scholarly journals Interactions of the lanthanide- and hapten-binding sites in the Fv fragment from the myeloma protein MOPC 315

1976 ◽  
Vol 155 (1) ◽  
pp. 37-53 ◽  
Author(s):  
R A Dwek ◽  
D Givol ◽  
R Jones ◽  
A C McLaughlin ◽  
S Wain-Hobson ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Metal Binding ◽  
Spin Label ◽  
Binding Sites ◽  
Binding Constants ◽  
Kinetic Scheme ◽  
Difference Spectrum ◽  
Protein Fluorescence ◽  
Myeloma Protein ◽  
Fluorescence Studies

1. The interactions of lanthanide metals and dinitrophenyl spin-label haptens with the Fv fragment of the mouse myeloma protein MOPC 315 were investigated by the techniques of fluorescence, e.s.r. (electron spin resonance) and high-resolution n.m.r. (nuclear magnetic resonance). 2. The protein fluorescence of Fv fragment at 340nm is quenched by the haptens (fluorescence enhancement, epsilon=0.15) and enhanced by Gd(III) (epsilon=1.14) and other lanthanides. The binding of the haptens studied here is insensitive to pH in the range 5.5-7.0 (dissociation constant KH=0.3-1.0 muM) and shows 1:1 stoicheiometry. The binding of Gd(III) also shows 1:1 stoicheiometry, but is pH-dependent; the binding constant (KM) varies from 10 muM at pH7.0 to 700 muM at pH4.8. La(III) binding is less sensitive to pH. The pH-dependences of the metal-binding constants imply that a group in the protein with pKa greater than or equal to 6.2 is involved in the binding, and probably also other groups with lower pKa values. 3. The apparent binding of the haptens is weakened about 20-fold by Gd(III), and vice versa. An equilibrium scheme involving a ternary complex with an interaction between the two binding sites is derived in Appendix I to explain the experimental results at two pH values. 4. Time-dependent fluorescence changes are observed in the presence of Gd(III) at pH5.5. A two-state kinetic scheme involving a ‘slow’ conformational change in the Fv fragment is derived in Appendix II to explain this time-dependence. This scheme is consistent with the antagonistic equilibrium behaviour. 5. The e.s.r. changes in the spin-label haptens on binding to Fv fragment and on the subsequent addition of lanthanides are consistent with the binding scheme for haptens and lanthanides proposed from the fluorescence studies. A difference between the limiting quenching of the e.s.r. signal from the bound haptens in the presence of saturating concentrations of Gd(III) and La(III) is attributed to dipolar interactions between bound Gd(III) and the nitroxide moiety of the bound hapten. The residual quenching with Gd(III) allows an estimate of 1.2nm to be made for the distance between the two paramagnetic centres. 6. The 270 MHz proton difference spectrum of the Fv fragment resulting from the addition of La(III) suggests that any metal-induced conformational changes are small and involve relatively few amino acid residues on the Fv fragment.

scholarly journals Positive co-operative binding at two weak lysine-binding sites governs the Glu-plasminogen conformational change

1992 ◽  
Vol 285 (2) ◽  
pp. 419-425 ◽  
Author(s):  
U Christensen ◽  
L Mølgaard
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Conformational Change ◽  
Conformational Changes ◽  
Binding Sites ◽  
High Specificity ◽  
Stopped Flow ◽  
Protein Fluorescence ◽  
Lysine Residues ◽  
Kinetics Of

The kinetics of a series of Glu-plasminogen ligand-binding processes were investigated at pH 7.8 and 25 degrees C (in 0.1 M-NaCl). The ligands include compounds analogous to C-terminal lysine residues and to normal lysine residues. Changes of the Glu-plasminogen protein fluorescence were measured in a stopped-flow instrument as a function of time after rapid mixing of Glu-plasminogen and ligand at various concentrations. Large positive fluorescence changes (approximately 10%) accompany the ligand-induced conformational changes of Glu-plasminogen resulting from binding at weak lysine-binding sites. Detailed studies of the concentration-dependencies of the equilibrium signals and the rate constants of the process induced by various ligands showed the conformational change to involve two sites in a concerted positive co-operative process with three steps: (i) binding of a ligand at a very weak lysine-binding site that preferentially, but not exclusively, binds C-terminal-type lysine ligands, (ii) the rate-determining actual-conformational-change step and (iii) binding of one more lysine ligand at a second weak lysine-binding site that then binds the ligand more tightly. Further, totally independent initial small negative fluorescence changes (approximately 2-4%) corresponding to binding at the strong lysine-binding site of kringle 1 [Sottrup-Jensen, Claeys, Zajdel, Petersen & Magnusson (1978) Prog. Chem. Fibrinolysis Thrombolysis 3, 191-209] were observed for the C-terminal-type ligands. The finding that the conformational change in Glu-plasminogen involves two weak lysine-binding sites indicates that the effect cannot be assigned to any single kringle and that the problem of whether kringle 4 or kringle 5 is responsible for the process resolves itself. Probably kringle 4 and 5 are both participating. The involvement of two lysine binding-sites further makes the high specificity of Glu-plasminogen effectors more conceivable.

scholarly journals Investigation of the nature of the two metal-binding sites in 5-aminolaevulinic acid dehydratase from Escherichia coli

1994 ◽  
Vol 300 (2) ◽  
pp. 373-381 ◽  
Author(s):  
P Spencer ◽  
P M Jordan
Keyword(s):  
Escherichia Coli ◽  
Metal Ions ◽  
Metal Binding ◽  
Binding Sites ◽  
Metal Ion ◽  
Protein Fluorescence ◽  
Metal Binding Sites ◽  
Aminolaevulinic Acid ◽  
Acid Dehydratase ◽  
Aminolaevulinic Acid Dehydratase

Two distinct metal-binding sites, termed alpha and beta, have been characterized in 5-aminolaevulinic acid dehydratase from Escherichia coli. The alpha-site binds a Zn2+ ion that is essential for catalytic activity. This site can also utilize other metal ions able to function as a Lewis acid in the reaction mechanism, such as Mg2+ or Co2+. The beta-site is exclusively a transition-metal-ion-binding site thought to be involved in protein conformation, although a metal bound at this site only appears to be essential for activity if Mg2+ is to be bound at the alpha-site. The alpha- and beta-sites may be distinguished from one another by their different abilities to bind divalent-metal ions at different pH values. The occupancy of the beta-site with Zn2+ results in a decrease of protein fluorescence at pH 6. Occupancy of the alpha- and beta-sites with Co2+ results in u.v.-visible spectral changes. Spectroscopic studies with Co2+ have tentatively identified three cysteine residues at the beta-site and one at the alpha-site. Reaction with N-ethyl[14C]maleimide preferentially labels cysteine-130 at the alpha-site when Co2+ occupies the beta-site.

scholarly journals Investigating the Conformation of S100β Protein Under Physiological Parameters Using Computational Modeling: A Clue for Rational Drug Design

2018 ◽  
Vol 12 (1) ◽  
pp. 36-50 ◽  
Author(s):  
Elvis K. Tiburu ◽  
Ibrahim Issah ◽  
Mabel Darko ◽  
Robert E. Armah-Sekum ◽  
Stephen O. A. Gyampo ◽  
...  
Keyword(s):  
Computational Modeling ◽  
Conformational Changes ◽  
Metal Binding ◽  
Binding Sites ◽  
Conformational Dynamics ◽  
Protein Molecule ◽  
Rational Drug Design ◽  
Characteristic Appearance ◽  
Secondary Structure Analysis ◽  
S100β Protein

Background: Physiochemical factors such as temperature, pH and cofactors are well known parameters that confer conformational changes in a protein structure. With S100β protein being a metal binding brain-specific receptor for both extracellular and intracellular functions, a change in conformation due to the above-mentioned factors, can compromise their cellular functions and therefore result in several pathological conditions such as Alzheimer’s disease, Ischemic stroke, as well as Myocardial Infarction. Objective: The studies conducted sought to elucidate the effect of these physiological factors on the conformational dynamics of S100β protein using computational modeling approaches. Method: Temperature-dependent and protein-cofactor complexes molecular dynamics simulations were conducted by varying the temperature from 100 to 400K using GROMACS 5.0.3. Additionally, the conformational dynamics of the protein was studied by varying the pH at 5.0, 7.4 and 9.0 using Ambertools17. This was done by preparing the protein molecule, solvating and minimizing its energy level as well as heating it to the required temperature, equilibrating and simulating under desired conditions (NVT and NPT ensembles). Results: The results show that the protein misfolds as a function of increasing temperature with alpha helical content at 100K and 400K being 57.8% and 43.3%, respectively. However, the binding sites of the protein was not appreciably affected by temperature variations. The protein displayed high conformational instability in acidic medium (pH ~5.0). The binding sites of Ca2+, Mg2+ and Zn2+ were identified and each exhibited different groupings of the secondary structural elements (binding motifs). The secondary structure analysis revealed different conformational changes with the characteristic appearance of two beta hairpins in the presence of Zn2+and Mg2+. Conclusion: High temperatures, different cofactors and acidic pH confer conformational changes to the S100β structure and these results may inform the design of novel drugs against the protein.

scholarly journals Serological and fluorescence studies of the heat stability of bovine lactoferrin

1979 ◽  
Vol 46 (1) ◽  
pp. 83-93 ◽  
Author(s):  
Augustin Baer ◽  
Marko Oroz ◽  
Bernard Blanc
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
Complement Fixation ◽  
Heat Stability ◽  
Heat Denaturation ◽  
Bovine Lactoferrin ◽  
Iron Binding ◽  
Binding Ability ◽  
Fluorescence Studies ◽  
Tryptophan Residues

SUMMARYThe heat denaturation of Fe-saturated lactoferrin (If) and Fe-free lactoferrin (apo-lf) was studied using the methods of micro-complement fixation and fluorescence. It was established that the change in conformation of apo-lf, induced by iron binding, conferred a higher heat stability to the molecule: the changes were observed at temperatures above 40 °C for apo-lf and above 60 °C for If. The Fe-binding ability of the protein was partially independent of the degree of denaturation. Fluorescence analyses indicated that tryptophan residues were probably not directly involved in the metal binding. There was no evidence of antibodies interfering with the binding sites.

scholarly journals Investigation of the effect of metal ions on the reactivity of thiol groups in human 5-aminolaevulinate dehydratase

1985 ◽  
Vol 225 (3) ◽  
pp. 573-580 ◽  
Author(s):  
P N B Gibbs ◽  
M G Gore ◽  
P M Jordan
Keyword(s):  
Metal Ions ◽  
Binding Sites ◽  
The Other ◽  
Stopped Flow ◽  
Thiol Groups ◽  
Protein Fluorescence ◽  
Fluorescence Studies ◽  
Nitrobenzoic Acid ◽  
Rate Of Reaction ◽  
Molar Equivalent

The reaction of human 5-aminolaevulinate dehydratase with 5,5′-dithiobis-(2-nitrobenzoic acid) (Nbs2) results in the release of 4 molar equivalents of 5-mercapto-2-nitrobenzoic acid (Nbs) per subunit. Two of the thiol groups reacted very rapidly (groups I and II), and their rate constants were determined by stopped-flow spectrophotometry; the other two thiol groups (groups III and IV) were observed by conventional spectroscopy. Titration of the enzyme with a 1 molar equivalent concentration of Nbs2 resulted in the release of 2 molar equivalents of Nbs and the concomitant formation of an intramolecular disulphide bond between groups I and II. Removal of zinc from the holoenzyme increased the reactivity of groups I and II without significantly affecting the rate of reaction of the other groups. The reactions of the thiol groups in both the holoenzyme and apoenzyme were little affected by the presence of Pb2+ ions at concentrations that strongly inhibit the enzyme, suggesting that Zn2+ and Pb2+ ions may have independent binding sites. Protein fluorescence studies with Pb2+ and Zn2+ have shown that the binding of both metal ions results in perturbation of the protein fluorescence.

Conformational changes in the metal-binding sites of cardiac troponin C induced by calcium binding

Biochemistry ◽  
1992 ◽  
Vol 31 (6) ◽  
pp. 1595-1602 ◽  
Author(s):  
George A. Krudy ◽  
Rui M. M. Brito ◽  
John A. Putkey ◽  
Paul R. Rosevear
Keyword(s):  
Conformational Changes ◽  
Metal Binding ◽  
Binding Sites ◽  
Calcium Binding ◽  
Cardiac Troponin ◽  
Troponin C ◽  
Metal Binding Sites ◽  
Cardiac Troponin C

Antibody-hapten interactions in solution

1975 ◽  
Vol 272 (915) ◽  
pp. 53-74 ◽  
Keyword(s):  
Amino Acid ◽  
Molecular Mass ◽  
Conformational Changes ◽  
Difference Spectrum ◽  
Spin Labels ◽  
Amino Acid Residues ◽  
Difference Spectroscopy ◽  
Relaxation Rates ◽  
Reciprocal Effect ◽  
Myeloma Protein

This paper reports the initial progress in a research programme to identify and obtain the relative orientations, in solution, of the amino acid residues that constitute the combining site of the myeloma protein MOPC 315. This protein has a molecular mass of 150000, but enzymic digestion yields the Fv fragment of molecular mass 25000 which still has the combining site intact, as judged by the affinity for dinitrophenyl haptens. Analysis of the e.s.r. spectra of a series of dinitrophenyl spin labelled haptens has allowed the dimensions, rigidity and polarity profile of the combining site to be determined. The combining site is a cleft of overall dimensions 1.1 nm x 0.9 nm x 0.6 nm which has considerable structural rigidity. One of these spin labels has also been used to perturb the n.m.r. spectrum of the Fv and using difference spectroscopy the 270 MHz proton n.m.r. spectrum of the amino acid residues in and around the combining site has been obtained. This spectrum contains only the equivalent of about 30 aromatic and 21 aliphatic protons. Comparison of this difference spectrum with that obtained using a diamagnetic analogue suggests that any conformational changes on hapten binding are mainly localized to the combining site. By the use of (n.m.r.) difference spectroscopy the protons of the three histidine residues in the Fv are observed to titrate with pH and have pK a values of about 8.1, 6.9 and 6.1. The histidine resonances with pK a values 6.9 and 6.1 alter slightly in the presence of haptens and also appear in the spin label difference spectrum, and must therefore be in or near to the combining site. These are assigned to His 102 H and His 97 L . The existence of lanthanide binding sites on the Fv, necessary for the mapping studies, has been demonstrated by measurements of Gd hi water relaxation rates in Fv solutions and also by the changes in the Fv tryptophan fluorescence on addition of Gd hi. At pH 5.5 there is one tight binding site for the lanthanides (K D ≈ 80 μm) but in the presence of hapten this is weakened 10-20 fold with a reciprocal effect on the hapten binding. Measurements of the Gd hi quenching of the e.s.r. spectrum of a spin labelled hapten bound to Fv indicate that the lanthanide site is ca. 1.5 nm from the nitroxide moiety.

scholarly journals Molecular Modeling and Spectroscopic Studies on the Interaction of Transresveratrol with Bovine Serum Albumin

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Xiaoli Liu ◽  
Yonghui Shang ◽  
Xudong Ren ◽  
Hua Li
Keyword(s):  
Molecular Modeling ◽  
Bovine Serum Albumin ◽  
Serum Albumin ◽  
Conformational Changes ◽  
Binding Sites ◽  
Bovine Serum ◽  
Electrostatic Interactions ◽  
Binding Constants ◽  
Binding Mode ◽  
Spectroscopic Studies

The interaction of transresveratrol (TRES) with bovine serum albumin (BSA) has been investigated by ultraviolet-visible, fluorescence, Fourier transform infrared spectroscopic methods and molecular modeling techniques. The fluorescence results show that the intrinsic fluorescence of BSA is quenched by TRES through a static quenching procedure. The binding constants of TRES with BSA at 292, 297 and 302 K are calculated as10.22×104,8.71×104, and7.59×104 L mol−1, respectively, and corresponding numbers of binding sites are approximately equal to unity. The thermodynamic parameters ΔHand ΔSare estimated to be −21.82 kJ mol−1and +21.15 J mol−1 K−1, which indicates that the interaction of TRES with BSA is driven mainly by hydrophobic forces and there are also hydrogen bonds and electrostatic interactions. The competitive experiments suggest that the binding site of TRES to BSA is probably located on site II. The results of infrared spectra show that the binding of TRES with BSA leads to conformational changes of BSA, and the binding stabilizes theα-helix andβ-sheet at the cost of a corresponding loss in theβ-turn structure of BSA. The results of molecular modeling calculation clarify the binding mode and the binding sites which are in good accordance with the experiment results.

scholarly journals The binding of lanthanides to non-immune rabbit immunoglobulin G and its fragments

1975 ◽  
Vol 149 (1) ◽  
pp. 73-82 ◽  
Author(s):  
S K Dower ◽  
R A Dwek ◽  
A C McLaughlin ◽  
L E Mole ◽  
E M Press ◽  
...  
Keyword(s):  
Heavy Chain ◽  
Immunoglobulin G ◽  
Metal Binding ◽  
Binding Sites ◽  
Water Proton ◽  
Proton Relaxation ◽  
Relaxation Rates ◽  
Protein Fluorescence ◽  
Chain Dimer ◽  
Rabbit Igg

The binding of Gd(III) to rabbit IgG (immunoglobulin G) and the Fab (N-terminal half of heavy and light chain), (Fab')2 (N-terminal half of heavy and light chains joined by inter-chain disulphide bond), Fc (C-terminal half of heavy-chain dimer)and pFc' (C-terminal quarter of heavy-chain dimer) fragments was demonstrated by measurements of the enhancement of the solvent-water proton relaxation rates in the appropriate Gd(III) solutions. At pH 5.5 there are six specific Gd(III)-binding sites on the IgG. These six sites can be divided into two classes; two very ‘tight’ sites on the Fc fragment (Kd approx. 5 μM) and two weaker sites on each Fab region (Kd approx. 140 μM). Ca(II) does not apparently compete for these metal-binding sites. The metal-binding parameters for IgG can be explained as the sum of the metal binding to the isolated Fab and Fc fragments, suggesting that there is no apparent interaction between the Fab and Fc regions in the IgG molecule. The binding of Gd(III) to Fab and Fc fragments was also monitored by measuring changes in the electron-spin-resonance spectrum of Gd(III) in the presence of each fragment and also by monitoring the effects of Gd(III) on the protein fluorescence at 340 nm (excitation 295 nm). The fluorescence of Tb(III) solutions of 545 nm (excitation 295 nm) is enhanced slightly on addition of Fab or Fc.

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