Myosin-V as a mechanical sensor: an elastic network study

Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling

Allosteric regulation is crucial for the operation of protein machines and molecular motors. A major challenge is to characterize and quantify the information exchange underlying allosteric communication between remote functional sites in a protein, and to identify the involved relevant pathways. We review applications of two topical approaches of dynamical protein modeling, a kinetic-based single-molecule stochastic model, which employs information thermodynamics to quantify allosteric interactions, and structure-based coarse-grained modeling to characterize intra-molecular couplings in terms of conformational motions and propagating mechanical strain. Both descriptions resolve the directionality of allosteric responses within a protein, emphasizing the concept of causality as the principal hallmark of protein allostery. We discuss the application of techniques from information thermodynamics to dynamic protein elastic networks and evolutionary designed model structures, and the ramifications for protein allostery.

Simple mechanics of protein machines

While belonging to the nanoscale, protein machines are so complex that tracing even a small fraction of their cycle requires weeks of calculations on supercomputers. Surprisingly, many aspects of their operation can be however already reproduced by using very simple mechanical models of elastic networks. The analysis suggests that, similar to other self-organized complex systems, functional collective dynamics in such proteins is effectively reduced to a low-dimensional attractive manifold.

Oscillating Piconewton Force Manipulation on Single-Molecule Enzymatic Conformational and Reaction Dynamics

Oscillation force has been demonstrated in theoretical studies as a critical role in unraveling the comprehensive enzymatic dynamics and addressing its regulation on enzyme activity. Utilizing the imposed external mechanical oscillation force by our newly developed magnetic tweezers coupled with a single-molecule photon-stamping imaging spectroscopic microscope, we experimentally studied a millisecond-scale oscillation force manipulation on single horseradish peroxidase enzymatic conformational and reaction dynamics. We have studied the enzymatic reaction dynamics and found that the enzyme activity changes under the real-time oscillatory force manipulation. Moreover, the oscillation force shows the capability of manipulating the enzyme active-site conformational state as well as the nascent-formed product's interaction with the active site of the enzyme, which impacts on the product release pathways. Specifically, we have identified that there are two product releasing pathways, the solvation-mediated diffusion releasing pathway and the spilling-out releasing pathway. We have observed that the spilling-out pathway can be significantly perturbed by the oscillatory force manipulation. Our correlated interpretation of enzymatic conformational and reaction dynamics provides a new insight into the comprehensive understanding of the complex conformational dynamics evolved in an enzymatic reaction. Technically, we have also demonstrated a novel approach capable of unfolding an enzyme under an enzymatic reaction condition in real time and, furthermore, by using an oscillatory mechanical weak piconewton force to manipulate enzyme conformations, and the enzyme thermal fluctuation is fully maintained. The real-time in situ fluorescence probe at the enzymatic active site reports the active-site conformational dynamics through each enzymatic reaction turnovers.

Coarse-Grained Protein Dynamics Studies Using Elastic Network Models

Elastic networks have been used as simple models of proteins to study their slow structural dynamics. They consist of point-like particles connected by linear Hookean springs and hence are convenient for linear normal mode analysis around a given reference structure. Furthermore, dynamic simulations using these models can provide new insights. As the computational cost associated with these models is considerably lower compared to that of all-atom models, they are also convenient for comparative studies between multiple protein structures. In this review, we introduce examples of coarse-grained molecular dynamics studies using elastic network models and their derivatives, focusing on the nonlinear phenomena, and discuss their applicability to large-scale macromolecular assemblies.

Designed Elastic Networks: Models of Complex Protein Machinery

Recently, the design of mechanical networks with protein-inspired responses has become increasingly popular. Here, we review contributions which were motivated by studies of protein dynamics employing coarse-grained elastic network models. First, the concept of evolutionary optimization that we developed to design network structures which execute prescribed tasks is explained. We then review what presumably marks the origin of the idea to design complex functional networks which encode protein-inspired behavior, namely the design of an elastic network structure which emulates the cycles of ATP-powered conformational motion in protein machines. Two recent applications are reviewed. First, the construction of a model molecular motor, whose operation incorporates both the tight coupling power stroke as well as the loose coupling Brownian ratchet mechanism, is discussed. Second, the evolutionary design of network structures which encode optimal long-range communication between remote sites and represent mechanical models of allosteric proteins is presented. We discuss the prospects of designed protein-mimicking elastic networks as model systems to elucidate the design principles and functional signatures underlying the operation of complex protein machinery.

High-speed atomic force microscopy and its future prospects

Various techniques have been developed and used to investigate how proteins produce complex biological architectures and phenomena. Among these techniques, high-speed atomic force microscopy (HS-AFM) holds a unique position. It is only HS-AFM that allows the simultaneous assessment of structure and dynamics of single protein molecules in action. This new microscopy tool has been successfully applied to a variety of proteins, from motor proteins to membrane proteins, antibodies, enzymes, and even to intrinsically disordered proteins. And yet there still remain many biomolecular phenomena that cannot be addressed by HS-AFM in its current form. Here, I present a brief history of HS-AFM development, describe the current state of HS-AFM, and then discuss which new biological scanning probe microscopy techniques will be coming up next.

Molecular mechanisms underlying the impact of mutations in SOD1 on its conformational properties associated with amyotrophic lateral sclerosis as revealed with molecular modelling

Background

So far, little is known about the molecular mechanisms of amyotrophic lateral sclerosis onset and progression caused by SOD1 mutations. One of the hypotheses is based on SOD1 misfolding resulting from mutations and subsequent deposition of its cytotoxic aggregates. This hypothesis is complicated by the fact that known SOD1 mutations of similar clinical effect could be distributed over the whole protein structure.

Results

In this work, a measure of hydrogen bond stability in conformational states was studied with elastic network analysis of 35 SOD1 mutants. Twenty-eight hydrogen bonds were detected in nine of 35 mutants with their stability being significantly different from that with the wild-type. These hydrogen bonds were formed by the amino acid residues known from the literature to be located in contact between SOD1 aggregates. Additionally, residues disposed between copper binding sites of both protein subunits were found from the models to form a stiff core, which can be involved in mechanical impulse transduction between these active centres.

Conclusions

The modelling highlights that both stability of the copper binding site and stability of the dimer can play an important role in ALS progression.

Electronic supplementary material

The online version of this article (10.1186/s12900-018-0080-9) contains supplementary material, which is available to authorized users.

High-speed atomic force microscopy and its future prospects

Various techniques have been developed and used to investigate how proteins produce complex biological architectures and phenomena. Among these techniques, high-speed atomic force microscopy (HS-AFM) holds a unique position. It is only HS-AFM that allows the simultaneous assessment of structure and dynamics of single protein molecules in action. This new microscopy tool has been successfully applied to a variety of proteins, from motor proteins to membrane proteins, antibodies, enzymes, and even to intrinsically disordered proteins. And yet there still remain many biomolecular phenomena that cannot be addressed by HS-AFM in its current form. Here, I present a brief history of HS-AFM development, describe the current state of HS-AFM, and then discuss which new biological scanning probe microscopy techniques will be coming up next.

Analysis of an ATP-induced conformational transition of ABC transporter MsbA using a coarse-grained model

Upon the binding of ATP molecules to nucleotide binding domains (NBDs), ATP-binding cassette (ABC) exporters undergo a conformational transition from an inward-facing (IF) to an outward-facing (OF) state. This molecular event is a typical example of chemo-mechanical coupling. However, the underlying mechanism remains unclear. In this study, we analyzed the IF→OF transition of a representative ABC exporter, MsbA, by solving the equation of motion under an elastic network model (ENM). ATP was represented as a single node in ENM or replaced by external forces. When two ATP nodes were added to the ENM of the IF state protein, the two NBDs dimerized; subsequently, the two transmembrane domains opened toward the extracellular side, resulting in the formation of the OF structure. Such a conformational transition was also reproduced by applying external forces, which caused the rotational motion of the NBDs instead of the addition of ATP nodes. The process of the conformational transition was analyzed in detail using cross-correlation maps for node-node interactions. More importantly, it was revealed that the ATP binding energy is converted into distortion energy of several transmembrane helices. These results are useful for understanding the chemo-mechanical coupling in ABC transporters.

Design of Elastic Networks with Evolutionary Optimized Long-Range Communication as Mechanical Models of Allosteric Proteins

Allosteric effects often underlie the activity of proteins, and elucidating generic design aspects and functional principles unique to allosteric phenomena represent a major challenge. Here an approach consisting of the in silico design of synthetic structures, which, as the principal element of allostery, encode dynamical long-range coupling among two sites, is presented. The structures are represented by elastic networks, similar to coarse-grained models of real proteins. A strategy of evolutionary optimization was implemented to iteratively improve allosteric coupling. In the designed structures, allosteric interactions were analyzed in terms of strain propagation, and simple pathways that emerged during evolution were identified as signatures through which long-range communication was established. Moreover, robustness of allosteric performance with respect to mutations was demonstrated. As it turned out, the designed prototype structures reveal dynamical properties resembling those found in real allosteric proteins. Hence, they may serve as toy models of complex allosteric systems, such as proteins. Application of the developed modeling scheme to the allosteric transition in the myosin V molecular motor was also demonstrated.

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

Recent structure-based computational studies suggest that, in contrast to the classical description of equilibrium fluctuations as wigglings and jigglings, proteins have access to well-defined spectra of collective motions, called intrinsic dynamics, encoded by their structure under native state conditions. In particular, the global modes of motions (at the low frequency end of the spectrum) are shown by multiple studies to be highly robust to minor differences in the structure or to detailed interactions at the atomic level. These modes, encoded by the overall fold, usually define the mechanisms of interactions with substrates. They can be estimated by low-resolution models such as the elastic network models (ENMs) exclusively based on interresidue contact topology. The ability of ENMs to efficiently assess the global motions intrinsically favored by the overall fold as well as the relevance of these predictions to the dominant changes in structure experimentally observed for a given protein in the presence of different substrates suggest that the intrinsic dynamics plays a role in mediating protein-substrate interactions. These observations underscore the functional significance of structure-encoded dynamics, or the importance of the predisposition to favor functional global modes in the evolutionary selection of structures.

Coarse-grain simulations of active molecular machines in lipid bilayers

A coarse-grain method for simulations of the dynamics of active protein inclusions in lipid bilayers is described. It combines the previously proposed hybrid simulations of bilayers [M.-J. Huang, R. Kapral, A. S. Mikhailov, and H.-Y. Chen, J. Chem. Phys. 137, 055101 (2012)], based on molecular dynamics for the lipids and multi-particle collision dynamics for the solvent, with an elastic-network description of active proteins. The method is implemented for a model molecular machine which performs active conformational motions induced by ligand binding and its release after reaction. The situation characteristic for peripheral membrane proteins is considered. Statistical investigations of the effects of single active or passive inclusions on the shape of the membrane are carried out. The results show that the peripheral machine produces asymmetric perturbations of the thickness of two leaflets of the membrane. It also produces a local saddle in the midplane height of the bilayer. Analysis of the power spectrum of the fluctuations of the membrane midplane shows that the conformational motion of the machine perturbs these membrane fluctuations. The hydrodynamic lipid flows induced by cyclic conformational changes in the machine are analyzed. It is shown that such flows are long-ranged and should provide an additional important mechanism for interactions between active inclusions in biological membranes.

Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics

The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or on their ability to perform wider and sometimes highly elaborated motions. Hence, there is considerable interest in the definition of accurate coarse-grained descriptions of protein dynamics, as an alternative to more computationally expensive approaches. In particular, the elastic network model, in which residue motions are subjected to pairwise harmonic potentials, is known to capture essential aspects of conformational dynamics in proteins, but has so far remained mostly phenomenological, and unable to account for the chemical specificities of amino acids. We propose, for the first time, a method to derive residue- and distance-specific effective harmonic potentials from the statistical analysis of an extensive dataset of NMR conformational ensembles. These potentials constitute dynamical counterparts to the mean-force statistical potentials commonly used for static analyses of protein structures. In the context of the elastic network model, they yield a strongly improved description of the cooperative aspects of residue motions, and give the opportunity to systematically explore the influence of sequence details on protein dynamics.

Membrane trafficking in podocyte health and disease

Podocytes are highly specialized epithelial cells localized in the kidney glomerulus. The distinct cell signaling events and unique cytoskeletal architecture tailor podocytes to withstand changes in hydrostatic pressure during glomerular filtration. Alteration of glomerular filtration leads to kidney disease and frequently manifests with proteinuria. It has been increasingly recognized that cell signaling and cytoskeletal dynamics are coupled more tightly to membrane trafficking than previously thought. Membrane trafficking coordinates the cross-talk between protein networks and signaling cascades in a spatially and temporally organized fashion and may be viewed as a communication highway between the cell exterior and interior. Membrane trafficking involves transport of cargo from the plasma membrane to the cell interior (i.e., endocytosis) followed by cargo trafficking to lysosomes for degradation or to the plasma membrane for recycling. Yet, recent studies indicate that the conventional classification does not fully reflect the complex and versatile nature of membrane trafficking. While the increasing complexity of elaborate protein scaffolds and signaling cascades is being recognized in podocytes, the role of membrane trafficking is less well understood. This review will focus on the role of membrane trafficking in podocyte health and disease.

Complex intramolecular mechanics of G-actin--an elastic network study

Systematic numerical investigations of conformational motions in single actin molecules were performed by employing a simple elastic-network (EN) model of this protein. Similar to previous investigations for myosin, we found that G-actin essentially behaves as a strain sensor, responding by well-defined domain motions to mechanical perturbations. Several sensitive residues within the nucleotide-binding pocket (NBP) could be identified, such that the perturbation of any of them can induce characteristic flattening of actin molecules and closing of the cleft between their two mobile domains. Extending the EN model by introduction of a set of breakable links which become effective only when two domains approach one another, it was observed that G-actin can possess a metastable state corresponding to a closed conformation and that a transition to this state can be induced by appropriate perturbations in the NBP region. The ligands were roughly modeled as a single particle (ADP) or a dimer (ATP), which were placed inside the NBP and connected by elastic links to the neighbors. Our approximate analysis suggests that, when ATP is present, it stabilizes the closed conformation of actin. This may play an important role in the explanation why, in the presence of ATP, the polymerization process is highly accelerated.