Motions in proteins

Frizzleds act as dynamic pharmacological entities

The Frizzled family of transmembrane receptors (FZD1-10) belongs to the class F of G protein-coupled receptors (GPCRs). FZDs bind to and are activated by Wingless/Int1 (WNT) proteins. The WNT/FZD signaling system regulates crucial aspects of developmental biology and stem-cell regulation. Dysregulation of WNT/FZD communication can lead to developmental defects and diseases such as cancer and fibrosis. Recent insight into the activation mechanisms of FZDs has underlined that protein dynamics and conserved microswitches are essential for FZD-mediated information flow and build the basis for targeting these receptors pharmacologically. In this review, we summarize recent advances in our understanding of FZD activation, and how novel concepts merge and collide with existing dogmas in the field.

Ratcheting synthesis

Synthetic chemistry has traditionally relied on reactions between reactants of high chemical potential and transformations that proceed energetically downhill to either a global or local minimum (thermodynamic or kinetic control). Catalysts can be used to manipulate kinetic control, lowering activation energies to influence reaction outcomes. However, such chemistry is still constrained by the shape of one-dimensional reaction coordinates. Coupling synthesis to an orthogonal energy input can allow ratcheting of chemical reaction outcomes, reminiscent of the ways that molecular machines ratchet random thermal motion to bias conformational dynamics. This fundamentally distinct approach to synthesis allows multi-dimensional potential energy surfaces to be navigated, enabling reaction outcomes that cannot be achieved under conventional kinetic or thermodynamic control. In this Review, we discuss how ratcheted synthesis is ubiquitous throughout biology and consider how chemists might harness ratchet mechanisms to accelerate catalysis, drive chemical reactions uphill and programme complex reaction sequences.

Ligands-induced open-close conformational change during DapE catalysis: Insights from molecular dynamics simulations

The microbial enzyme DapE plays a critical role in the lysine biosynthetic pathway and is considered as a potentially safe antibiotic target. In this study, atomistic simulations are employed to identify the modes of essential dynamics that define the conformational response of the enzyme to ligand binding and unbinding. The binding modes and the binding affinities of the products to the DapE enzyme are estimated from the MM-PBSA method, and the residues contributing to the ligand binding are identified. Various structural analyses and the principal component analysis of the molecular dynamics trajectories reveal that the removal of products from the active site causes a significant change in the overall enzyme structure. Both Cartesian and dihedral principal component analyses are used to characterize the structural changes in terms of domain unfolding and domain twisting motions. In the most dominant mode, that is, the domain unfolding motion, the two catalytic domains move away from the two dimerization domains of the dimeric enzyme, representing a closed-to-open conformational change. The conformational changes are initiated by the coordinated movement of three loops (Asp75-Pro82, Gly240-Asn244, and Thr347-Glu353) that trigger a domain-level movement. From multiple short trajectories, the time constant associated with the domain opening motion is estimated as 43.6 ns. Physiologically, this close-to-open conformational change is essential for the regeneration of the initial state of the enzyme for the subsequent cycle of catalytic action and provides the apo enzyme enough flexibility for efficient substrate binding.

D3PM: a comprehensive database for protein motions ranging from residue to domain

Background

Knowledge of protein motions is significant to understand its functions. While currently available databases for protein motions are mostly focused on overall domain motions, little attention is paid on local residue motions. Albeit with relatively small scale, the local residue motions, especially those residues in binding pockets, may play crucial roles in protein functioning and ligands binding.

Results

A comprehensive protein motion database, namely D3PM, was constructed in this study to facilitate the analysis of protein motions. The protein motions in the D3PM range from overall structural changes of macromolecule to local flip motions of binding pocket residues. Currently, the D3PM has collected 7679 proteins with overall motions and 3513 proteins with pocket residue motions. The motion patterns are classified into 4 types of overall structural changes and 5 types of pocket residue motions. Impressively, we found that less than 15% of protein pairs have obvious overall conformational adaptations induced by ligand binding, while more than 50% of protein pairs have significant structural changes in ligand binding sites, indicating that ligand-induced conformational changes are drastic and mainly confined around ligand binding sites. Based on the residue preference in binding pocket, we classified amino acids into “pocketphilic” and “pocketphobic” residues, which should be helpful for pocket prediction and drug design.

Conclusion

D3PM is a comprehensive database about protein motions ranging from residue to domain, which should be useful for exploring diverse protein motions and for understanding protein function and drug design. The D3PM is available on www.d3pharma.com/D3PM/index.php.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04595-0.

The nature of efficacy at G protein-coupled receptors

G protein-coupled receptors (GPCRs) participate in many pathophysiological processes as well as almost all aspects of normal physiology. They are present at the surface of all cell types making them amenable and attractive targets for pharmaceutical therapeutics. GPCRs possess complex pharmacology with the ability to be turned on to various extents, have their constitutive activity suppressed and even switch between signaling pathways to which they couple. Underlying this complex pharmacology is GPCR signaling efficacy, and differences in efficacy promoted by alternative ligands and in different tissues is of great interest to biology in general and also the pharmaceutical industry. In this review we hope to discuss what the molecular foundations of efficacy are and whether a new approach utilizing a rate-dependent model may provide new insights into this phenomenon.

Conformational Transitions and the Activation of Heterotrimeric G Proteins by G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) are particularly attractive targets for therapeutic pharmaceuticals. This is because they are involved in almost all facets of physiology, in many pathophysiological processes, they are tractable due to their cell surface location, and can exhibit highly textured pharmacology. While the development of new drugs does not require the molecular details of the mechanism of activity for a particular target, there has been increasing interest in the GPCR field in these details. In part, this has come with the recognition that differential activity at a particular target might be a way in which to leverage drug activity, either through manipulation of efficacy or through differential coupling (signaling bias). To this end, the past few years have seen a number of publications that have specifically attempted to address one or more aspects of the molecular reaction pathway, leading to activation of heterotrimeric G proteins by GPCRs.

In vitro evaluation of the conjugations of neonicotinoids with transport protein: photochemistry, ligand docking and molecular dynamics studies

The flexibility of ligand structures and the property of substituents in neonicotinoids play a pivotal role in protein–neonicotinoid and this type of biorecognition may have a great impact on the potential toxicity of these widely used agrochemicals.

Psychrophilic enzymes: from folding to function and biotechnology

Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.

A surprising role for conformational entropy in protein function

Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a great challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to access experimentally is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned, and what the future may hold for this emerging view of protein function.

The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation

Historically it has been virtually impossible to experimentally determine the contribution of residual protein entropy to fundamental protein activities such as the binding of ligands. Recent progress has illuminated the possibility of employing NMR relaxation methods to quantitatively determine the role of changes in conformational entropy in molecular recognition by proteins. The method rests on using fast internal protein dynamics as a proxy. Initial results reveal a large and variable role for conformational entropy in the binding of ligands by proteins. Such a role for conformational entropy in molecular recognition has significant implications for enzymology, signal transduction, allosteric regulation and the development of protein-directed pharmaceuticals.

Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events

We present a computational methodology to sample rare events in large biological enzymes that may involve electronically polarizing, reactive processes. The approach includes simultaneous dynamical treatment of electronic and nuclear degrees of freedom, where contributions from the electronic portion are computed using hybrid density functional theory and the computational costs are reduced through a hybrid quantum mechanics/molecular mechanics (QM/MM) treatment. Thus, the paper involves a QM/MM dynamical treatment of rare events. The method is applied to probe the effect of the active site elements on the critical hydrogen transfer step in the soybean lipoxygenase-1 (SLO-1) catalyzed oxidation of linoleic acid. It is found that the dynamical fluctuations and associated flexibility of the active site are critical toward maintaining the electrostatics in the regime where the reactive process can occur smoothly. Physical constraints enforced to limit the active site flexibility are akin to mutations and, in the cases studied, have a detrimental effect on the electrostatic fluctuations, thus adversely affecting the hydrogen transfer process.

Protein stability and enzyme activity at extreme biological temperatures

Psychrophilic microorganisms thrive in permanently cold environments, even at subzero temperatures. To maintain metabolic rates compatible with sustained life, they have improved the dynamics of their protein structures, thereby enabling appropriate molecular motions required for biological activity at low temperatures. As a consequence of this structural flexibility, psychrophilic proteins are unstable and heat-labile. In the upper range of biological temperatures, thermophiles and hyperthermophiles grow at temperatures > 100 °C and synthesize ultra-stable proteins. However, thermophilic enzymes are nearly inactive at room temperature as a result of their compactness and rigidity. At the molecular level, both types of extremophilic proteins have adapted the same structural factors, but in opposite directions, to address either activity at low temperatures or stability in hot environments. A model based on folding funnels is proposed accounting for the stability-activity relationships in extremophilic proteins.

Molecular dynamics of an alpha-helical polypeptide: Temperature dependence and deviation from harmonic behavior

The mean square amplitudes of atomic fluctuations for a polypeptide (decaglycine) alpha-helix evaluated from molecular dynamics simulations at seven temperatures between 5 and 300 K are compared with analytic harmonic results and with experimental values. Above 100 K the harmonic approximation significantly underestimates the amplitudes of the displacements. Analysis of the time dependence of the fluctuations shows that low-frequency modes (<75 cm(-1)) dominate the atomic fluctuations and that there is a contribution with a very long relaxation time (>10 ps). Quantum corrections to the amplitude of the fluctuations are found to be small above 50 K. The mean square amplitudes obtained from the molecular dynamics simulations are compared with the values derived from x-ray temperature (Debye-Waller) factors for metmyoglobin (80, 250, and 300 K) and ferrocytochrome c (300 K).

Mobility and active-site coupling in 2-oxo acid dehydrogenase complexes

The 2-oxo acid dehydrogenase complexes consist of multiple copies of each of three enzymes, 2-oxo acid decarboxylase (E1), lipoate acetyltransferase (E2) and lipoamide dehydrogenase (E3), which catalyse successive steps in the overall reaction. The complexes are based on a structural core made up of the E2 chains, which also contain lipoic acid residues covalently attached to lysine residues. These lipoic acid residues are involved in transferring the substrate between the different active sites. A combination of limited proteolysis and 1H NMR experiments has shown that the E2 component has an unusual structure, having a substantial segment of polypeptide chain in the form of a highly flexible random coil. This flexibility allows the lipoyl-lysine residues to move rapidly over considerable distances, and provides a mechanism for the system of active-site coupling observed in these complexes.

The role of mobility in the substrate binding and catalytic machinery of enzymes

Recent theoretical and experimental studies have demonstrated that proteins are fluctuating systems capable of large, seemingly random, excursions from the equilibrium conformation. Attention is now focusing on the functional consequences of these motions. X-ray diffraction is a powerful tool for mapping the spatial distribution of protein dynamics; studies on the temperature dependence of the apparent Debye-Waller factors of crystalline myoglobin demonstrate that proteins are flexible in the solid state. Crystallographic studies of a Michaelis complex of ribonuclease A show that a mobile lysine adapts its conformation to the changes in stereochemistry and charge distribution in the substrate during catalysis. The structure of the triose phosphate isomerase-substrate complex shows that a mobile region of 10 amino acids becomes ordered when ligand binds. These studies suggest several roles for protein mobility in enzymic catalysis: providing access to internal sites, allowing changes in substrate structure during the reaction, and reducing the observed binding constant of substrate and product to the enzyme by decreasing entropy. A flexible enzyme also does not need a communication system to signal binding or transformation, since a pre-existing equilibrium can be used. More speculative ideas, such as the guiding of thermal vibrations along the reaction coordinate, can only be tested when more detailed data are available.

Influence of local structure on the location of antigenic determinants in tobacco mosaic virus protein

Early work on protein antigenicity led to the common belief that proteins possess a finite number of antigenic determinants located in accessible regions of the molecule's surface. This view is now changing. As a result of extensive studies, seven continuous epitopes have been located on tobacco mosaic virus (TMV) protein by measuring the antigenic activity of short peptides with anti-protein antibodies. The structure of the viral protein has been refined in Cambridge, enabling the Strasbourg workers to correlate the position of these epitopes with regions of high segmental mobility in the protein. Surface accessibility is not a sufficient condition for antigenicity, because six short peptides corresponding to accessible regions of the protein possess no antigenic activity. Recent work in Strasbourg shows that when longer peptides of TMV protein are used, more antigenic determinants are found and these lie in more structured regions of the protein (e.g. helices). In these cases the longer peptide may be folding up in solution to mimic part of the native structure.

Conformational transitions and glycation of serum albumin in patients with minimal-change glomerulopathy

BACKGROUND

There has been a lack of study on the structural changes of serum albumin in patients with minimal change disease (MCD). To determine whether glycation and/or conformational transitions of albumin are involved in the pathogenesis of albuminuria, nine patients with MCD were enrolled in a prospective follow-up study for comparison of these parameters in serum albumin during the remission and relapse of nephrotic syndrome.

METHODS

Circular dichroism measurements were made with purified albumin. Ellipticities at each wavelength were transformed to mean residue ellipticity. Monosaccharide composition was analyzed by high-pH anion-exchange chromatography with pulsed amperometric detection.

RESULTS

There was no difference in the proportions of alpha-helix, beta-conformation, and beta-turn of albumin between the sera of control patients and those with nephrotic syndrome. However, the proportion of the random configuration was slightly higher in the plasma albumin of patients in relapse than in those in remission. The proportion of the random configuration was lower in the albumin of the serum than in the urine of patients with nephrotic syndrome, but there was no difference in the proportions of alpha-helix, beta-conformation, and beta-tum of albumin between their plasma and urine.

CONCLUSION

Our results suggest that conformational changes in albumin are involved in albuminuria in patients with MCD.

Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation

Binding of the HIV tat protein to the TAR (transactivating response region) RNA element activates transcription of the HIV viral genome. The complex of TAR with argininamide serves as a model for the RNA conformation in the tat-TAR complex. The dynamics of the HIV-2 TAR-argininamide complex was investigated by measurements of the relaxation rates of protonated base carbon and nitrogen nuclei. Six auto-correlation rates as well as cross-correlation rates were measured to map the frequencies of base motion in the HIV-2 TAR-argininamide complex. These measurements reveal a broad range of dynamic heterogeneity exhibited by hexanucleotide loop, the dinucleotide bulge, and the A-form helical regions. U23 in the bulge undergoes the largest dynamic change on binding argininamide, while U25 remains flexible, reflecting the large conformational change that is triggered upon ligand binding.

Microsecond to minute dynamics revealed by EX1-type hydrogen exchange at nearly every backbone hydrogen bond in a native protein

A previous comprehensive analysis of the pH dependence of native-state amide hydrogen (NH) exchange in turkey ovomucoid third domain (OMTKY3) yielded apparent opening and closing rate constants (k(op) and k(cl)) at 14 NH groups involved in global conformational changes. This analysis has been extended to 18 additional slowly exchanging NH groups. Quench-flow experiments were performed to monitor NH exchange in native OMTKY3 from neutral to very alkaline pH ( approximately 12) conditions. Above pH 10 the mechanism of exchange switched from one governed by a rapid equilibrium preceding the chemistry of exchange (i.e. EX2 exchange), to one where exchange was limited by the rate of opening (i.e. EX1 exchange). Kinetics of solvent exposure are now known for nearly all backbone NH groups in native OMTKY3, yielding rate constants that span five orders of magnitude, 0.004 to 200 s(-1).

From genes to protein structure and function: novel applications of computational approaches in the genomic era

The genome-sequencing projects are providing a detailed 'parts list' of life. A key to comprehending this list is understanding the function of each gene and each protein at various levels. Sequence-based methods for function prediction are inadequate because of the multifunctional nature of proteins. However, just knowing the structure of the protein is also insufficient for prediction of multiple functional sites. Structural descriptors for protein functional sites are crucial for unlocking the secrets in both the sequence and structural-genomics projects.

Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin

The influence of hydration on the internal dynamics of a typical EF-hand calciprotein, parvalbumin, was investigated by incoherent quasi-elastic neutron scattering (IQNS) and solid-state 13C-NMR spectroscopy using the powdered protein at different hydration levels. Both approaches establish an increase in protein dynamics upon progressive hydration above a threshold that only corresponds to partial coverage of the protein surface by the water molecules. Selective motions are apparent by NMR in the 10-ns time scale at the level of the polar lysyl side chains (externally located), as well as of more internally located side chains (from Ala and Ile), whereas IQNS monitors diffusive motions of hydrogen atoms in the protein at time scales up to 20 ps. Hydration-induced dynamics at the level of the abundant lysyl residues mainly involve the ammonium extremity of the side chain, as shown by NMR. The combined results suggest that peripheral water-protein interactions influence the protein dynamics in a global manner. There is a progressive induction of mobility at increasing hydration from the periphery toward the protein interior. This study gives a microscopic view of the structural and dynamic events following the hydration of a globular protein.

Fractal ion-channel behavior generates fractal firing patterns in neuronal models

Fractal behavior has been observed in both ion-channel gating and neuronal spiking patterns, but a causal relationship between the two has not yet been established. Here, we examine the effects of fractal ion-channel activity in modifications of two classical neuronal models: Fitzhugh-Nagumo (FHN) and Hodgkin-Huxley (HH). For the modified FHN model, the recovery variable was represented as a population of ion channels with either fractal or Markov gating characteristics. Fractal gating characteristics changed the form of the interspike interval histogram (ISIH) and also induced fractal behavior in the firing rate. For the HH model, the K+ conductance was represented as a collection of ion channels with either quasifractal or Markov gating properties. Fractal gating induced fractal-rate behavior without changing the ISIH. We conclude that fractal ion-channel gating activity is sufficient to account for fractal-rate firing behavior.

The protein state of matter

Three ways are generally used to visualize proteins: (1) a static model in which the atomic positions are defined, (2) a dynamic model taking into account fluctuations, and (3) a reactive model that reflects the internal and external electric fields of the molecule. The properties of chromophoric prosthetic groups can be probed by optical spectroscopy, and when high resolution techniques are used, the results reveal information about the local electric fields in proteins, as influenced and determined by atomic positions and dynamics.

Conformational dynamics and enzyme activity

Conformational flexibility and structural fluctuations play an important role in enzyme activity. A great variety of internal motions ranging over different time scales and of different amplitudes are involved in the catalytic cycle. These different types of motions and their functional consequences are considered in the light of experimental data and theoretical analyses. The conformational changes upon substrate binding, and particularly the hinge-bending motion which occurs in enzymes made of two domains, are analyzed from several well documented examples. The conformational events accompanying the different steps of the catalytic cycle are discussed. The last section concerns the motions involved in the allosteric transition which regulates the enzyme activity.

Theory and practice of nuclear spin relaxation in proteins

NMR relaxation experiments can provide information on overall and internal motions in proteins. This review consists of a concise report on the evolution of the theories for nuclear relaxation followed by an overview of mathematical models for internal motions in proteins. Next, the method of spectral density mapping with recent developments is reviewed. This is followed by a discussion of pulse sequences for relaxation experiments. Finally, we review recent studies correlating relaxation parameters, in particular spectral density functions, with structural features of proteins and with results of molecular dynamics simulations.

Access of ligands to cavities within the core of a protein is rapid

We have investigated the magnitude and timescale of fluctuations within the core of a protein using the exchange kinetics of indole and benzene binding to engineered hydrophobic cavities in T4 lysozyme. The crystal structures of variant-benzene complexes suggest that relatively large scale fluctuations (1-2 angstrom) of backbone atoms are required for entry of these ligands into the core. Nonetheless, these ligands enter the cavities rapidly, with bimolecular rate constants of approximately 10(6)-10(7) M(-1) s(-1) and a low activation barrier, 2-5 kcal mol(-1). These results suggest that protein cores undergo substantial fluctuations on the millisecond to microsecond timescale and that entry of small molecules into protein interiors is not strongly limited by steric occlusion.

Study of global motions in proteins by weighted masses molecular dynamics: adenylate kinase as a test case

The weighted masses molecular dynamics (WMMD) technique is applied to the protein adenylate kinase. A novel set of restraints has been developed to allow the use of this technique with proteins. The WMMD simulation is successful in predicting the flexibility of the two mobile domains of the protein. The end product of the simulation is similar to the known open and AMP bound forms of the enzyme. The biological relevance of the restraints used and potential methods of improving the technique are discussed.

Molecular dynamics of alamethicin transmembrane channels from open-channel current noise analysis

Conductance noise measurement of the open states of alamethicin transmembrane channels reveals excess noise attributable to cooperative low-frequency molecular dynamics that can generate fluctuations approximately 1 A rms in the effective channel pore radius. Single-channel currents through both persistent and nonpersistent channels with multiple conductance states formed by purified polypeptide alamethicin in artificial phospholipid bilayers isolated onto micropipettes with gigaohm seals were recorded using a voltage-clamp technique with low background noise (rms noise < 3 pA up to 20 kHz). Current noise power spectra between 100 Hz and 20 kHz of each open channel state showed little frequency dependence. Noise from undetected conductance state transitions was insignificant. Johnson and shot noises were evaluated. Current noise caused by electrolyte concentration fluctuation via diffusion was isolated by its dependence on buffer concentration. After removing these contributions, significant current noise remains in all persistent channel states and increases in higher conductance states. In nonpersistent channels, remaining noise occurs primarily in the lowest two states. These fluctuations of channel conductance are attributed to thermal oscillations of the channel molecular conformation and are modeled as a Langevin translational oscillation of alamethicin molecules moving radially from the channel pore, damped mostly by lipid bilayer viscosity.

A statistical mechanical model for hydrogen exchange in globular proteins

We develop a statistical mechanical theory for the mechanism of hydrogen exchange in globular proteins. Using the HP lattice model, we explore how the solvent accessibilities of chain monomers vary as proteins fluctuate from their stable native conformations. The model explains why hydrogen exchange appears to involve two mechanisms under different conditions of protein stability: (1) a "global unfolding" mechanism by which all protons exchange at a similar rate, approaching that of the denatured protein, and (2) a "stable-state" mechanism by which protons exchange at rates that can differ by many orders of magnitude. There has been some controversy about the stable-state mechanism: does exchange take place inside the protein by solvent penetration, or outside the protein by the local unfolding of a subregion? The present model indicates that the stable-state mechanism of exchange occurs through an ensemble of conformations, some of which may bear very little resemblance to the native structure. Although most fluctuations are small-amplitude motions involving solvent penetration or local unfolding, other fluctuations (the conformational distant relatives) can involve much larger transient excursions to completely different chain folds.

An in vitro model of aging: the influence of increasing physical density on enzyme activities of trypsin, xanthine oxidase and superoxide dismutase

The enzyme activities of trypsin (using an artificial substrate, Nalpha-benzoyl-L-arginine-ethylester = BAEE), xanthine oxidase (XOD) and superoxide dismutase (SOD) were measured in the absence and presence of various concentrations of the following inert, water-soluble polymer viscogens: polyvinylpyrrolidone (PVP-40), polyethyleneglycol (PEG-6000) and bovine serum albumin (BSA). Enzyme activities measured in the absence of viscogens were taken as 100%. In the presence of the viscogens, enzyme activities decreased considerably as follows: (i) Trypsin: to 2 or 12% in reaction mixtures containing 64 mg/ml PVP-40 or 481 mg/ml PEG-6000, respectively. (ii) XOD: to 29.3% in a reaction mixture containing 116 mg/ml PVP-40, to 68.9% in a medium containing 266 mg/ml PEG-6000, and 38.1% in the presence of 138 mg/ml BSA. (iii) SOD: to 40.0, 19.9 and 16.6% in the same media as listed for XOD, respectively. The observations are consistent with the predictions of the molecular enzyme kinetic model (MEKM), and are also of importance for the membrane hypothesis of aging, since the latter explains the loss of cell functions by an age-dependent increase of intracellular density which may cause serious enzyme inhibitions.

Models of cooperativity in protein folding

What is the basis for the two-state cooperativity of protein folding? Since the 1950s, three main models have been put forward. 1. In 'helix-coil' theory, cooperativity is due to local interactions among near neighbours in the sequence. Helix-coil cooperativity is probably not the principal basis for the folding of globular proteins because it is not two-state, the forces are weak, it does not account for sheet proteins, and there is no evidence that helix formation precedes the formation of a hydrophobic core in the following pathways. 2. In the 'sidechain packing' model, cooperativity is attributed to the jigsaw-puzzle-like complementary fits of sidechains. This too is probably not the basis of folding cooperativity because exact models and experiments on homopolymers with sidechains give no evidence that sidechain freezing is two-state, sidechain complementarities in proteins are only weak trends, and the molten globule model predicted by this model is far more native-like than experiments indicate. 3. In the 'hydrophobic core collapse' model, cooperativity is due to the assembly of non-polar residues into a good core. Exact model studies show that this model gives two-state behaviour for some sequences of hydrophobic and polar monomers. It is based on strong forces. There is considerable experimental evidence for the kinetics this model predicts: the development of hydrophobic clusters and cores is concurrent with secondary structure formation. It predicts compact denatured states with sizes and degrees of disorder that are in reasonable agreement with experiments.

Side-chain entropy and packing in proteins

What role does side-chain packing play in protein stability and structure? To address this question, we compare a lattice model with side chains (SCM) to a linear lattice model without side chains (LCM). Self-avoiding configurations are enumerated in 2 and 3 dimensions exhaustively for short chains and by Monte Carlo sampling for chains up to 50 main-chain monomers long. This comparison shows that (1) side-chain degrees of freedom increase the entropy of open conformations, but side-chain steric exclusion decreases the entropy of compact conformations, thus producing a substantial entropy that opposes folding; (2) there is side-chain "freezing" or ordering, i.e., a sharp decrease in entropy, near maximum compactness; and (3) the different types of contacts among side chains (s) and main-chain elements (m) have different frequencies, and the frequencies have different dependencies on compactness. mm contacts contribute significantly only at high densities, suggesting that main-chain hydrogen bonding in proteins may be promoted by compactness. The distributions of mm, ms, and ss contacts in compact SCM configurations are similar to the distributions in protein structures in the Brookhaven Protein Data Bank. We propose that packing in proteins is more like the packing of nuts and bolts in a jar than like the pairwise matching of jigsaw puzzle pieces.

Conformational dynamics of bovine Cu, Zn superoxide dismutase revealed by time-resolved fluorescence spectroscopy of the single tyrosine residue

The structural dynamics of bovine erythrocyte Cu, Zn superoxide dismutase (BSOD) was studied by time-resolved fluorescence spectroscopy. BSOD is a homodimer containing a single tyrosine residue (and no tryptophan) per subunit. Frequency-domain fluorometry revealed a heterogeneous fluorescence decay that could be described with a Lorentzian distribution of lifetimes. The lifetime distribution parameters (center and width) were markedly dependent on temperature. The distribution center (average lifetime) displayed Arrhenius behavior with an Ea of 4.2 kcal/mol, in contrast with an Ea of 7.4 kcal/mol for the single-exponential decay of L-tyrosine. This indicated that thermal quenching of tyrosine emission was not solely responsible for the effect of temperature on the lifetimes of BSOD. The distribution width was broad (1 ns at 8 degrees C) and decreased significantly at higher temperatures. Furthermore, the width of the lifetime distribution increased in parallel to increasing viscosity of the medium. The combined effects of temperature and viscosity on the fluorescence decay suggest the existence of multiple conformational substrates in BSOD that interconvert during the excited-state lifetime. Denaturation of BSOD by guanidine hydrochloride produced an increase in the lifetime distribution width, indicating a larger number of conformations probed by the tyrosine residue in the denatured state. The rotational mobility of the tyrosine in BSOD was also investigated. Analysis of fluorescence anisotropy decay data enabled resolution of two rotational correlation times. One correlation time corresponded to a fast (picosecond) rotation that contributed 62% of the anisotropy decay and likely reported local mobility of the tyrosine ring. The longer correlation time was 50% of the expected value for rotation of the whole (dimeric) BSOD molecule and appeared to reflect segmental motions in the protein in addition to overall tumbling. Comparison between rotational correlation times and fluorescence lifetimes of BSOD indicates that the heterogeneity in lifetimes does not arise from mobility of the tyrosine per se, but rather from dynamics of the protein matrix surrounding this residue which affect its fluorescence decay.

Thermal expansion of hen egg-white lysozyme. Comparison of the 1.9 A resolution structures of the tetragonal form of the enzyme at 100 K and 298 K

The average structural and dynamic properties of tetragonal hen egg-white lysozyme have been compared, in structures refined at 1.9 A resolution, using data collected at 100 K and 298 K. The molecule expands by 1.8% over this temperature range with the expansion occurring primarily in its small sub-atomic-sized spaces in an anisotropic manner. Hen egg-white lysozyme consists of two domains: domain 1 (residues 40 to 88) is composed primarily of beta-sheet and is observed to expand by only 0.3%; domain 2 (residues 1 to 39 and 89 to 129) is chiefly alpha-helix and is observed to expand by 2.2%. This is consistent with previous observations that proteins composed primarily of alpha-helix expand more with temperature than do those composed primarily of beta-sheet. The largest movement in the molecule is undergone by the two domains of the structure that move further apart as the temperature is raised. This motion is not a cleft opening but rather consists of a tilt by 2.3 degrees of domain 1 away from domain 2. Within the individual domains the largest movement is undergone by loop T1 of domain 2, consisting of residues 17 to 23. This loop moves in the opposite direction to the rest of the molecule as the temperature is raised. Average temperature factors for the room-temperature and low-temperature structures are 15.2 A2 and 8.1 A2, respectively, when all protein atoms are considered, while these values are 14.0 A2 and 7.8 A2, when only main-chain atoms (N, C alpha, C) are taken into account. An examination of the main-chain averaged B-factor per residue shows that residues involved in intermolecular protein-protein contacts, with symmetry-related molecules, have somewhat lower B-factors than the average and undergo smaller than average changes in B-factor as the temperature is lowered.

Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex

Although antibodies are highly specific, cross-reactions are frequently observed. To understand the molecular basis of this phenomenon, we studied the anti-hen egg lysozyme (HEL) monoclonal antibody (mAb) D11.15, which cross-reacts with several avian lysozymes, in some cases with a higher affinity (heteroclitic binding) than for HEL. We have determined the crystal structure of the Fv fragment of D11.15 complexed with pheasant egg lysozyme (PHL). In addition, we have determined the structure of PHL, Guinea fowl egg lysozyme, and Japanese quail egg lysozyme. Differences in the affinity of D11.15 for the lysozymes appear to result from sequence substitutions in these antigens at the interface with the antibody. More generally, cross-reactivity is seen to require a stereochemically permissive environment for the variant antigen residues at the antibody-antigen interface.

Glycerol effects on protein flexibility: a tryptophan phosphorescence study

In exploring the dynamic properties of protein structure, numerous studies have focussed on the dependence of structural fluctuations on solvent viscosity, but the emerging picture is still not well defined. Exploiting the sensitivity of the phosphorescence lifetime of tryptophan to the viscosity of its environment we have used the delayed emission as an intrinsic probe of protein flexibility and investigated the effects of glycerol as a viscogenic cosolvent. The phosphorescence lifetime of alcohol dehydrogenase, alkaline phosphatase, apoazurin and RNase T1, as a function of glycerol concentration was studied at various temperatures. Flexibility data, which refer to rather rigid sites of the globular structures, point out that, for some concentration ranges glycerol, effects on the rate of structural fluctuations of alcohol dehydrogenase and RNase T1 do not obey Kramers' a power law on solvent viscosity and emphasize that cosolvent-induced structural changes can be important, even for inner cores of the macromolecule. When the data is analyzed in terms of Kramers' model, for the temperature range 0-30 degrees C one derives frictional coefficients that are relatively large (0.6-0.7) for RNase T1, where the probe is in a flexible region near the surface of the macromolecule and much smaller, less than 0.2, for the rigid sites of the other proteins. For the latter sites the frictional coefficient rises sharply between 40 and 60 degrees C, and its value correlates weakly with molecular parameters such as the depth of burial or the rigidity of a particular site. For RNase T1, coupling to solvent viscosity increases at subzero temperatures, with the coefficient becoming as large as 1 at -20 degrees C. Temperature effects were interpreted by proposing that solvent damping of internal protein motions is particularly effective for low frequency, large amplitude, structural fluctuations yielding highly flexible conformers of the macromolecule.