Simulations of reversible protein aggregate and crystal structure

Selective Chiral Interactions between Hydrophilic/Hydrophobic Amino Acids and Growing Gypsum Crystals

In nature, selective interactions between chiral amino acids and crystals are important for the formation of chiral biominerals and provide insight into the mysterious origin of homochirality. Here, we show that chiral amino acids with different hydrophilicities/hydrophobicities exhibit different chiral selectivity preferences in the dynamically growing gypsum [001] steps. Hydrophilic amino acids show a chiral selectivity preference for their d-isomers, whereas hydrophobic amino acids prefer their l-isomers. These differences in chiral recognition can be attributed to the different stereochemical matching between the hydrophilic and hydrophobic amino acids on the [001] steps of growing gypsum. These different chiral selectivities resulting from the amino acid hydrophilicity/hydrophobicity are confirmed by the experimental crystallization investigations from nano regulation on dynamic steps, to microscopic modification of gypsum morphology, and to macroscopic precipitation. Furthermore, as the hydrophilicity of amino acids increases, the disparity in chiral selection rises; conversely, the increase in the hydrophobicity of amino acids results in a decline in chiral selection. These insights improve our understanding of the interaction mechanism between amino acids and crystals and provide insights into the formation process of chiral biominerals and the origin of homochirality in nature.

Chaperone-Like Activity of HSPB5: The Effects of Quaternary Structure Dynamics and Crowding

Small heat-shock proteins (sHSPs) are ATP-independent molecular chaperones that interact with partially unfolded proteins, preventing their aberrant aggregation, thereby exhibiting a chaperone-like activity. Dynamics of the quaternary structure plays an important role in the chaperone-like activity of sHSPs. However, relationship between the dynamic structure of sHSPs and their chaperone-like activity remains insufficiently characterized. Many factors (temperature, ions, a target protein, crowding etc.) affect the structure and activity of sHSPs. The least studied is an effect of crowding on sHSPs activity. In this work the chaperone-like activity of HSPB5 was quantitatively characterized by dynamic light scattering using two test systems, namely test systems based on heat-induced aggregation of muscle glycogen phosphorylase b (Phb) at 48 °C and dithiothreitol-induced aggregation of α-lactalbumin at 37 °C. Analytical ultracentrifugation was used to control the oligomeric state of HSPB5 and target proteins. The possible anti-aggregation functioning of suboligomeric forms of HSPB5 is discussed. The effect of crowding on HSPB5 anti-aggregation activity was characterized using Phb as a target protein. The duration of the nucleation stage was shown to decrease with simultaneous increase in the relative rate of aggregation of Phb in the presence of HSPB5 under crowded conditions. Crowding may subtly modulate sHSPs activity.

Visual Detection of Denatured Glutathione Peptides: A Facile Method to Visibly Detect Heat Stressed Biomolecules

Every year pharmaceutical companies use significant resources to mitigate aggregation of pharmaceutical drug products. Specifically, peptides and proteins that have been denatured or degraded can lead to adverse patient reactions such as undesired immune responses. Current methods to detect aggregation of biological molecules are limited to costly and time consuming processes such as high pressure liquid chromatography, ultrahigh pressure liquid chromatography and SDS-PAGE gels. Aggregation of pharmaceutical drug products can occur during manufacturing, processing, packaging, shipment and storage. Therefore, a facile in solution detection method was evaluated to visually detect denatured glutathione peptides, utilizing gold nanoparticle aggregation via 3-Aminopropyltreithoxysilane. Glutathione was denatured using a 70 °C water bath to create an accelerated heat stressed environment. The peptide, gold nanoparticle and aminosilane solution was then characterized via, UV-Vis spectroscopy, FTIR spectroscopy, dynamic light scattering and scanning electron microscopy. Captured images and resulting absorbance spectra of the gold nanoparticle, glutathione, and aminosilane complex demonstrated visual color changes detectable with the human eye as a function of the denaturation time. This work serves as an extended proof of concept for fast in solution detection methods for glutathione peptides that have experienced heat stress.

Impact of additives on the formation of protein aggregates and viscosity in concentrated protein solutions

In concentrated protein solutions attractive protein interactions may not only cause the formation of undesired aggregates but also of gel-like networks with elevated viscosity. To guarantee stable biopharmaceutical processes and safe formulations, both phenomenons have to be avoided as these may hinder regular processing steps. This work screens the impact of additives on both phase behavior and viscosity of concentrated protein solutions. For this purpose, additives known for stabilizing proteins in solution or modulating the dynamic viscosity were selected. These additives were PEG 300, PEG 1000, glycerol, glycine, NaCl and ArgHCl. Concentrated lysozyme and glucose oxidase solutions at pH 3 and 9 served as model systems. Fourier-transformed-infrared spectroscopy was chosen to determine the conformational stability of selected protein samples. Influencing protein interactions, the impact of additives was strongly dependent on pH. Of all additives investigated, glycine was the only one that maintained protein conformational and colloidal stability while decreasing the dynamic viscosity. Low concentrations of NaCl showed the same effect, but increasing concentrations resulted in visible protein aggregation.

Thermal stability of high concentration lysozyme across varying pH: A Fourier Transform Infrared study

AIM:

The current work is aimed at understanding the effect of pH on the thermal stability of hen egg white lysozyme (HEWL) at high concentration (200 mg/mL).

MATERIALS AND METHODS:

Fourier Transform Infrared (FTIR) Spectroscopy with modified hardware and software to overcome some of the traditional challenges like water subtraction, sample evaporation, proper purging etc., are used in this study.

RESULTS:

HEWL was subjected to thermal stress at pH 3.0-7.0 between 25°C and 95°C and monitored by FTIR spectroscopy. Calculated T_m values showed that the enzyme exhibited maximum thermal stability at pH 5.0. Second derivative plots constructed in the amide I region suggested that at pH 5.0 the enzyme possessed higher amount of α-helix and lower amount of aggregates, when compared to other pHs.

CONCLUSIONS:

Considering the fact that HEWL has attractive applications in various industries and being processed under different experimental conditions including high temperatures, our work is able to reveal the reason behind the pH dependent thermal stability of HEWL at high concentration, when subjected to heat denaturation. In future, studies should aim at using various excipients that may help to increase the stability and activity of the enzyme at this high concentration.

Serous cutaneous glands in anurans: Fourier transform analysis of the repeating secretory granule substructure

A combined transmission electron microscopy (TEM) and Fourier transform analysis has been performed on the secretory granules storing active peptides/proteins in serous cutaneous glands of n = 12 anuran species. Previous TEM investigation showed that the granules are provided with remarkable repeating substructures based on discrete subunits, arranged into a consistent framework. Furthermore, TEM findings revealed that this recurrent arrangement is acquired during a prolonged post-Golgian (or maturational) processing that affects the secretory product. Maturation leads to a variety of patterns depending on the degree of subunit clustering. This variety of recurrent patterns has been plotted into a range of frequency spectra. Through this quantitative approach, we found that the varying granule substructure can be reduced to a single mechanism of peptide/protein aggregation.

A protein aggregation based test for screening of the agents affecting thermostability of proteins

To search for agents affecting thermal stability of proteins, a test based on the registration of protein aggregation in the regime of heating with a constant rate was used. The initial parts of the dependences of the light scattering intensity (I) on temperature (T) were analyzed using the following empiric equation: I = K_agg(T−T₀)², where K_agg is the parameter characterizing the initial rate of aggregation and T₀ is a temperature at which the initial increase in the light scattering intensity is registered. The aggregation data are interpreted in the frame of the model assuming the formation of the start aggregates at the initial stages of the aggregation process. Parameter T₀ corresponds to the moment of the origination of the start aggregates. The applicability of the proposed approach was demonstrated on the examples of thermal aggregation of glycogen phosphorylase b from rabbit skeletal muscles and bovine liver glutamate dehydrogenase studied in the presence of agents of different chemical nature. The elaborated approach to the study of protein aggregation may be used for rapid identification of small molecules that interact with protein targets.

Neurocognitive derivation of protein surface property from protein aggregate parameters

Current work targeted to predicate parametric relationship between aggregate and individual property of a protein. In this approach, we considered individual property of a protein as its Surface Roughness Index (SRI) which was shown to have potential to classify SCOP protein families. The bulk property was however considered as Intensity Level based Multi-fractal Dimension (ILMFD) of ordinary microscopic images of heat denatured protein aggregates which was known to have potential to serve as protein marker. The protocol used multiple ILMFD inputs obtained for a protein to produce a set of mapped outputs as possible SRI candidates. The outputs were further clustered and largest cluster centre after normalization was found to be a close approximation of expected SRI that was calculated from known PDB structure. The outcome showed that faster derivation of individual protein's surface property might be possible using its bulk form, heat denatured aggregates.

Mechanism of suppression of dithiothreitol-induced aggregation of bovine alpha-lactalbumin by alpha-crystallin

The kinetics of dithiothreitol (DTT)-induced aggregation of alpha-lactalbumin from bovine milk has been studied using dynamic light-scattering technique. Analysis of the distribution of the particles formed in the solution of alpha-lactalbumin after the addition of DTT by size showed that the initial stage of the aggregation process was the stage of formation of the start aggregates with the hydrodynamic radius (R(h)) of 80-100nm. Further growth of the protein aggregates proceeds as a result of sticking of the start aggregates. Suppression of alpha-lactalbumin aggregation by alpha-crystallin is mainly due to the increase in the duration of the lag period on the kinetic curves of aggregation. It is assumed that the initially formed complexes of unfolded alpha-lactalbumin with alpha-crystallin were transformed to the primary clusters prone to aggregation as a result of the redistribution of the denatured protein molecules on the surface of the alpha-crystallin particles.

Simulations of nucleation and elongation of amyloid fibrils

We present a coarse-grained model for the growth kinetics of amyloid fibrils from solutions of peptides and address the fundamental mechanism of nucleation and elongation by using a lattice Monte Carlo procedure. We reproduce the three main characteristics of nucleation of amyloid fibrils: (1) existence of lag time, (2) occurrence of a critical concentration, and (3) seeding. We find the nucleation of amyloid fibrils to require a quasi-two-dimensional configuration, where a second layer of beta sheet must be formed adjunct to a first layer, which in turn leads to a highly cooperative nucleation barrier. The elongation stage is found to involve the Ostwald ripening (evaporation-condensation) mechanism, whereby bigger fibrils grow at the expense of smaller ones. This new mechanism reconciles the debate as to whether protofibrils are precursors or monomer reservoirs. We have systematically investigated the roles of time, peptide concentration, temperature, and seed size. In general, we find that there are two kinds of lag time arising from two different mechanisms. For higher temperatures or low enough concentrations close to the disassembly boundary, the fibrillization follows the nucleation mechanism. However, for low temperatures, where the nucleation time is sufficiently short, there still exists an apparent lag time due to slow Ostwald ripening mechanism. Consequently, the lag time is nonmonotonic with temperature, with the shortest lag time occurring at intermediate temperatures, which in turn depend on the peptide concentration. While the nucleation dominated regime can be controlled by seeding, the Ostwald ripening regime is insensitive to seeding. Simulation results from our coarse-grained model on the fibril size, lag time, elongation rate, and solubility are consistent with available experimental observations on many specific amyloid systems.

Dynamic alpha-helices: conformations that do not conform

Structural transitions are important for the stability and function of proteins, but these phenomena are poorly understood. An extensive analysis of Protein Data Bank entries reveals 103 regions in proteins with a tendency to transform from helical to nonhelical conformation and vice versa. We find that these dynamic helices, unlike other helices, are depleted in hydrophobic residues. Furthermore, the dynamic helices have higher surface accessibility and conformational mobility (P-value = 3.35e-07) than the rigid helices. Contact analyses show that these transitions result from protein-ligand, protein-nucleic acid, and crystal-contacts. The immediate structural environment differs quantitatively (P-value = 0.003) as well as qualitatively in the two alternate conformations. Often, dynamic helix experiences more contacts in its helical conformation than in the nonhelical counterpart (P-value = 0.001). There is differential preference for the type of short contacts observed in two conformational states. We also demonstrate that the regions in protein that can undergo such large conformational transitions can be predicted with a reasonable accuracy using logistic regression model of supervised learning. Our findings have implications in understanding the molecular basis of structural transitions that are coupled with binding and are important for the function and stability of the protein. Based on our observations, we propose that several functionally relevant regions on the protein surface can switch over their conformation from coil to helix and vice-versa, to regulate the recognition and binding of their partner and hence these may work as "molecular switches" in the proteins to regulate certain biological process. Our results supports the idea that protein structure-function paradigm should transform from static to a highly dynamic one.

Self-assembly of β-sheet forming peptides into chiral fibrillar aggregates

The authors introduce a novel mid-resolution off-lattice coarse-grained model to investigate the self-assembly of beta-sheet forming peptides. The model retains most of the peptide backbone degrees of freedom as well as one interaction center describing the side chains. The peptide consists of a core of alternating hydrophobic and hydrophilic residues, capped by two oppositely charged residues. Nonbonded interactions are described by Lennard-Jones and Coulombic terms. The influence of different levels of "hydrophobic" and "steric" forces between the side chains of the peptides on the thermodynamics and kinetics of aggregation was investigated using Langevin dynamics. The model is simple enough to allow the simulation of systems consisting of hundreds of peptides, while remaining realistic enough to successfully lead to the formation of chiral, ordered beta tapes, ribbons, as well as higher order fibrillar aggregates.

Computational models of molecular self-organization in cellular environments

The cellular environment creates numerous obstacles to efficient chemistry, as molecular components must navigate through a complex, densely crowded, heterogeneous, and constantly changing landscape in order to function at the appropriate times and places. Such obstacles are especially challenging to self-organizing or self-assembling molecular systems, which often need to build large structures in confined environments and typically have high-order kinetics that should make them exquisitely sensitive to concentration gradients, stochastic noise, and other non-ideal reaction conditions. Yet cells nonetheless manage to maintain a finely tuned network of countless molecular assemblies constantly forming and dissolving with a robustness and efficiency generally beyond what human engineers currently can achieve under even carefully controlled conditions. Significant advances in high-throughput biochemistry and genetics have made it possible to identify many of the components and interactions of this network, but its scale and complexity will likely make it impossible to understand at a global, systems level without predictive computational models. It is thus necessary to develop a clear understanding of how the reality of cellular biochemistry differs from the ideal models classically assumed by simulation approaches and how simulation methods can be adapted to accurately reflect biochemistry in the cell, particularly for the self-organizing systems that are most sensitive to these factors. In this review, we present approaches that have been undertaken from the modeling perspective to address various ways in which self-organization in the cell differs from idealized models.

Mapping electrostatic potential of a protein on its hydrophobic surface: Implications for crystallization of Cytochrome P450scc

Calculation and combined visualization of electrostatic and hydrophobic properties of Cytochrome P450scc based on two very different homology models allowed to identify extensive hydrophobic patches with neutral electrostatic potential and mutations removing such patches and thus expecting to facilitate crystallization of Cytochrome P450scc, especially for the nanotemplate crystallization method. Implications are discussed for optimizing crystallization and other aspects of protein surface properties and protein recognition.

Change in kinetic regime of protein aggregation with temperature increase. Thermal aggregation of rabbit muscle creatine kinase

Creatine kinase thermal aggregation kinetics has been studied in 30 mM Hepes-NaOH buffer, pH 8.0, at two temperatures: 50.6 and 60 degrees C. Aggregation kinetics was analyzed by measuring the growth of apparent absorption (A) at 400 nm. It was found that the limiting value of apparent absorption (A(lim)) is proportional to protein concentration at both temperatures. The first order rate constant (k(I)) does not depend on protein concentration in the range 0.05-0.2 mg/ml at temperature 50.6 degrees C, but at temperature 60 degrees C it increases with the growth of protein concentration in the range 0.1-0.4 mg/ml. Kinetic curves, shown in coordinates {A/A(lim); t}, in experiments at 50.6 degrees C fuse to a common curve, which coincides with the theoretical curve of creatine kinase denaturation calculated using the denaturation rate constant determined from differential scanning calorimetry. At temperature 60 degrees C, half-transformation time t(1/2) = ln2/k(I) decreases when protein concentration grows. We conclude that when temperature increased from 50.6 to 60 degrees C, change in the kinetic regime of thermal creatine kinase aggregation took place: at 50.6 degrees C aggregation rate is limited by the stage of protein molecule denaturation, but at 60 degrees C it is limited by the stage of protein aggregate growth, which proceeds as a reaction of pseudo-first order. Small heat shock protein Hsp 16.3 Mycobacterium tuberculosis suppresses the creatine kinase aggregation.

Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations

Fibrillary protein aggregates rich in beta-sheet structure have been implicated in the pathology of several neurodegenerative diseases. In this work, we investigate the formation of fibrils by performing discontinuous molecular dynamics simulations on systems containing 12 to 96 model Ac-KA(14)K-NH(2) peptides using our newly developed off-lattice, implicit-solvent, intermediate-resolution model, PRIME. We find that, at a low concentration, random-coil peptides assemble into alpha-helices at low temperatures. At intermediate concentrations, random-coil peptides assemble into alpha-helices at low temperatures and large beta-sheet structures at high temperatures. At high concentrations, the system forms beta-sheets over a wide range of temperatures. These assemble into fibrils above a critical temperature which decreases with concentration and exceeds the isolated peptide's folding temperature. At very high temperatures and all concentrations, the system is in a random-coil state. All of these results are in good qualitative agreement with those by Blondelle and co-workers on Ac-KA(14)K-NH(2) peptides. The fibrils observed in our simulations mimic the structural characteristics observed in experiments in terms of the number of sheets formed, the values of the intra- and intersheet separations, and the parallel peptide arrangement within each beta-sheet. Finally, we find that when the strength of the hydrophobic interaction between nonpolar side chains is high compared to the strength of hydrogen bonding, amorphous aggregates, rather than fibrillar aggregates, are formed.

Anion Binding and Controlled Aggregation of Human Interleukin-1 Receptor Antagonist

Highly concentrated human recombinant interleukin-1 receptor antagonist (IL-1ra) aggregates at elevated temperature without perturbation in its secondary structure. The protein aggregation can be suppressed depending on the buffer ionic strength and the type of anion present in the sample solution. Phosphate is an approximately 4-fold weaker suppressant than either citrate or pyrophosphate on the basis of the measured protein aggregation rates. This is in agreement with the strength of protein-anion interactions at the IL-1ra single anion-binding site as judged by the estimated dissociation constant values of 2.9 mM, 3.8 mM, and 13.7 mM for pyrophosphate, citrate, and phosphate, respectively. The strength of binding also correlates with the anion size and with the number of ionized groups available per molecule at a given pH. Affinity probing of IL-1ra with methyl acetyl phosphate (MAP) in combination with proteolytic digestion and mass spectral analysis show that an anion-binding site location on the IL-1ra surface is contributed by lysine-93 and lysine-96 of the loop 84-98 as well as by lysine-6 of the unstructured N-terminal region 1-7. The replacement of lysine-93 with alanine by site-directed mutagenesis results in dramatically suppressed IL-1ra aggregation. Furthermore, when the unstructured N-terminal region of IL-1ra is removed by limited proteolysis, a 2-fold increase in the time course of the aggregation lag phase is observed for the truncated protein. An anion-controlled mechanism of IL-1ra aggregation is proposed by which the anion competition for the protein cationic site prevents formation of intermolecular cation-pi interactions and, thus, interferes with the protein asymmetric self-association pathway.

Induction and analysis of aggregates in a liquid IgG1-antibody formulation

The objective of this study was to compare different agitation stress methods (stirring in Reacti Vials versus horizontal shaking) in their effect on protein destabilization, to assess several analytical techniques (light obscuration, turbidimetric and light scattering analysis) for detection of aggregates of various sizes and to evaluate the protecting effect of polysorbate 80 on protein aggregation. A monoclonal IgG1 antibody was used as model protein. Both mechanical stress methods can provoke aggregate formation. The method of stirring induces particles in the range of 10-25 microm comparable to shaking stress. However, stirred samples show a much higher absorbance and reveal a second particle species in DLS analysis, suggesting that stirring stress induces a higher amount of smaller protein aggregates. Addition of polysorbate 80 protects the antibody against aggregation. Only in stirred samples a slight increase in sub-visible particles and turbidity was noted. However, a greater extent of aggregation products was detected by DLS as compared to surfactant-free formulations. Thus, polysorbate 80 appears to stabilise small aggregates and prevents further proceeding of the aggregation process. The induction of aggregates by stirring stress in Reacti Vials analysed by absorbance measurement seems to be a good combination for high-throughput formulation studies.

Kinetics of heat- and acidification-induced aggregation of firefly luciferase

The general approach to analysis of the kinetics of protein aggregation registered by the turbidimetric method has been elaborated. The terminal part of the kinetic curves is analyzed using a theoretical equation connecting the derivative of the apparent absorbance (A) with respect to time (dA/dt) and A (t is time). This analysis allows the limiting value of A at t--> infinity (A(lim)) and the order of aggregation with respect to protein (n) to be calculated. Approach proposed was applied to analysis of thermal and acidification-induced aggregation of firefly luciferase. In both cases the A(lim) value is a linear function of the protein concentration. The terminal part of the kinetic curves of thermal aggregation follows the first-order kinetics (n=1), whereas the kinetics of acidification-induced aggregation are characterized by the value of n higher than unity (n=1.29). The mechanism of nucleation-dependent aggregation has been discussed.

Effect of rate of chemical or thermal renaturation on refolding and aggregation of a simple lattice protein

We used dynamic Monte Carlo simulation to investigate how changing the rate of chemical or thermal renaturation affects the folding and aggregation behavior of a system of simple, two-dimensional lattice protein molecules. Four renaturation methods were simulated: infinitely slow cooling; slow but finite cooling; quenching; and pulse renaturation. The infinitely slow cooling method, which is equivalent to dialysis or diafiltration, provides refolding yields that are relatively high and aggregates that are relatively small (mostly dimers or trimers). The slow but finite cooling method, which is equivalent to multiple-step dilution, provides refolding yields that are almost as high as those observed in the infinitely slow cooling case, but in a relatively short period of time. Quenching, which is equivalent to one-step dilution or quick quenching, is extremely slow and has low re- folding yields. A maximum appears in the refolding yield as a function of denaturant concentration in the simulation but disappears after a very long duration. Finally, the pulse renaturation method provides refolding yields that are substantially higher than those observed in the other three methods, even at high packing fractions. As in the early stages of quenching, there is a maximum in the refolding yield as a function of denaturant concentration when relatively large numbers of denatured chains are added to the refolding solution at each step.

Use of a hydrophobic dye to indirectly probe the structural organization and conformational plasticity of molecules in amorphous aggregates of carbonic anhydrase

Understanding protein aggregation may hold important clues to understanding what goes wrong with protein folding in neurodegenerative disorders and in bioreactors in which proteins are overexpressed. Unfortunately, aggregates tend to be intractable to most standard methods of biochemical investigation. Thus, relatively little is even now known about the micro- and macro-structural features of aggregates. To gain insights into the thermal aggregation of a model globular protein [bovine carbonic anhydrase (BCA)], we have used spectrofluorimetry to examine the binding of a hydrophobic dye, 8-anilinonaphthalene sulfonate (ANS), to hydrophobic clusters on the protein's surface both before and after heat-induced aggregation and upon cooling. Whereas native BCA shows no surface hydrophobicity, thermally aggregated BCA displays significant hydrophobicity both in the heated state and upon cooling. The timing of the addition of ANS in the course of aggregation makes no net difference to the ANS bound; we argue that this suggests that aggregates are essentially porous. Cooling of aggregates results in a dramatic, fully reversible increase in ANS binding that cannot be explained by the temperature dependence of fluorescence quantum yield alone; we argue that the enhancement of fluorescence upon cooling indicates possible structural consolidation of unfolded regions within aggregates (akin to refolding), with the required structural reorganization being facilitated by porosity. Finally, implications of porosity in aggregates are discussed, in particular, for the possible immobilization of enzymes through fusion with aggregation-prone protein domains.

Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model

Computer simulations are performed on a system of eight model peptide chains to study how the competition between protein refolding and aggregation affects the optimal conditions for refolding of four-helix bundles. The discontinuous molecular dynamics algorithm is utilized along with an intermediate-resolution protein model that we developed for this work. Physically, the model is much more detailed than any model used to date for simulations of protein aggregation. Each model residue consists of a detailed, three-bead backbone and a simplified, single-bead side-chain. Excluded volume, hydrogen bond, and hydrophobic interactions are modeled with discontinuous (i.e. hard-sphere and square-well) potentials. Simulations efficiently sample conformational space, and complete folding trajectories from random initial configurations to two four-helix bundles are possible within two days on a single processor workstation. Folding of the bundles follows two main pathways, one through a trimeric intermediate and the other through an intermediate with two dimers. The proportion of trajectories that follow each route is significantly different for the eight-peptide system in this work than in a previously studied four-peptide system, which yields one four-helix bundle, suggesting, as our previous simulations have, that protein folding properties are strongly influenced by the presence of other proteins. Folding of the bundles is optimal within a fixed temperature range, with the high-temperature boundary a function of the complexity of the protein (or oligomer) to be folded and the low-temperature boundary a function of the complexity of the protein's environment. Above the optimal temperature range for folding, the model chains tend to unfold; below the optimal range, the model chains tend to aggregate. As has been seen previously, aggregates have substantial levels of native secondary structure, suggesting that aggregates are composed largely of partially folded intermediates, not denatured chains.

Models of protein crystal growth

The growth of large and well ordered protein crystals remains the major obstacle in protein structure determination by means of X-ray crystallography. One of the reasons is that the physico-chemical aspect of protein crystallization process is not understood. This article reviews efforts towards formulation of models that could become theoretical frameworks for the interpretation of voluminous experimental data collected on protein crystal growth. Special attention is devoted to microscopic models that recognize the role of the shape of protein molecules in crystal formation.

Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues

Patterns of hydrophobic and hydrophilic residues play a major role in protein folding and function. Long, predominantly hydrophobic strings of 20-22 amino acids each are associated with transmembrane helices and have been used to identify such sequences. Much less attention has been paid to hydrophobic sequences within globular proteins. In prior work on computer simulations of the competition between on-pathway folding and off-pathway aggregate formation, we found that long sequences of consecutive hydrophobic residues promoted aggregation within the model, even controlling for overall hydrophobic content. We report here on an analysis of the frequencies of different lengths of contiguous blocks of hydrophobic residues in a database of amino acid sequences of proteins of known structure. Sequences of three or more consecutive hydrophobic residues are found to be significantly less common in actual globular proteins than would be predicted if residues were selected independently. The result may reflect selection against long blocks of hydrophobic residues within globular proteins relative to what would be expected if residue hydrophobicities were independent of those of nearby residues in the sequence.

Microscopic model of protein crystal growth

A microscopic, reversible model to study protein crystal nucleation and growth is presented. The probability of monomer attachment to the growing crystal was assumed to be proportional to the protein volume fraction and the orientational factor representing the anisotropy of protein molecules. The rate of detachment depended on the free energy of association of the given monomer in the lattice, as calculated from the buried surface area. The proposed algorithm allowed the simulation of the process of crystal growth from free monomers to complexes having 10(5) molecules, i.e. microcrystals with already formed faces. These simulations correctly reproduced the crystal morphology of the chosen model system--the tetragonal lysozyme crystal. We predicted the critical size, after which the growth rate rapidly increased to approximately 50 protein monomers. The major factors determining the protein crystallisation kinetics were the geometry of the protein molecules and the resulting number of kinetics traps on the growth pathway.

Single-step purification of a recombinant thermostable alpha-amylase after solubilization of the enzyme from insoluble aggregates

The expression of the gene encoding a thermostable alpha-amylase (EC 3.2.1.1) (optimal activity at 100 degrees C) from the hyperthermophilic archaeon Pyrococcus woesei in the mesophilic hosts Escherichia coli and Halomonas elongata resulted in the formation of insoluble aggregates. More than 85% of the recombinant enzyme was present within the cells as insoluble but catalytically active aggregates. The recombinant alpha-amylase was purified to homogeneity in a single step by hydrophobic interaction chromatography on a phenyl superose column after solubilization of the enzyme under nondenaturing conditions. The enzyme was purified 258-fold with a final yield of 54%.

Instability, stabilization, and formulation of liquid protein pharmaceuticals

One of the most challenging tasks in the development of protein pharmaceuticals is to deal with physical and chemical instabilities of proteins. Protein instability is one of the major reasons why protein pharmaceuticals are administered traditionally through injection rather than taken orally like most small chemical drugs. Protein pharmaceuticals usually have to be stored under cold conditions or freeze-dried to achieve an acceptable shelf life. To understand and maximize the stability of protein pharmaceuticals or any other usable proteins such as catalytic enzymes, many studies have been conducted, especially in the past two decades. These studies have covered many areas such as protein folding and unfolding/denaturation, mechanisms of chemical and physical instabilities of proteins, and various means of stabilizing proteins in aqueous or solid state and under various processing conditions such as freeze-thawing and drying. This article reviews these investigations and achievements in recent years and discusses the basic behavior of proteins, their instabilities, and stabilization in aqueous state in relation to the development of liquid protein pharmaceuticals.

Lattice simulations of aggregation funnels for protein folding

A computer model of protein aggregation competing with productive folding is proposed. Our model adapts techniques from lattice Monte Carlo studies of protein folding to the problem of aggregation. However, rather than starting with a single string of residues, we allow independently folding strings to undergo collisions and consider their interactions in different orientations. We first present some background into the nature and significance of protein aggregation and the use of lattice Monte Carlo simulations in understanding other aspects of protein folding. The results of a series of simulation experiments involving simple versions of the model illustrate the importance of considering aggregation in simulations of protein folding and provide some preliminary understanding of the characteristics of the model. Finally, we discuss the value of the model in general and of our particular design decisions and experiments. We conclude that computer simulation techniques developed to study protein folding can provide insights into protein aggregation, and that a better understanding of aggregation may in turn provide new insights into and constraints on the more general protein folding problem.

Lattice simulations of protein crystal formation

A new algorithm is presented for the lattice simulation of protein crystal growth. The algorithm allows the calculation of the size distribution of microcrystals in the volume and timescale of experiments and within the framework of the previously-published microscopic model [A.M. Kierzek, W.M. Wolf, P. Zielenkiewicz, Biophys. J. 73 (1997) 571-580]. Simulations for the tetragonal lysozyme crystal show that there are two critical sizes in the development of ordered phase. The first one corresponds to the size of the smallest stable complex which, in the case of the tetragonal lysozyme crystal, is the particular tetramer. In a volume of 5 mul the tetramer appears in the millisecond timescale. The second critical radius of approximately 100 monomers is only reached by a few of all the smallest stable complexes formed in the solution. The model predicts that out of 10(7) tetramers which appear in solution, only eight reach the size of 100 monomers within 8 h. After exceeding the second critical radius the microcrystals grow to the size of 10(4) monomers in the minute timescale and are thus assumed to quickly lead to macroscopic crystals. The predicted number of crystals formed during 8 h of nucleation is in qualitative agreement with arrested nucleation experiments.

Theoretical analysis of protein organization in lipid membranes

The fundamental physical principles of the lateral organization of trans-membrane proteins and peptides as well as peripheral membrane proteins and enzymes are considered from the point of view of the lipid-bilayer membrane, its structure, dynamics, and cooperative phenomena. Based on a variety of theoretical considerations and model calculations, the nature of lipid-protein interactions is considered both for a single protein and an assembly of proteins that can lead to aggregation and protein crystallization in the plane of the membrane. Phenomena discussed include lipid sorting and selectivity at protein surfaces, protein-lipid phase equilibria, lipid-mediated protein-protein interactions, wetting and capillary condensation as means of protein organization, mechanisms of two-dimensional protein crystallization, as well as non-equilibrium organization of active proteins in membranes. The theoretical findings are compared with a variety of experimental data.

Small-scale lipid-membrane structure: simulation versus experiment

Recently, it has become obvious that the conventional picture of the fluid lipid-bilayer component of biological membranes being a fairly structureless 'fluid mosaic' solvent is far from correct. The lipid bilayer displays distinct static and dynamic structural organization on a small scale, for example in terms of differentiated lipid domains, and evidence is accumulating that these structures are of importance for the functioning of biological membranes, including the activity of membrane-bound enzymes and receptors and morphological changes at the cell surface. Insight into the relationship between this small-scale structure and biological functioning holds promise for a more rational approach to modulate function via manipulation of the lipid microenvironment and the lipid/protein interface in particular. Computer simulation has proved to be a useful tool in investigating membrane structure on a small scale-specifically the nanometer scale (1-100 nm), which is in between the molecular scale accessible by various spectroscopic techniques and molecular dynamics calculations, and the micrometer scale accessible by scattering and microscopy techniques.

Simulations of nucleation and early growth stages of protein crystals

Analysis of known protein crystal structures reveals that interaction energies between monomer pairs alone are not sufficient to overcome entropy loss related to fixing monomers in the crystal lattice. Interactions with several neighbors in the crystal are required for stabilization of monomers in the lattice. A microscopic model of nucleation and early growth stages of protein crystals, based on the above observations, is presented. Anisotropy of protein molecules is taken into account by assigning free energies of association (proportional to the buried surface area) to individual monomer-monomer contacts in the lattice. Lattice simulations of the tetragonal lysozyme crystal based on the model correctly reproduce structural features of the movement of dislocation on the (110) crystal face. The dislocation shifts with the speed equal to the one determined experimentally if the geometric probability of correct orientation is set to 10(-5), in agreement with previously published estimates. At this value of orientational probability, the first nuclei, the critical size of which for lysozyme is four monomers, appear in 1 ml of supersaturated solution on a time scale of microseconds. Formation of the ordered phase proceeds through the growth of nuclei (rather then their association) and requires nucleations on the surface at certain stages.

Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers

A survey was compiled of several characteristics of the intersubunit contacts in 58 oligomeric proteins, and of the intermolecular contracts in the lattice for 223 protein crystal structures. The total number of atoms in contact and the secondary structure elements involved are similar in the two types of interfaces. Crystal contact patches are frequently smaller than patches involved in oligomer interfaces. Crystal contacts result from more numerous interactions by polar residues, compared with a tendency toward nonpolar amino acids at oligomer interfaces. Arginine is the only amino acid prominent in both types of interfaces. Potentials of mean force for residue-residue contacts at both crystal and oligomer interfaces were derived from comparison of the number of observed residue-residue interactions with the number expected by mass action. They show that hydrophobic interactions at oligomer interfaces favor aromatic amino acids and methionine over aliphatic amino acids; and that crystal contacts form in such a way as to avoid inclusion of hydrophobic interactions. They also suggest that complex salt bridges with certain amino acid compositions might be important in oligomer formation. For a protein that is recalcitrant to crystallization, substitution of lysine residues with arginine or glutamine is a recommended strategy.