Small Globular Proteins Research Articles

Thermal Energy Transport through Nonbonded Native Contacts in Protein.

Within the protein interior, where we observe various types of interactions, nonuniform flow of thermal energy occurs along the polypeptide chain and through nonbonded native contacts, leading to inhomogeneous transport efficiencies from one site to another. The folded native protein serves not merely as thermal transfer medium but, more importantly, as sophisticated molecular nanomachines in cells. Therefore, we are particularly interested in what sort of "communication" is mediated through native contacts in the folded proteins and how such features are quantitatively depicted in terms of local transport coefficients of heat currents. To address the issue, we introduced a concept of inter-residue thermal conductivity and characterized the nonuniform thermal transport properties of a small globular protein, HP36, using equilibrium molecular dynamics simulation and the Green-Kubo formula. We observed that the thermal transport of the protein was dominated by that along the polypeptide chain, while the local thermal conductivity of nonbonded native contacts decreased in the order of H-bonding > π-stacking > electrostatic > hydrophobic contacts. Furthermore, we applied machine learning techniques to analyze the molecular mechanism of protein thermal transport. As a result, the contact distance, variance in contact distance, and H-bonding occurrence probability during MD simulations are found to be the top three important determinants for predicting local thermal transport coefficients.

Staphylococcal Enterotoxins: Description and Importance in Food.

Staphylococcus aureus stands out as one of the most virulent pathogens in the genus Staphylococcus. This characteristic is due to its ability to produce a wide variety of staphylococcal enterotoxins (SEs) and exotoxins, which in turn can cause staphylococcal food poisoning (SFP), clinical syndromes such as skin infections, inflammation, pneumonia, and sepsis, in addition to being associated with the development of inflammation in the mammary glands of dairy cattle, which results in chronic mastitis and cell necrosis. SEs are small globular proteins that combine superantigenic and emetic activities; they are resistant to heat, low temperatures, and proteolytic enzymes and are tolerant to a wide pH range. More than 24 SE genes have been well described (SEA-SEE, SEG, SEH, SEI, SEJ, SElK, SElL, SElM, SElN, SElO, SElP, SElQ, SElR, SElS, SElT, SElU, SElV, SElW, SElX, SElY, and SElZ), being a part of different SFP outbreaks, clinical cases, and isolated animal strains. In recent years, new genes (sel26, sel27, sel28, sel31, sel32, and sel33) from SEs have been described, as well as two variants (seh-2p and ses-3p) resulting in a total of thirty-three genes from Ses, including the nine variants that are still in the process of genetic and molecular structure evaluation. SEs are encoded by genes that are located in mobile genetic elements, such as plasmids, prophages, pathogenicity islands, and the enterotoxin gene cluster (egc), and housed in the genomic island of S. aureus. Both classical SEs and SE-like toxins (SEls) share phylogenetic relationships, structure, function, and sequence homology, which are characteristics for the production of new SEs through recombination processes. Due to the epidemiological importance of SEs, their rapid assessment and detection have been crucial for food security and public health; for this reason, different methods of identification of SEs have been developed, such as liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS), molecular methods, and whole-genome sequencing; providing the diagnosis of SEs and a better understanding of the occurrence, spread, and eradication of SEs. This review provides scientific information on the enterotoxins produced by S. aureus, such as structural characteristics, genetic organization, regulatory mechanisms, superantigen activity, mechanisms of action used by SEs at the time of interaction with the immune system, methods of detection of SEs, and recent biocontrol techniques used in food.

Quantitative entropy-enthalpy compensation in intraprotein interactions from model compound data.

Many small globular proteins exist in only two states-the physiologically relevant folded state and an inactive unfolded state. The active state is stabilized by numerous weak attractive contacts, including hydrogen bonds, other polar interactions, and the hydrophobic effect. Knowledge of these interactions is key to understanding the fundamental equilibrium thermodynamics of protein folding and stability. We focus on one such interaction, that between amide and aromatic groups. We provide a statistically convincing case for quantitative, linear entropy-enthalpy compensation in forming aromatic-amide interactions using published model compound transfer-free energy data.

Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model.

The Martini coarse-grain force-field has emerged as an important framework to probe cellular processes at experimentally relevant time- and length-scales. However, the recently developed version, the Martini3 force-field with the implemented Go̅ model (Martini3Go̅), as well as previous variants of the Martini model have not been benchmarked and rigorously tested for globular proteins. In this study, we consider three globular proteins, ubiquitin, lysozyme, and cofilin, and compare protein dynamics and hydration with observables from experiments and all-atom simulations. We show that the Martini3Go̅ model is able to accurately model the structural and dynamic features of small globular proteins. Overall, the structural integrity of the proteins is maintained, as validated by contact maps, radii of gyration (Rg), and SAXS profiles. The chemical shifts predicted from the ensemble sampled in the simulations are consistent with the experimental data. Further, a good match is observed in the protein-water interaction energetics, and the hydration levels of the residues are similar to atomistic simulations. However, the protein-water interaction dynamics is not accurately represented and appears to depend on the protein structural complexity, residue specificity, and water dynamics. Our work is a step toward testing and assessing the Martini3Go̅ model and provides insights into future efforts to refine Martini models with improved solvation effects and better correspondence to the underlying all-atom systems.

Protein-Functionalized Gold Nanospheres with Tunable Photothermal Efficiency for the Near-Infrared Photothermal Ablation of Biofilms.

Temperature-responsive nanostructures with high antimicrobial efficacy are attractive for therapeutic applications against multidrug-resistant bacteria. Here, we report temperature-responsive nanospheres (TRNs) engineered to undergo self-association and agglomeration above a tunable transition temperature (Tt). The temperature-responsive behavior of the nanoparticles is obtained by functionalizing citrate-capped spherical gold nanoparticles (AuNPs) with elastin-like polypeptides (ELPs). Using protein design principles, we achieve a broad range of attainable Tt values and photothermal conversion efficiencies (η). Two approaches were used to adjust this range: First, by altering the position of the cysteine residue used to attach ELP to the AuNP, we attained a Tt range from 34 to 42 °C. Then, by functionalizing the AuNP with an additional small globular protein, we could extend this range to 34-50 °C. Under near-infrared (NIR) light exposure, all TRNs exhibited reversible agglomeration. Moreover, they showed an enhanced photothermal conversion efficiency in their agglomerated state relative to the dispersed state. Despite their spherical shape, TRNs have a photothermal conversion efficiency approaching that of gold nanorods (η = 68 ± 6%), yet unlike nanorods, the synthesis of TRNs requires no cytotoxic compounds. Finally, we tested TRNs for the photothermal ablation of biofilms. Above Tt, NIR irradiation of TRNs resulted in a 10,000-fold improvement in killing efficiency compared to untreated controls (p < 0.0001). Below Tt, no enhanced antibiofilm effect was observed. In conclusion, engineering the interactions between proteins and nanoparticles enables the tunable control of TRNs, resulting in a novel antibiofilm nanomaterial with low cytotoxicity.

Modulation of the electrostatic potential around α-lactalbumin using oligoelectrolyte chains, pH and salt concentration.

In this study, we conducted a comprehensive computational investigation of the interaction between α-lactalbumin, a small globular protein, and strong anionic oligoelectrolyte chains with a polymerization degree from 2 to 9. Both the protein and oligoelectrolyte chains are represented using coarse-grained models, and their properties were calculated by the Monte Carlo method under constant pH conditions. We were able to estimate the effects of this interaction on the electrostatic potential around the protein. At acidic pH, the protein had a net positive charge; therefore, the electrostatic potential around it was also positive. To neutralize or reverse this electrostatic potential, oligoelectrolyte chains with a minimum size of six monomers were necessary. Simultaneously, low salt concentrations were required as elevated salt levels led to a significant attenuation of the electrostatic interactions and the corresponding electrostatic potential.

Fluorescent Labeling of Outer Membrane Proteins Using the SpyCatcher-SpyTag System.

The SpyCatcher-SpyTag system has become a popular and versatile tool for protein ligation. It is based on a small globular protein (SpyCatcher) that binds to a 13-residue peptide (SpyTag), which subsequently leads to the formation of a covalent isopeptide bond. Thus, the reaction is essentially irreversible. Here, we describe how the SpyCatcher-SpyTag system can be used to label surface-exposed bacterial outer membrane proteins, e.g., for topology mapping or fluorescent time-course experiments. We cover using fluorescence measurements and microscopy to measure labeling efficiency using SpyCatcherfused with superfolderGFPin this chapter.

Results from the Completed Dose Escalation Portion of the Phase 1 Study of HPN217, a Half-Life Extended Tri-Specific T Cell Activating Construct (TriTAC®) Targeting B Cell Maturation Antigen (BCMA) for Relapsed/Refractory Multiple Myeloma (MM)

Background HPN217 is a B Cell Maturation Antigen (BCMA)-targeting tri-specific T cell engager (TCE). HPN217 contains three binding domains including anti-BCMA for MM cell binding, anti-albumin for half-life extension, and anti-CD3 for T cell engagement and activation. HPN217 is a small (~50 kDa) globular protein, designed to increase the therapeutic window by minimizing off-target toxicities and cytokine release syndrome (CRS). HPN217 is under investigation in patients (pts) with heavily pretreated relapsed/refractory MM (RRMM). Methods This study is designed to assess the safety, pharmacology and early clinical activity of HPN217 using fixed and step-dose (prime dose followed by target doses) regimens in dose escalation cohorts along with expansion of selected regimens for further evaluation. Pts with RRMM who have received at least 3 prior therapies including a proteasome inhibitor, an immunomodulatory drug, and CD38-targeted therapy are eligible. Prior exposure to a BCMA-targeting agent is permitted. Primary objectives include evaluation of safety, tolerability, pharmacokinetics (PK), and determination of the Recommended Phase 2 Dose(s) (RP2D). Secondary objectives include preliminary efficacy. HPN217 is administered IV once weekly or once every 2 weeks. Adverse events (AEs) are graded by CTCAE 5.0, and ASTCT for cytokine release syndrome (CRS) and ICANS. Clinical activity is assessed per IMWG Response Criteria. Results Dose escalation has been completed. 97 pts were enrolled across 15 dose escalation cohorts and expansion of 3 regimens with the highest target dose levels from dose escalation (12mg weekly; 24mg every 2 weeks; 24mg weekly for 1 cycle followed by 24mg every 2 weeks). As of 26 June 2023, across all cohorts, 94 pts were treated and had received a median (range) of 6 (2-19) prior lines of treatment (62% penta-exposed, 17% BCMA-targeted therapy, 68% prior transplantation). Median age was 70 (38-85) years. 36 pts (38%) remain on treatment. The most common (≥25%) treatment-emergent adverse events (TEAEs) across all cohorts and in the 12mg and 24mg cohorts are summarized in Table 1. Dose limiting toxicities (DLTs) of reversible transaminitis (Gr 3, n=1; Gr 4, n=1) in 2 pts at 2.86 mg fixed dose during dose escalation informed the choice of 2.15 mg as priming dose in the highest step dose cohorts; a maximum tolerated dose (MTD) has not been reached in step dose cohorts. All CRS events were grade 1-2 except one event of grade 3 CRS at 24 mg. Grade 1 ICANS was reported in 2 pts. Responses were observed at doses ≥ 2.15 mg. Among the 12mg and 24mg cohorts, 55% (22/40) of efficacy-evaluable pts currently have had a confirmed response (PR or better) including 2 pts with prior BCMA directed CAR-T cell therapy; disease assessments for recently enrolled patients are pending. Among pts with a response, 73% (16/22) have had a confirmed response of VGPR or better. Across all dose levels, the median time on treatment for pts with a confirmed response was 40 weeks (range 8.3-114 weeks), including 9 patients on treatment for over 12 months, with data maturing to include longer follow-up on patients recently enrolled. HPN217 exhibited linear and dose proportional PK across all dose groups with a median half-life of 68 hours (range 26-197 hours). Transient cytokine increases were higher with the initial/priming dose compared to subsequent/target doses. Conclusions Dose escalation of HPN217, a novel half-life extended BCMA-targeting T-cell engager, has been completed; the MTD was not reached in step dose cohorts. The 12mg and 24mg target doses are well tolerated with manageable adverse event profiles similar to those at lower dose levels and are associated with robust and durable clinical responses. Additional follow up of recently enrolled pts in 12 mg and 24 mg cohorts will inform the choice of the RP2D(s), and complete data on all pts enrolled will be presented. NCT04184050

Replacement of the native cis prolines by alanine leads to simplification of the complex folding mechanism of a small globular protein

The folding mechanism of MNEI, a single-chain variant of naturally occurring double-chain monellin, is complex, with multiple parallel refolding channels. To determine whether its folding energy landscape could be simplified, the two native cis-prolines, Pro41 and Pro93, were mutated, singly and together, to Ala. The stability of P93A was the same as that of the wild-type protein, pWT; however, P41A and P41AP93A were destabilized by ∼0.9 kcal mol−1. The effects of the mutations on the very fast, fast, slow, and very slow phases of folding were studied. They showed that heterogeneity in the unfolded state arises due to cis to trans isomerization of the Gly92-Pro93 peptide bond. The Pro41 to Ala mutation abolished the very slow phase of folding, whereas surprisingly, the Pro93 to Ala mutation abolished the very fast phase of folding. Double-jump, interrupted folding experiments indicated that two sequential trans to cis proline isomerization steps, of the Gly92-Pro93 peptide bond followed by the Arg40-Pro41 peptide bond, lead to the formation of the native state. They also revealed the accumulation of a late native-like intermediate, N∗, which differs from the native state in the isomeric status of the Arg40-Pro41 bond, as well as in a few tertiary contacts as monitored by near-UV CD measurements. The Pro to Ala mutations not only eliminated the cis to trans Pro isomerization reaction in the unfolded state, but also the two trans to cis Pro isomerization reactions during folding. By doing so, and by differentially affecting the relative stabilities of folding intermediates, the mutations resulted in a simplification of the folding mechanism. The two Pro to Ala mutations together accelerate folding to such an extent that the native state forms more than 1000-fold faster than in the case of pWT.

Uncertainties in Markov State Models of Small Proteins.

Markov state models are widely used to describe and analyze protein dynamics based on molecular dynamics simulations, specifically to extract functionally relevant characteristic time scales and motions. Particularly for larger biomolecules such as proteins, however, insufficient sampling is a notorious concern and often the source of large uncertainties that are difficult to quantify. Furthermore, there are several other sources of uncertainty, such as choice of the number of Markov states and lag time, choice and parameters of dimension reduction preprocessing step, and uncertainty due to the limited number of observed transitions; the latter is often estimated via a Bayesian approach. Here, we quantified and ranked all of these uncertainties for four small globular test proteins. We found that the largest uncertainty is due to insufficient sampling and initially increases with the total trajectory length T up to a critical tipping point, after which it decreases as , thus providing guidelines for how much sampling is required for given accuracy. We also found that single long trajectories yielded better sampling accuracy than many shorter trajectories starting from the same structure. In comparison, the remaining sources of the above uncertainties are generally smaller by a factor of about 5, rendering them less of a concern but certainly not negligible. Importantly, the Bayes uncertainty, commonly used as the only uncertainty estimate, captures only a relatively small part of the true uncertainty, which is thus often drastically underestimated.

REVIEW ON PROTEIN FOOTPRINTING AS A TOOL IN STRUCTURAL BIOLOGY

Structural characterization of proteins is fundamental for understanding their functions and interactions within cellular environments. Protein footprinting has emerged as a powerful and versatile technique in structural biology, providing valuable insights into protein structure, dynamics, and conformational changes. This study comprehensively explores the principles, methodologies, and applications of protein footprinting as an indispensable tool in structural biology. Protein footprinting encompasses a range of innovative techniques, including hydroxyl radical footprinting, mass spectrometry-based footprinting, and chemical footprinting, each offering unique advantages for probing different aspects of protein structure. The study elucidates the underlying principles of these methods, discussing the mechanisms by which protein-footprinting agents interact with amino acid residues and elucidate structural details. The application of protein footprinting in studying protein-protein interactions, ligand binding, and conformational changes is highlighted through a detailed examination of key studies and experimental approaches. The review emphasizes the versatility of protein footprinting in investigating diverse protein systems, from small globular proteins to large multi-subunit complexes. Furthermore, the integration of protein footprinting with other structural biology techniques, such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy, is explored to showcase the complementary nature of these approaches in achieving a comprehensive understanding of protein structure and function. The study addresses recent advancements and technological innovations in protein footprinting methodologies, including advancements in mass spectrometry instrumentation and data analysis strategies. Additionally, it discusses challenges associated with the technique, such as data interpretation and accessibility, and proposes future directions for overcoming these hurdles. Protein footprinting stands as a valuable tool in the structural biologist’s arsenal, providing unique perspectives on protein structure and dynamics. As the field continues to evolve, with ongoing refinements in methodologies and expanded applications, protein footprinting is poised to play a pivotal role in unraveling the complexities of biological macromolecules. This study serves as a comprehensive resource for researchers and practitioners seeking an in-depth understanding of protein footprinting and its contributions to advancing structural biology.

Biophysical studies of amorphous protein aggregation and in vivo immunogenicity.

Amorphous protein aggregates are oligomers that lack specific, high-order structures.Soluble amorphous aggregates are smaller than ~1µm. Despite their lack of high-order structure, amorphous protein aggregates exhibit specific biophysical properties such as reversibilityof formation, density, conformation, and biochemical stability. Our mutational analysis using a Solubility Controlling Peptide (SCP) tag strongly suggests that amorphous aggregation of small globular proteins can significantly increase in vivo immune response and that the magnitude of enhanced immune responses depends on the aggregates' biophysical and biochemical properties. We propose that SCP tags might help develop subunit (protein) adjuvant-free (immunostimulant-free) vaccinesby controlling the aggregation propensity of target proteins.

Site-Directed Spin Labeling EPR Spectroscopy for Determination of Albumin Structural Damage and Hypoalbuminemia in Critical COVID-19.

The main factors in the COVID-19 pathology, which can initiate extensive structural changes at the cellular and molecular levels, are the generation of free radicals in abnormal amounts, and oxidative stress. Under "oxidative shock" conditions, the proteins undergo various modifications that affect their function and activity, and as a result distribute malfunctioning protein derivatives in the body. Human serum albumin is a small globular protein characterized by a high overall binding capacity for neutral lipophilic and acidic dosage forms. The albumin concentration is crucial for the maintenance of plasma oncotic pressure, the transport of nutrients, amino acids, and drugs, the effectiveness of drug therapy, and the prevention of drug toxicity. Hypoalbuminemia and structural defects molecule in the protein suggest a risk of changed metabolism and increased plasma concentration of unbound drugs. Therefore, the albumin structural and functional changes accompanied by low protein levels can be a serious prerequisite for ineffective therapy, frequent complications, and high mortality in patients with SARS-CoV-2 infection. The current opinion aims the research community the application of Site-Directed Spin Labeling Electron Paramagnetic Resonance spectroscopy (SDSL-EPR) and 3-Maleimido-PROXYL radical in determining abnormalities of the albumin dynamics and protein concentrations in COVID-19 critical patients.

Effects of Radiation on Cross-Linking Reaction, Microstructure, and Microbiological Properties of Whey Protein-Based Tissue Adhesive Development.

Whey proteins are mainly a group of small globular proteins. Their structures can be modified by physical, chemical, and other means to improve their functionality. The objectives of this study are to investigate the effect of radiation on protein–protein interaction, microstructure, and microbiological properties of whey protein–water solutions for a novel biomaterial tissue adhesive. Whey protein isolate solutions (10%, 27%, 30%, 33%, and 36% protein) were treated by different intensities (10–35 kGy) of gamma radiation. The protein solutions were analyzed for viscosity, turbidity, soluble nitrogen, total plate count, and yeast and mold counts. The interactions between whey proteins were also analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and scanning electron microscopy. The viscosity of protein solution (27%, w/w) was increased by the treatment of gamma radiation and by the storage at 23 °C. The 35 kGy intensity irradiated soluble nitrogen (10%, w/w) was reduced to about half of the sample treated by 0 kGy gamma radiation. The effects of gamma radiation and storage time can significantly increase the viscosity of whey protein solutions (p < 0.05). Radiation treatment had significant impact on soluble nitrogen of whey protein solutions (p < 0.05). SDS-PAGE results show that the extent of oligomerization of whey protein isolate solutions are increased by the enhancement in gamma radiation intensity. Photographs of SEM also indicate that protein–protein interactions are induced by gamma radiation in the model system. Consistent with above results, the bonding strength increases by the addition of extent of gamma radiation and the concentration of glutaraldehyde. Our results revealed that the combination of gamma-irradiated whey protein isolate solutions and glutaraldehyde can be used as a novel biomaterial tissue adhesive.

Combining High-Pressure NMR and Geometrical Sampling to Obtain a Full Topological Description of Protein Folding Landscapes: Application to the Folding of Two MAX Effectors from Magnaporthe oryzae.

Despite advances in experimental and computational methods, the mechanisms by which an unstructured polypeptide chain regains its unique three-dimensional structure remains one of the main puzzling questions in biology. Single-molecule techniques, ultra-fast perturbation and detection approaches and improvement in all-atom and coarse-grained simulation methods have greatly deepened our understanding of protein folding and the effects of environmental factors on folding landscape. However, a major challenge remains the detailed characterization of the protein folding landscape. Here, we used high hydrostatic pressure 2D NMR spectroscopy to obtain high-resolution experimental structural information in a site-specific manner across the polypeptide sequence and along the folding reaction coordinate. We used this residue-specific information to constrain Cyana3 calculations, in order to obtain a topological description of the entire folding landscape. This approach was used to describe the conformers populating the folding landscape of two small globular proteins, AVR-Pia and AVR-Pib, that belong to the structurally conserved but sequence-unrelated MAX effectors superfamily. Comparing the two folding landscapes, we found that, in spite of their divergent sequences, the folding pathway of these two proteins involves a similar, inescapable, folding intermediate, even if, statistically, the routes used are different.

Effects of macromolecular crowding on folding of small globular proteins

The effects of inert spherical crowders on the melting temperature and the folding stability of small globular proteins are investigated by using molecular dynamics simulations with a Gō-like model for the proteins. The energy parameter in the Gō-like model is obtained individually for each protein by matching the model’s melting temperature to the experimental meltingtemperature in the absence of crowders. It is shown that both the melting temperature and the folding stability of protein increase in the presence of the crowders. Specifically, as the crowders’ volume fraction φc increases from 0 to 0.4 the melting temperature increases by more than 20 Kelvins, whereas the folding stability is enhanced by up to ∼3.6 kcal/mol depending on the protein and the temperature. At room temperature (300 K), the stability enhancement is 1.2–1.4 kcal/mol, which is close to prior experimental data. It is also shown that the dependence of the folding free energy change on φc can be fitted well to the scaled particle theory by assuming a linear dependence of the effective size of the unfolded state on φc .

Estimating ruggedness of free-energy landscapes of small globular proteins from principal component analysis of molecular dynamics trajectories.

The internal dynamics of biomolecules, and hence their function, is governed by the structure of their free-energy landscape. Early flash-photolysis experiments on myoglobin suggested that the free-energy landscapes of proteins are hierarchically structured, with a characteristic distribution of free-energy barriers which gives rise to anomalous diffusion. Analytical results have been derived for one-dimensional or high-dimensional hierarchical free-energy landscapes. Recent improvements in methods and computer performance enable generating sufficiently long molecular dynamics (MD) trajectories to extract dynamics information covering many orders of magnitude, such that the broad distributions of energy barriers of proteins become accessible to quantitative studies of intermediate dimensions. In this work, we present a nonequilibrium method to estimate barrier height distributions from microsecond-long MD simulations. It infers barrier height distributions from anomalous diffusion exponents derived from principal component analysis and by comparison to simple hierarchical lattice models. These models are d-dimensional lattices of states separated by free-energy barriers, the heights of which are distributed as p(ΔG)=1/γexp(-ΔG/γ). The parameter γ quantifies the "ruggedness" of the free-energy landscape in such models. We show that both parameters, i.e., ruggedness and effective dimensionality d, can be inferred from anomalous diffusion exponents. Assuming a similar dependency of anomalous diffusion exponents on γ and d for proteins, we estimate the ruggedness of the free-energy landscapes of 500 small, single-domain globular proteins between 15 and 20 kT per dimension with an estimated accuracy of 4.2 kT and dimensionality between 40 and 60 with an estimated accuracy of 10 dimensions. Remarkably, neither effective dimensionality nor the ruggedness correlates with protein size and both ruggedness and effective dimensionality are much smaller than the scatter of protein sizes. From this finding, we conclude that these two properties of the free-energy landscape of a protein are rather adapted to the particular function of each single protein and that, quite generally, are functionally relevant for globular proteins.

Computational Study on the Thermal Conductivity of a Protein.

Protein molecules are thermally fluctuating and tightly packed amino acid residues strongly interact with each other. Such interactions are characterized in terms of heat current at the atomic level. We calculated the thermal conductivity of a small globular protein, villin headpiece subdomain, based on the linear response theory using equilibrium molecular dynamics simulation. The value of its thermal conductivity was 0.3 ± 0.01 [W m-1 K-1], which is in good agreement with experimental and computational studies on the other proteins in the literature. Heat current along the main chain was dominated by local vibrations in the polypeptide bonds, with amide I, II, III, and A bands on the Fourier transform of the heat current autocorrelation function.

Physical properties of the cytoplasm modulate the rates of microtubule polymerization and depolymerization.

The cytoplasm is a crowded, visco-elastic environment whose physical properties change according to physiological or developmental states. How the physical properties of the cytoplasm impact cellular functions invivo remains poorly understood. Here, we probe the effects of cytoplasmic concentration on microtubules by applying osmotic shifts to fission yeast, moss, and mammalian cells. We show that the rates of both microtubule polymerization and depolymerization scale linearly and inversely with cytoplasmic concentration; an increase in cytoplasmic concentration decreases the rates of microtubule polymerization and depolymerization proportionally, whereas a decrease in cytoplasmic concentration leads to the opposite. Numerous lines of evidence indicate that these effects are due to changes in cytoplasmic viscosity rather than cellular stress responses or macromolecular crowding per se. We reconstituted these effects on microtubules invitro by tuning viscosity. Our findings indicate that, even in normal conditions, the viscosity of the cytoplasm modulates the reactions that underlie microtubule dynamic behaviors.

Blocking PSD95-PDZ3's amyloidogenesis through point mutations that inhibit high-temperature reversible oligomerization (RO).

The third PDZ domain of the postsynaptic density protein 95 (PSD95-PDZ3; 11 kDa, 103 residues) has a propensity to form amyloid fibrils at high temperatures. At neutral pH, PDZ3 is natively folded, but it exhibits a peculiar three-state thermal unfolding with a reversible oligomerization (RO) equilibrium at high temperatures, which is uncharacteristic in the unfolding of a small globular protein as PDZ3 is. Here, we examined the RO's role in PDZ3's amyloidogenesis at high-temperature using two variants (F340A and L342A) that suppress the high-temperature RO and five single-alanine-mutated variants, where we mutated surface-exposed hydrophobic residues to alanine. Circular Dichroism (CD), Analytical Ultracentrifuge (AUC), and other spectroscopic measurements confirmed the retention of the native structure at ambient temperature. Differential Scanning Calorimetry (DSC) was used to assess the presence or absence of the high-temperature RO, and the amyloidogenicity of the variants was measured by Thioflavin T (ThT) fluorescence and Transmission Electron Microscopy (TEM). By comparing the fraction of RO and the ThT signal, we found that mutations that suppressed the high-temperature RO strongly inhibited amyloidogenesis. On the other hand, all variants forming RO also formed amyloids under the same conditions as the wild-type PDZ3.