Protein-interface Interactions Research Articles

In Silico Prediction of Plasmodium falciparum Cytoadherence Inhibitors That Disrupt Interaction between gC1qR-DBLβ12 Complex.

Malaria causes about half a million deaths per year, mainly in children below 5 years of age. Cytoadherence of Plasmodium falciparum infected erythrocytes in brain and placenta has been linked to severe malaria and malarial related deaths. Cytoadherence is mediated by binding of human receptor gC1qR to the DBLβ12 domain of a P. falciparum erythrocyte membrane protein family 1 (PfEMP1) protein. In the present work, molecular dynamic simulation was extensively studied for the gC1qR-DBLβ12 complex. The stabilized protein complex was used to study the protein–protein interface interactions and mapping of interactive amino acid residues as hotspot were performed. Prediction of inhibitors were performed by using virtual protein–protein inhibitor database Timbal screening of about 15,000 compounds. In silico mutagenesis studies, binding profile and protein ligand interaction fingerprinting were used to strengthen the screening of the potential inhibitors of gC1qR-DBLβ12 interface. Six compounds were selected and were further subjected to the MAIP analysis and ADMET studies. From these six compounds, the compounds 3, 5, and 6 were found to outperform on all screening criteria from the rest selected compounds. These compounds may provide novel drugs to treat and manage severe falciparum malaria. Additionally. the identified hotspots can be used in future for designing novel interventions for disruption of interface interactions, such as through peptides or vaccines. Futher in vitro and in vivo studies are required for the confirmation of these compounds as potential inhibitors of gC1qR-DBLβ12 interaction.

Structural Changes in Insulin at a Soft Electrochemical Interface.

Understanding the interaction of proteins at interfaces, which occurs at or within cell membranes and lipoprotein vesicles, is central to our understanding of protein function. Therefore, new experimental approaches to understand how protein structure is influenced by protein-interface interactions are important. Herein we build on our previous work exploring electrochemistry at the interface between two immiscible electrolyte solutions (ITIES) to investigate changes in protein secondary structure that are modulated by protein-interface interactions. The ITIES provides an experimental framework to drive protein adsorption at an interface, allowing subsequent spectroscopic analysis (e.g., Fourier transform infrared spectroscopy) to monitor changes in protein structure. Here, we reveal that the interaction between insulin and the interface destabilizes native insulin secondary structure, promoting formation of α helix secondary structures. These structural alterations result from protein-interface rather than protein-protein interactions at the interface. Although this is an emerging approach, our results provide a foundation highlighting the value of the ITIES as a tool to study protein structure and interactions at interfaces. Such knowledge may be useful to elucidate protein function within biological systems or to aid sensor development.

Controlling Experimental Parameters to Improve Characterization of Biomaterial Fouling.

Uncontrolled protein adsorption and cell binding to biomaterial surfaces may lead to degradation, implant failure, infection, and deleterious inflammatory and immune responses. The accurate characterization of biofouling is therefore crucial for the optimization of biomaterials and devices that interface with complex biological environments composed of macromolecules, fluids, and cells. Currently, a diverse array of experimental conditions and characterization techniques are utilized, making it difficult to compare reported fouling values between similar or different biomaterials. This review aims to help scientists and engineers appreciate current limitations and conduct fouling experiments to facilitate the comparison of reported values and expedite the development of low-fouling materials. Recent advancements in the understanding of protein–interface interactions and fouling variability due to experiment conditions will be highlighted to discuss protein adsorption and cell adhesion and activation on biomaterial surfaces.

Self-Assembly of Switchable Protein Nanocages via Allosteric Effect

Protein cages have promising applications in highly efficient gene transportation. Many methods of engineering protein–interface interactions have been developed to build such viral mimics. Missing...

Analyzing protein-ligand and protein-interface interactions using high pressure

All protein function is based on interactions with the environment. Proteins can bind molecules for their transport, their catalytic conversion, or for signal transduction. They can bind to each other, and they adsorb at interfaces, such as lipid membranes or material surfaces. An experimental characterization is needed to understand the underlying mechanisms, but also to make use of proteins in biotechnology or biomedicine. When protein interactions are studied under high pressure, volume changes are revealed that directly describe spatial contributions to these interactions. Moreover, the strength of protein interactions with ligands or interfaces can be tuned in a smooth way by pressure modulation, which can be utilized in the design of drugs and bio-responsive interfaces. In this short review, selected studies of protein-ligand and protein-interface interactions are presented that were carried out under high pressure. Furthermore, a perspective on bio-responsive interfaces is given where protein-ligand binding is applied to create functional interfacial structures.

Understanding Protein-Interface Interactions of a Fusion Protein at Silicone Oil-Water Interface Probed by Sum Frequency Generation Vibrational Spectroscopy

Protein adsorbed at the silicone oil-water interface can undergo a conformational change that has the potential to induce protein aggregation on storage. Characterization of the protein structures at interface is therefore critical for understanding the protein-interface interactions. In this article, we have applied sum frequency generation (SFG) spectroscopy for studying the secondary structures of a fusion protein at interface and the surfactant effect on protein adsorption to silicone oil-water interface. SFG and chiral SFG spectra from adsorbed protein in the amide I region were analyzed. The presence of beta-sheet vibrational band at 1635 cm−1 implies the protein secondary structure was likely perturbed when protein adsorbed at silicone oil interface. The time-dependent SFG study showed a significant reduction in the SFG signal of preadsorbed protein when polysorbate 20 was introduced, suggesting surfactant has stronger interaction with the interface leading to desorption of protein from the interface. In the preadsorbed surfactant and a mixture of protein/polysorbate 20, SFG analysis confirmed that surfactant can dramatically prevent the protein adsorption to silicone oil surface. This study has demonstrated the potential of SFG for providing the detailed molecular level understanding of protein conformation at interface and assessing the influence of surfactant on protein adsorption behavior.

The Conformation of Interfacially Adsorbed Ranaspumin-2 Is an Arrested State on the Unfolding Pathway

Ranaspumin-2 (Rsn-2) is a surfactant protein found in the foam nests of the túngara frog. Previous experimental work has led to a proposed model of adsorption that involves an unusual clam-shell-like unhinging of the protein at an interface. Interestingly, there is no concomitant denaturation of the secondary structural elements of Rsn-2 with the large-scale transformation of its tertiary structure. In this work we use both experiment and simulation to better understand the driving forces underpinning this unusual process. We develop a modified Gō-model approach where we have included explicit representation of the side chains to realistically model the interaction between the secondary structure elements of the protein and the interface. Doing so allows for the study of the underlying energy landscape that governs the mechanism of Rsn-2 interfacial adsorption. Experimentally, we study targeted mutants of Rsn-2, using the Langmuir trough, pendant drop tensiometry, and circular dichroism, to demonstrate that the clam-shell model is correct. We find that Rsn-2 adsorption is in fact a two-step process: the hydrophobic N-terminal tail recruits the protein to the interface after which Rsn-2 undergoes an unfolding transition that maintains its secondary structure. Intriguingly, our simulations show that the conformation Rsn-2 adopts at an interface is an arrested state along the denaturation pathway. More generally, our computational model should prove a useful, and computationally efficient, tool in studying the dynamics and energetics of protein-interface interactions.

Pressure-Induced Protein Adsorption at Aqueous–Solid Interfaces

There seems to be a general relation between the standard Gibbs energy change of unfolding, ΔG°unf, of a protein and its affinity to aqueous-solid interfaces. So-called "hard" proteins (ΔG°unf is large) are found to adsorb less strongly to such interfaces than "soft" proteins (ΔG°unf is small). Here, we provide direct support for this rule by using high pressure to modulate the folding stability of a protein. We have performed high-pressure total internal reflection fluorescence (HP-TIRF) spectroscopy and high-pressure neutron reflectometry (HP-NR) to measure the degree of adsorption and the structure of lysozyme on planar solid surfaces as a function of pressure for the first time. By carrying out these experiments at hydrophilic and hydrophobic surfaces with varying concentrations of glycerol, we have found strong evidence that ΔG°unf has indeed a direct influence. At high pressures, there is a larger degree of lysozyme adsorption, probably because lysozyme becomes a "soft" protein under these conditions. The results of this study demonstrate that high pressure is a very useful tool to explore thermodynamics of protein-interface interactions.

Effects of Pressure on the Adsorption of Proteins at Aqueous-Solid Interfaces

The spontaneous adsorption of proteins at aqueous-solid interfaces plays an important role in nature, medicine, and biotechnology. A sound understanding of the molecular mechanisms and interactions upon protein adsorption is required for the development of new materials coatings and for the choice of solvent conditions. So far, protein adsorption studies have been carried out mainly as a function of protein solution concentration, pH-value, and surface chemistry. In addition, several temperature-dependent studies have shed some light on the thermodynamics underlying protein adsorption. In contrast, effects of pressure on this process are widely unknown. Applying pressure to molecular systems generally offers access to all kinds of volume changes occurring during assembly of molecules, phase transitions, and chemical reactions. In the case of protein adsorption, using pressure as a thermodynamic variable allows for the determination of volume changes of adsorption, volume changes of unfolding in the adsorbed state, and changes of protein-interface interactions that determine the degree of protein adsorption. We have designed new high pressure cells for total internal reflection fluorescence (TIRF) spectroscopy and neutron reflectometry (NR) for pressures up to 2500 bar in order to access these quantities. The results obtained so far indicate a pressure-induced increase of the degree of protein adsorption at both the water-silica and water-poly(styrene) interfaces. Moreover, a drastic decrease of the volume change of unfolding has been found when proteins are adsorbed at the water-silica interface. Apparently, pressure exerts a distinct influence on the process of protein adsorption and provides a new complemental view on the underlying mechanism.

High Pressure Protein Unfolding at Model Interfaces

Protein adsorption often plays the central role in a wide variety of processes occurring in medicine, biochemistry and biotechnology. In order to develop novel material coatings, a detailed insight into the underlying adsorption mechanisms at the molecular level and the knowledge of thermodynamic parameters is of great importance. So far, protein adsorption has been investigated in terms of concentration, pH-value and temperature of the protein solution. However, volume effects on protein adsorption are still unknown in spite of their fundamental contribution to protein-interface interactions. in order to investigate volume effects and protein conformational transitions, two model proteins, SNase and lysozyme, were adsorbed onto silica nanoparticles and subjected to high hydrostatic pressures. At pressures up to 2500 bar, we have observed much smaller volumes of protein unfolding in the adsorbed state as compared to the solution behavior. These changes are directly linked to volume changes upon protein adsorption at the aqueous-solid model interface.

Allostery in the ferredoxin protein motif does not involve a conformational switch

Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the iron-sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.

The physics and bioinformatics of binding and folding-an energy landscape perspective.

It has been recognized in the last few years that unstructured proteins play an important role in biological organisms, often participating in signal transduction, transcriptional regulation, and a variety of other regulatory activities. Various hypotheses have been put forward for the ubiquity of the unfolded state; rapid turnover, faster or more specific binding kinetics, multifunctionality may all possibly explain apparent ubiquitousness of unfolded proteins in eukaryotic cells. In this paper we extend the energy landscape theory of protein folding to construct an analytical model of how binding and folding are coupled thermodynamically when the energy landscape is partially rugged. To deduce the parameters that enter the theory, which is based on Generalized Random Energy Model, we have analyzed in a bioinformatic sense a large structural database of more than 500 protein complexes. We find that Miyazawa-Jernigan contact potential shows similar energy gaps for folding for both hydrophobic and hydrophilic proteins, but that for binding contacts hydrophobic interfaces turn out to be funneled while hydrophilic ones are antifunneled. This suggests evolution has found a mechanism for avoiding frustration between folding and binding by making use of indirect water-mediated interactions. By juxtaposing the monomeric protein folding free energy profile in the protein complex database with another database consisting of only well-folded monomers, we estimate that at least 15% of monomers in the former database are unfolded in the absence of partner protein interface interactions. When employing the parameters characteristic of these unfolded monomers to construct binding/folding phase diagrams, we find that these monomers would indeed fold if sufficiently stabilizing binding contacts, consistent with that fold, are formed.