitive monitor for the thermally induced unfolding of proteins in H2O solution. A 2-dimensional correlation analysis was applied to the mid-IR and near-IR spectra of RNase A to establish correlations between IR bands in both regions. The correlation analysis demonstrates that the thermal unfolding of RNase A is not a completely cooperative process; rather it begins with some changes in beta-sheet structure, followed by the loss of alpha-helical structures, and then ending with the unfolding of the remaining beta-sheets.

Thermozymes

Enzymes synthesized by thermophiles (organisms with optimal growth temperatures > 60 degrees C) and hyperthermophiles (optimal growth temperatures > 80 degrees C) are typically thermostable (resistant to irreversible inactivation at high temperatures) and thermophilic (optimally active at high temperatures, i.e., > 60 degrees C). These enzymes, called thermozymes, share catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, thermozymes usually retain their thermal properties, suggesting that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, and crystal structure comparisons indicate that thermozymes are, indeed, very similar to mesophilic enzymes. No obvious sequence or structural features account for enzyme thermostability and thermophilicity. Thermostability and thermophilicity molecular mechanisms are varied, differing from enzyme to enzyme. Thermostability and thermophilicity are usually caused by the accumulation of numerous subtle sequence differences. This review concentrates on the mechanisms involved in enzyme thermostability and thermophilicity. Their relationships with protein rigidity and flexibility and with protein folding and unfolding are discussed. Intrinsic stabilizing forces (e.g., salt bridges, hydrogen bonds, hydrophobic interactions) and extrinsic stabilizing factors are examined. Finally, thermozymes' potential as catalysts for industrial processes and specialty uses are discussed, and lines of development (through new applications, and protein engineering) are also proposed.

Interaction of cisplatin with human serum albumin. Drug binding mode and protein secondary structure

Cis-diamminedichloroplatinum(II) (cisplatin) is an antitumor drug, which forms intrastrand cross-links DNA adducts. Protein interaction with cisplatin-DNA complexes induces DNA bending and biopolymer structural changes. This study is designed to examined the interaction of cisplatin with human serum albumin (HSA) in aqueous solution at physiological pH with drug concentrations of 0.0001 mM to 0.1 mM, and HSA (fatty acid free) concentration of 2% w/v. Absorption spectra and Fourier transform infrared (FTIR) spectroscopy with its self-deconvolution and second derivative resolution enhancement, as well as curve-fitting procedures, were used to determine the drug binding mode, drug binding constant and the protein secondary structure in aqueous solution. Spectroscopic evidence showed that at low drug concentration (0.0001 mM), minor cisplatin-protein interaction occurs, while at higher drug content (0.001 mM), major Pt-HSA complexation takes place via protein C=O, C-N and S-H donor groups with overall binding constant K = 8.52 x 10(2) M-1. At high drug concentration, cisplatin binding results in major protein secondary structural changes from that of the alpha-helix 55% (free HSA) to 45% and beta-sheet 22% (free HSA) to 32%, in the cisplatin-HSA complexes. The observed spectral changes indicate a partial unfolding of the protein structure, in the presence of cisplatin at high drug concentrations.

Conformation of thermally denatured RNase T1 with intact disulfide bonds: a study by small-angle X-ray scattering

Small-angle X-ray scattering of RNase T1 with intact disulfide bonds was measured at 20 degrees and 60 degrees C in order to get insight into the structural changes of the protein caused by thermal denaturation. The radius of gyration increases from R(G)= 1.43 nm to R(G) = 2.21 nm. The conformations of the molecules at 60 degrees C are similar to those of ring-shaped random walk chains. However, the molecules are more compact than one would expect under theta conditions due to attractive interactions between the chain segments. The volume needed for free rotation of the thermally unfolded protein molecules about any axis in solution is five times greater than in the native state whereas the hydrodynamic effective volume is increasing only two times.

Thermodynamics of protein unfolding: questions pertinent to testing the validity of the two-state model

We discuss a number of questions pertaining to the analysis of data to extract thermodynamic parameters for the reversible unfolding of proteins. Simulations are presented to illustrate problems in trying to test the validity of the two-state model, vis-a-vis a more complicated unfolding model. A conceptual and practical problem is how to consider the unfolded state and how to relate the observed signal to this state. We discuss the idea that the unfolded state can be described as a single macrostate, comprising a distribution of microstates having different degrees of solvent-accessible surface area. We also discuss the possibilities and thermodynamic consequences of having more than one unfolded state and of having a denaturant which both stabilizes and destabilizes the protein's native state.

Conformation of a water-soluble beta-sheet model peptide. A circular dichroism and Fourier-transform infrared spectroscopic study of double D-amino acid replacements

Among peptide secondary structures beta-sheet domains have been much less intensively studied than alpha-helical conformations, mainly because of the lack of well characterized model peptides. In the present paper the secondary structure of a water-soluble de novo peptide consisting of 26 amino acids (DPKGDPKGVTVTVTVTVTGKGDPKPD-NH2) and the corresponding double D-amino acid replacement set have been studied by circular dichroism and Fourier-transform infrared spectroscopy. The model peptide was found to be unstructured in aqueous solution at peptide concentrations < 10(-3) mol/L but to adopt a predominantly beta-sheet structure in the presence of 15 mM sodium dodecyl sulfate or at apolar/water interfaces. Although the peptide is composed of amino acids with low helical propensity, it formed a single-stranded helical structure in aqueous trifluoroethanol. The D-amino acid replacement set was synthesized in order to study the conformational stability of the model peptide selectively in distinct regions. The data show that both the alpha-helix present in 50% trifluoroethanol as well as the beta-sheet domain formed in the presence of sodium dodecyl sulfate or at apolar/water interfaces, are located in the region between Val9 and Thr18. Pairwise substitution of adjacent amino acids by their corresponding D-amino acids provides a pronounced beta-sheet disturbance. These findings demonstrate that double D-amino acid replacements may be used to locate beta-sheet domains in peptides.

A correlation between thermal stability and structural features of staphylokinase and selected mutants: a Fourier-transform infrared study

Variants of recombinant staphylokinase (Sak) were investigated by Fourier-transform infrared spectroscopy: Sak (wild type), Sak-M26A, Sak-M26L, and Sak-G34S/R36G/R43H (Sak-B). Estimation of the secondary structure and hydrogen-deuterium exchange experiments revealed the existence of fast-exchanging and strongly solvent-exposed fractions of the helical structures in the two samples Sak and Sak-M26L. These two samples are also thermally less stable with unfolding transition temperatures of 43.7 degrees C (Sak) and 43.5 degrees C (Sak-M26L), respectively. On contrast, Sak-M26A and Sak-G34S/R36G/R43H have a slower hydrogen-deuterium exchange, have a smaller solvent-exposed portion of the helical part, and are more resistant against thermal unfolding; the transition temperatures are 51.7 degrees C and 59.3 degrees C, respectively. The secondary structure analysis was performed by two different approaches, by curve-fitting after band narrowing and by pattern recognition (factor analysis) based upon reference spectra of proteins with known crystal structure. Within the limits of the used methods, we are unable to detect significant differences in the secondary structure of the four variants of Sak. According to the results of the factor analysis, the portions of secondary structure elements were obtained to 16-20% alpha-helix, 28-30% beta-sheet, 23-27% turns, 28-30% irregular (random) and other structure. The sharp differences in the specific plasminogen-activating capacity (Sak, Sak-G34S/R36G/R43H and Sak-M26L are fully active, but Sak-M26A does not form a stable complex with plasminogen) are not reflected in the structural features revealed by the infrared spectra of this study.

Thermally induced hydrogen exchange processes in small proteins as seen by FTIR spectroscopy

Fourier-transform infrared (FTIR) spectroscopy has been used to study the thermally induced exchange characteristics of those backbone amide protons which persist H-D exchange at ambient conditions in ribonuclease A, in wild type ribonuclease T1 and some of its variants, and in the histone-like protein HBsu. The H-D exchange processes were induced by increasing the thermal energy of the protein solutions in two ways: (i) by linearly increasing the temperature, and (ii) by a temperature jump. To trace the H-D exchange in the proteins, various infrared absorption bands known to be sensitive to H-D exchange were used as specific monitors. Characteristic H-D exchange curves were obtained from which the endpoints (TH/D) of H-D exchange could be determined. The H-D exchange curves, the TH/D-values and the phase transition temperatures Tm were used to estimate the structural flexibility and stability of the given proteins. It is suggested that time-resolved FTIR spectroscopy can be used to determine global stability parameters of proteins.

Interaction between superoxide dismutase and dipalmitoylphosphotidylglycerol bilayers: a fourier transform infrared (FT-IR) spectroscopic study

PURPOSE

Superoxide dismutase (SOD), an antioxidant enzyme, converts peroxide radicals into hydrogen peroxide. Liposomes have been used as carriers for SOD to enhance its antioxidant effect. Our previous DSC study has suggested that SOD binding to dipalmitoylphosphatidylglycerol (DPPG) may protect lipid membranes against oxygen-mediated injury. We now present FT-IR studies on the effect of DPPG binding on the temperature-induced SOD folding-unfolding process.

METHODS

The FT-IR spectra of SOD in D2O or DPPG membranes are measured as temperatures increase from 28 degrees to 121 degrees C at a rate of 0.5 degrees C/min. From the quantitative determination of the changes in the amide I band components of the Fourier self-deconvoluted spectra, the DPPG-induced changes of SOD secondary structure could be detected as a function of temperature.

RESULTS

We observe that the relative intensity of the SOD bands from 28 degrees C to 77 degrees C show graduate loss of beta-sheet "distorted" structure, loss of turns, and existence of an intermediate state around 50 degrees C. Beginning at 80 degrees C, changes are obtained in three temperature regions: (i) 80 degrees C, (ii) 92 degrees C, (iii) 109 degrees C. The result suggests that SOD folding/unfolding transition involves mostly the relative changes within the regions of helix-like hydrogen bonding pattern, turn, twisted beta-bend and irregular structures. When SOD is bound to DPPG, the conformational changes shift to lower temperatures, indicating a reduction of SOD thermal stability. In addition, the gel to liquid crystalline phase transition temperature of DPPG increases from 42 degrees C to 43.5 degrees C.

CONCLUSIONS

These results suggest that the thermal stability of SOD is reduced by DPPG binding. However, DPPG bilayer is stabilized by the presence of SOD.

Temperature-jump-induced refolding of ribonuclease A: a time-resolved FTIR spectroscopic study

FTIR difference spectroscopy has been used for the first time to investigate the kinetics of secondary structure formation during refolding. The refolding process of ribonuclease A (RNase A) as a model system was induced by applying a temperature-jump of 60 degrees. The temperature-jump was triggered by rapidly injecting a small volume of the thermally unfolded protein solution at 80 degrees C into a special cuvette system kept at 20 degrees C. The dead-time of the injection and the time resolution of the FTIR spectrometer permitted the observation of refolding processes in a time window ranging from 170 ms to several minutes. Specifically, the formation of beta-structures and the disappearance of irregular conformations could be observed in this time interval.

The use and misuse of FTIR spectroscopy in the determination of protein structure

Fourier transform infrared (FTIR) spectroscopy is an established tool for the structural characterization of proteins. However, many potential pitfalls exist for the unwary investigator. In this review we critically assess the application of FTIR spectroscopy to the determination of protein structure by (1) outlining the principles underlying protein secondary structure determination by FTIR spectroscopy, (2) highlighting the situations in which FTIR spectroscopy should be considered the technique of choice, (3) discussing the manner in which experiments should be conducted to derive as much physiologically relevant information as possible, and (4) outlining current methods for the determination of secondary structure from infrared spectra of proteins.