Immunochemical and spectroscopic evidence for protein conformational changes in phytochrome transformations

Phytochrome was examined by immunochemical and spectroscopic techniques to detect differences between the protein moieties of red- and far red-absorbing phytochrome (P_r and P_fr). No differences in the reaction of P_r and P_fr with phytochrome antibody were discernible on Ouchterlony double diffusion plates. However, the microcomplement fixation assay showed a greater degree of antibody reaction with P_fr than with P_r, indicating some difference in the surface characteristics of the two forms. Circular dichroism spectroscopy between 300 and 200 nanometers revealed differences between P_r and P_fr which may reflect differences in the protein conformation. The circular dichroism spectrum of P_r showed a negative band at 285 nanometers which was not present in the spectrum of P_fr, and the large negative circular dichroism band at 222 nanometers with P_fr, associated with the α-helical content, was shifted 2 nanometers to shorter wave length with P_r although there was no change of magnitude of this band. The absorbancy of P_r and P_fr is very nearly the same in the 280 nanometer spectral region, but sensitive difference spectra between P_r and P_fr did reveal spectra which were similar to solvent perturbation spectra obtained by others with different proteins. In total, the experiments indicate that there are conformational differences between the protein moieties of P_r and P_fr but that these differences are rather slight from a standpoint of gross structure.     

Topological aspects of conformational transformations in proteins

The topological aspects of the conformational transformations in proteins are investigated using a new peptide-ribbon representation of the tertiary structure. The topological parameters evaluated on a set of 49 proteins show striking regularities that extend beyond the secondary structures actually present and are interpreted as a manifestation of the topological invariance of conformational transformations in globular proteins.     

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

The decryption of sequence of structural events during protein conformational transitions is essential to a detailed understanding of molecular functions ofvarious biological nanomachines. Coarse‐grained models have proven useful by allowing highly efficient simulations of protein conformational dynamics. By combining two coarse‐grained elastic network models constructed based on the beginning and end conformations of a transition, we have developed an interpolated elastic network model to generate a transition pathway between the two protein conformations. For validation, we have predicted the order of local and global conformational changes during key ATP‐driven transitions in three important biological nanomachines (myosin, F₁ ATPase and chaperonin GroEL). We have found that the local conformational change associated with the closing of active site precedes the global conformational change leading to mechanical motions. Our finding is in good agreement with the distribution of intermediate experimental structures, and it supports the importance of local motions at active site to drive or gate various conformational transitions underlying the workings of a diverse range of biological nanomachines. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Analysis of conformational changes in WASP using a split YFP

WASP (Wiskott-Aldrich syndrome protein) has been proposed to adopt a closed conformation (autoinhibited conformation) due to interaction between the carboxy terminal and the GTPase binding domain. Various WASP-interacting proteins have been suggested to relieve this autoinhibition. We have used the split YFP (Yellow Fluorescent Protein) to analyze the conformation of WASP. Saccharomyces cerevisiae cells expressing YFP1-154-WASP-YFP155-238 were found to exhibit YFP fluorescence while cells expressing of YFP1-154-WASP and WASP-YFP155-238 did not suggesting an intramolecular complementation of the YFP molecule. The fluorescence signal of YFP1-154-WASP-YFP155-238 was enhanced in the presence of WIP (WASP-interacting protein) however this is not due to the increased stability of YFP1-154-WASP-YFP155-238. Expression of Toca-1 and Nck1 reduced the YFP fluorescence from YFP1-154-WASP-YFP155-238 even in the presence of WIP suggesting that binding of Toca-1 or Nck1 altered the conformation of YFP1-154-WASP-YFP155-238. Thus both Nck1 and Toca-1 can relieve the autoinhibition of the WASP molecule.     

A computational tool for designing FRET protein biosensors by rigid-body sampling of their conformational space

Biosensors relying on the fluorescence resonance energy transfer (FRET) between fluorescent proteins have been used for live-cell imaging of cellular events including Ca(2+) signaling. The efficiency of energy transfer between the donor and acceptor fluorescent proteins depends on the relative distance and orientation between them, which become altered by conformational changes of a fused sensory protein caused by a cellular event. In this way, changes in FRET efficiency of Ca(2+) biosensors can be correlated with Ca(2+) concentrations. The design of these FRET biosensors can be improved by modeling conformational changes before and after a cellular event. Hence, a computational tool called FPMOD was developed to predict FRET efficiency changes by constructing FRET biosensors and sampling their conformational space through rigid-body rotation. We showed with FPMOD that our computational modeling approach can qualitatively predict the FRET efficiencies of a range of biosensors, which had strong agreement with experimental results.     

Predicting large-scale conformational changes in proteins using energy-weighted normal modes

We report the development of a method to improve the sampling of protein conformational space in molecular simulations. It is shown that a principal component analysis of energy-weighted normal modes in Cartesian coordinates can be used to extract vectors suitable for describing the dynamics of protein substructures. The method can operate with either atomistic or user-defined coarse-grained models of protein structure. An implicit reverse coarse-graining allows the dynamics of all-atoms to be recovered when a coarse-grained model is used. For an external test set of four proteins, it is shown that the new method is more successful than normal mode analysis in describing the large-scale conformational changes observed on ligand binding. The method has potential applications in protein-ligand and protein-protein docking and in biasing molecular dynamics simulations.     

Alcohol-induced conformational changes of ubiquitin

Ubiquitin has been found to be soluble in ethylene glycol and alcohols as the perchlorate or hydrochloride salt. When the effect of alcohol on the structure of ubiquitin is examined, two reversible conformational transitions are observed. Upon lowering the dielectric constant of aqueous alcohol solutions of ubiquitin from 80 to 45, the native structure of ubiquitin is converted to a form consistent with 50% helical structure. This conformational change results in a change in exposure to solvent of the single methionine and the single tyrosine residues of ubiquitin. In agreement with crystallographic results, these residues are buried in the native conformation but become fully exposed to solvent upon undergoing this transition. Further lowering of the dielectric constant to 20 results in the accumulation of a conformation with almost complete helical structure. Thus, hydrophobic interactions cause facile conformational changes in the ubiquitin structure. These results are discussed in terms of a preferential solvation model. It is shown that the results obtained with different alcohols can be normalized by the use of a dielectric constant scale. This normalization corrects for the different molar volumes of different alcohols, allows comparison of results obtained with different alcohols, and should be useful in studying this phenomenon with different proteins.     

pH-induced conformational changes of DNA

The electrophoretic mobility of calf thymus DNA has been measured in aqueous buffered solutions as a function of pH. In the pH range 3.7–3.0, two electrophoretic species appear. The faster one migrates with the mobility of native DNA, the slower one migrates with a mobility close to that of thermally denatured DNA. The ratio of the two species varies with pH. Decreasing the pH increase the relative amount of the slower-moving component. These results may be interpreted by assuming that the DNA used in these experiments has a broad heterogeneity of base composition and that the conformational stability with respect to pH increases with increasing G + C content.     

Topological aspects of the conformational transformations in polypeptides and proteins

The topological aspects of the conformational transformations in a polypeptide chain are investigated in relation to the problem of selecting the minimum-energy pathways in protein folding.     

Study of conformational changes in immunoglobulin M using the method of differential spectroscopy

Using differential and solvent-perturbation spectrophotometry, the nature of conformational changes in immunoglobulin M (IgM) in different regimens was investigated. The quantities of tryptophan and tyrosine chromophores exposed on the surface of the molecule and screened, were evaluated. The changes in pH (7.8----2.0) of the surrounding medium and splitting of carbohydrate groups from IgM were shown to cause opposite effects, i. e., a "blue shift" of the spectrum and exposure of new chromophores by acidification, and a "red shift" and screening of chromophores by splitting of carbohydrate groups. The experimental results agree well with the previously made assumption on the differences in the spatial conformational changes in the IgM molecule under effects of pH of the surrounding medium and the loss of carbohydrate groups. Analysis of the spectral characteristics of some free Fab- and (Fc)5-fragments derived from the IgM molecules allowed a specification of the changes occurring in different parts of the whole molecule. The main conformational changes after acidification occur in the (Fc)5-fragment responsible for the effector function of IgM.     

Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol

A hybrid protocol combining Rosetta fullatom refinement and Multi-Conformation Continuum Electrostatics (MCCE) to estimate pK(a) is applied to the blind prediction of 94 mutated residues in Staphylococcal nuclease (SNase), as part of the pK(a)-cooperative benchmark test. The standard MCCE method is limited to sidechain conformational changes. The Rosetta refinement protocol is used to add the backbone conformational changes in pK(a) calculations. The non-electrostatic energy component from Rosetta and the electrostatic energy from MCCE are combined to weight the calculated ionization states. Of 63 measured pK(a)s, the root mean squared deviation (RMSD) between the calculated pK(a)s and the measured values is 4.3, showing an improvement compared to the RMSD of 6.6 in the standard MCCE calculations, using a low protein dielectric constant of 4. The breakdown of pK(a) shift from the solution values (ΔpK(a)) shows that the desolvation energy contributes the most in the standard MCCE calculations. Lowering desolvation penalties and optimizing electrostatic interactions with the Rosetta/MCCE protocol reduces the ΔpK(a) to favor the charged states. Analysis also showed that the Rosetta/MCCE protocol samples conformations with pK(a)s close to the solution values. The question remains whether the correct conformational changes coupled to the ionization changes are found here. Nevertheless, a challenge emerges to accurately estimate the reorganization energy, which is not directly measured from the electrostatic environment of the site of interest. Possible improvements to the protocol are also discussed.     

Investigating extracellular in situ EGFR structure and conformational changes using FRET microscopy

The crystallographic structures of functional fragments of ErbBs have provided excellent insights into the geometry of growth factor binding and receptor dimerization. By placing together receptor fragments to build structural models of entire receptors, we expect to understand how these enzymes are allosterically regulated; however, several predictions from these models are inconsistent with experimental evidence from cells. The opening of this gap underlines the need to investigate intact ErbBs by combining cellular and structural studies into a full picture.     

Studies of substrate-induced conformational changes in human cytomegalovirus protease using optical biosensor technology

The interaction between human cytomegalovirus (HCMV) protease and a peptide substrate was studied using a surface plasmon resonance (SPR)-based biosensor. Immobilization of the enzyme to the sensor chip surface by amine coupling resulted in an active enzyme with a higher catalytic efficiency than the enzyme in solution, primarily due to a lower K(m) value. The interaction between immobilized protease and substrate was characterized by a biphasic SPR signal. Rate constants for the formation of the initial enzyme-substrate complex could be determined from the sensorgrams. Simulated binding curves based on the determined k(cat) and the rate constants indicated that the complex binding signal did not originate from the accumulation of intermediates in the catalytic reaction. By chemical crosslinking of the immobilized HCMV protease, which was shown to limit the enzyme's structural flexibility, it was revealed that the obtained sensorgrams were composed of a signal caused by substrate binding and considerable structural alterations in the immobilized enzyme. Furthermore, HCMV protease was inactivated by chemical crosslinking, indicating that structural flexibility is essential for this enzyme. Parallel experiments with immobilized alpha-chymotrypsin revealed that it does not undergo similar conformational changes on peptide binding and that crosslinking did not inactivate the enzyme. The simultaneous detection of binding and conformational changes using optical biosensor technology is expected to be of importance for further characterization of the enzymatic properties of HCMV protease and for identification of inhibitors of this enzyme. It can also be of use for studies of other flexible proteins.     

Enzyme immunoassay using monoclonal antibodies to study conformational changes of human serum albumin

A method for studying conformational changes induced in the human albumin molecule, either in its purified form or in serum, is described. Plates were coated with albumin or human serum at varying pHs and were reacted with peroxidase-labeled anti-albumin monoclonal antibodies of different specificities. The data showed that albumin molecules were coated in conformations induced as a result of pH changes, allowing us to demonstrate that pH modifications involved the N-terminal portion of the albumin molecule whether in its purified form or in serum. This method should be applicable to the study of conformational modifications in other proteins as well.     

Complement driven by conformational changes

Complement in mammalian plasma recognizes pathogenic, immunogenic and apoptotic cell surfaces, promotes inflammatory responses and marks particles for cell lysis, phagocytosis and B-cell stimulation. At the heart of the complement system are two large proteins, complement component C3 and protease factor B. These two proteins are pivotal for amplification of the complement response and for labelling of the target particles, steps that are required for effective clearance of the target. Here we review the molecular mechanisms of complement activation, in which proteolysis and complex formation result in large conformational changes that underlie the key offensive step of complement executed by C3 and factor B. Insights into the mechanisms of complement amplification are crucial for understanding host defence and pathogen immune evasion, and for the development of complement-immune therapies.     

Conformational spectra--probing protein conformational changes

Stafford [Biophys. J. 17 (1996) MP452] has shown that it is possible, using the analytical ultracentrifuge in sedimentation velocity mode, to calculate the molecular weights of proteins with a precision of approximately 5%, by fitting Gaussian distributions to g(s*) profiles so long as partial specific volume and the radial position of the meniscus are known. This makes possible the analysis of systems containing several components by the fitting of multiple distributions to the total g(s*) profile. We have found the Stafford relationship to hold for a range of protein solutes, particularly good agreement being found when the g(s*) profiles are computed from Schlieren (dc/dr vs. r) data using the Bridgman equation [J. Am. Chem. Soc. 64 (1942) 2349] . On this basis, we have developed a new approach to the analysis of systems where two or more distinguishable conformations of a single species are present, either in the same sample cell or in different cells in the same rotor. In the former case, this allows us to analyse a given solution of pure protein (i.e. monodisperse with respect to M) to reveal the presence in that solution of two or more conformers under identical solvent conditions. In the latter case, we can detect with high sensitivity any conformational change occurring in the transition from one set of solvent conditions to another. Alternatively, in this case, we can analyse slightly different proteins (e.g. deletion mutants) for conformational changes under identical solvent conditions. Examples of these procedures using well-defined protein systems are given.