Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π–Cation Interaction

How Omecamtiv Modulates Myosin Motion

Myosin VI is a unique reverse-directed motor protein in the myosin family. The D179Y mutation in Myosin VI is associated with deafness in mammals. This mutation destroys the processive motion of myosin and inhibits its functional activity due to an elevated phosphate release rate. The current work explores the way by which this mutation affects the phosphate release rate and changes the action of Myosin VI. Our study involves a wide range of approaches comprising free energy-based simulations, contact map analysis, binding energy investigation, structural inspection, renormalization simulation, multiple sequence alignment, and bioinformatics analysis. It is found that when the evolutionary conserved aspartic acid (D179) of Myosin VI is mutated to tyrosine (Y179), it leads to premature phosphate release from Myosin VI. Most importantly, the drug omecamtiv rescues the processivity of the mutant by slowing down the actin-independent phosphate release from Myosin VI. Thus, we also explore the molecular mechanism behind the premature phosphate release of the D179Y mutant of Myosin VI and the actin-independent slowing down of the phosphate release in the presence of omecamtiv. This phosphate release modulation is related to Myosin VI's processivity as found experimentally. Overall, our proposed model indicates that omecamtiv significantly alters the interaction between the P-loop of Myosin VI and the interfacial residues, which is the driving force behind the slowing down of the phosphate release of the D179Y mutant in the presence of omecamtiv. Finally, our study provides additional support to our proposal that the directionality of myosins is determined by the highest barrier along the cycle and not by any dynamical effect.

On the Control of Directionality of Myosin

The origin of the unique directionality of myosin has been a problem of fundamental and practical importance. This work establishes in a conclusive way that the directionality is controlled by tuning the barrier for the rate-determining step, namely, the ADP release step. This conclusion is based on exploring the molecular origin behind the reverse directionality of myosins V and VI and the determination of the origin of the change in the barriers of the ADP release for the forward and backward motions. Our investigation is performed by combining different simulation methods such as steer molecular dynamics (SMD), umbrella sampling, renormalization method, and automated path searching method. It is found that in the case of myosin V, the ADP release from the postrigor (trailing head) state overcomes a lower barrier than the prepowerstroke (leading head) state, which is also evident from experimental observation. In the case of myosin VI, we noticed a different trend when compared to myosin V. Since the directionality of myosins V and VI follows a reverse trend, we conclude that such differences in the directionality are controlled by the free energy barrier for the ADP release. Overall, the proof that the directionality of myosin is determined by the activation barrier of the rate-determining step in the cycle, rather than by some unspecified dynamical effects, has general importance.

Energetic and structural insights behind calcium induced conformational transition in calmodulin

Calmodulin (CaM) is a key signaling protein that triggers several cellular and physiological processes inside the cell. Upon binding with calcium ion, CaM undergoes large scale conformational transition from a closed state to an open state that facilitates its interaction with various target protein and regulates their activity. This work explores the origin of the energetic and structural variation of the wild type and mutated CaM and explores the molecular origin for the structural differences between them. We first calculated the sequential calcium binding energy to CaM using the PDLD/S-LRA/β approach. This study  shows a very good correlation with experimental calcium binding energies. Next we calculated the calcium binding energies to the wild type CaM and several mutated CaM systems which were reported experimentally. On the structural aspect, it has been reported experimentally that certain mutation (Q41L-K75I) in calcium bound CaM leads to complete conformational transition from an open to a closed state. By using equilibrium molecular dynamics simulation, free energy calculation and contact frequency map analysis, we have shown that the formation of a cluster of long-range hydrophobic contacts, initiated by the Q41L-K75I CaM variant is the driving force behind its closing motion. This study unravels the energetics and structural aspects behind calcium ion induced conformational changes in wild type CaM and its variant.

Conformational dynamics of adenylate kinase in crystals

Adenylate kinase is a ubiquitous enzyme in living systems and undergoes dramatic conformational changes during its catalytic cycle. For these reasons, it is widely studied by genetic, biochemical, and biophysical methods, both experimental and theoretical. We have determined the basic crystal structures of three differently liganded states of adenylate kinase from Methanotorrus igneus, a hyperthermophilic organism whose adenylate kinase is a homotrimeric oligomer. The multiple copies of each protomer in the asymmetric unit of the crystal provide a unique opportunity to study the variation in the structure and were further analyzed using advanced crystallographic refinement methods and analysis tools to reveal conformational heterogeneity and, thus, implied dynamic behaviors in the catalytic cycle.

Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO

The structure of proteins has long been recognized to hold the key to understanding and engineering their function, and rapid advances in structural biology and protein structure prediction are now supplying researchers with an ever-increasing wealth of structural information. Most of the time, however, structures can only be determined in free energy minima, one at a time. While conformational flexibility may thus be inferred from static end-state structures, their interconversion mechanisms─a central ambition of structural biology─are often beyond the scope of direct experimentation. Given the dynamical nature of the processes in question, many studies have attempted to explore conformational transitions using molecular dynamics (MD). However, ensuring proper convergence and reversibility in the predicted transitions is extremely challenging. In particular, a commonly used technique to map out a path from a starting to a target conformation called steered MD (SMD) can suffer from starting-state dependence (hysteresis) when combined with techniques such as umbrella sampling (US) to compute the free energy profile of a transition. Here, we study this problem in detail on conformational changes of increasing complexity. We also present a new, history-independent approach that we term "MEMENTO" (Morphing End states by Modelling Ensembles with iNdependent TOpologies) to generate paths that alleviate hysteresis in the construction of conformational free energy profiles. MEMENTO utilizes template-based structure modelling to restore physically reasonable protein conformations based on coordinate interpolation (morphing) as an ensemble of plausible intermediates, from which a smooth path is picked. We compare SMD and MEMENTO on well-characterized test cases (the toy peptide deca-alanine and the enzyme adenylate kinase) before discussing its use in more complicated systems (the kinase P38α and the bacterial leucine transporter LeuT). Our work shows that for all but the simplest systems SMD paths should not in general be used to seed umbrella sampling or related techniques, unless the paths are validated by consistent results from biased runs in opposite directions. MEMENTO, on the other hand, performs well as a flexible tool to generate intermediate structures for umbrella sampling. We also demonstrate that extended end-state sampling combined with MEMENTO can aid the discovery of collective variables on a case-by-case basis.

Comparative study of the unbinding process of some HTLV-1 protease inhibitors using unbiased molecular dynamics simulations

The HTLV-1 protease is one of the major antiviral targets to overwhelm this virus. Several research groups have developed protease inhibitors, but none has been successful. In this regard, developing new HTLV-1 protease inhibitors to fix the defects in previous inhibitors may overcome the lack of curative treatment for this oncovirus. Thus, we decided to study the unbinding pathways of the most potent (compound 10, PDB ID 4YDF, Ki = 15 nM) and one of the weakest (compound 9, PDB ID 4YDG, Ki = 7900 nM) protease inhibitors, which are very structurally similar. We conducted 12 successful short and long simulations (totaling 14.8 μs) to unbind the compounds from two monoprotonated (mp) forms of protease using the Supervised Molecular Dynamics (SuMD) without applying any biasing force. The results revealed that Asp32 or Asp32′ in the two forms of mp state similarly exert powerful effects on maintaining both potent and weak inhibitors in the binding pocket of HTLV-1 protease. In the potent inhibitor’s unbinding process, His66′ was a great supporter that was absent in the weak inhibitor’s unbinding pathway. In contrast, in the weak inhibitor’s unbinding process, Trp98/Trp98′ by pi-pi stacking interactions were unfavorable for the stability of the inhibitor in the binding site. In our opinion, these results will assist in designing more potent and effective inhibitors for the HTLV-1 protease.

Curious Case of MAD2 Protein: Diverse Folding Intermediates Leading to Alternate Native States

Anfinsen's dogma postulates that for one sequence there will be only one unique structure that is necessary for the functioning of the protein. However, over the years there have been a number of departures from this postulate. As far as function is considered, there are growing examples of proteins that "moonlight", perform multiple unrelated functions. With the discovery of intrinsically disordered proteins, morpheeins, chameleonic sequences, and metamorphic proteins that can switch folds, we have acquired a more nuanced understanding of protein folding and dynamics. Appearing to apparently contradict the classical folding paradigm, metamorphic proteins are considered exotic species. In this work, we have explored the free energy landscape and folding pathways of the metamorphic protein MAD2 which is an important component of the spindle checkpoint. It coexists in two alternate states: the inactive open state and the active closed state. Using a dual-basin structure-based model approach we have shown that a variety of intermediates and multiple pathways are available to MAD2 to fold into its alternate forms. This approach involves performing molecular dynamics simulations of coarse-grained models of MAD2 where the structural information regarding both of its native conformations is explicitly included in terms of their native contacts in the force field used. Detailed analyses have indicated that some of the contacts within the protein play a key role in determining which folding pathway will be selected and point to a probable long-range communication between the N and the C termini of the protein that seems to control its folding. Finally, our work also provides a rationale for the experimentally observed preference of the ΔC₁₀ variant of MAD2 to exist in the open state.

An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules

In theoretical modeling of a physical system, a crucial step consists of the identification of those degrees of freedom that enable a synthetic yet informative representation of it. While in some cases this selection can be carried out on the basis of intuition and experience, straightforward discrimination of the important features from the negligible ones is difficult for many complex systems, most notably heteropolymers and large biomolecules. We here present a thermodynamics-based theoretical framework to gauge the effectiveness of a given simplified representation by measuring its information content. We employ this method to identify those reduced descriptions of proteins, in terms of a subset of their atoms, that retain the largest amount of information from the original model; we show that these highly informative representations share common features that are intrinsically related to the biological properties of the proteins under examination, thereby establishing a bridge between protein structure, energetics, and function.

Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution

Hydrophobic association is the key contributor behind the formation of well packed core of a protein which is often believed to be an important step for folding from an unfolded chain to its compact functional form. While most of the protein folding/unfolding studies have evaluated the changes in the hydrophobic interactions during chemical denaturation, the role of hydrophilic amino acids in such processes are not discussed in detail. Here we report the role of the hydrophilic amino acids behind ethanol induced unfolding of protein. Using free energy simulations, we show that chicken villin head piece (HP-36) protein unfolds gradually in presence of water-ethanol binary mixture with increasing composition of ethanol. However, upon mutation of hydrophilic amino acids by glycine while keeping the hydrophobic amino acids intact, the compact state of the protein is found to be stable at all compositions with gradual flattening of the free energy landscape upon increasing compositions. The local environment around the protein in terms of ethanol/water number significantly differs in wild type protein compared to the mutated protein. The calculated Wyman-Tanford preferential binding coefficient of ethanol for wild type protein reveals that a greater number of cosolutes (here ethanol) bind to the unfolded state compared to its folded state. However, no significant increase in binding coefficient of ethanol at the unfolded state is found for mutated protein. Local-bulk partition coefficient calculation also suggests similar scenarios. Our results reveal that the weakening of hydrophobic interactions in aqueous ethanol solution along with larger preferential binding of ethanol to the unfolded state mediated by hydrophilic amino acids combinedly helps unfolding of protein in aqueous ethanol solution.

Multiple Pathways and Time Scales for Conformational Transitions in apo-Adenylate Kinase

The open/close transition in adenylate kinase (AK) is regarded as a representative example for large-scale conformational transition in proteins, yet its mechanism remains unclear despite numerous experimental and computational studies. Using extensive (∼50 μs) explicit solvent atomistic simulations and Markov state analysis, we shed new lights on the mechanism of this transition in the apo form of AK. The closed basin of apo AK features an open NMP domain while the LID domain closes and rotates toward it. Therefore, although the computed structural properties of the closed ensemble are consistent with previously reported FRET and PRE measurements, our simulations suggest that NMP closure is likely to follow AMP binding, in contrast to the previous interpretation of FRET and PRE data that the apo state was able to sample the fully closed conformation for "ligand selection". The closed state ensemble is found to be kinetically heterogeneous; multiple pathways and time scales are associated with the open/close transition, providing new clues to the disparate time scales observed in different experiments. Besides interdomain interactions, a novel mutual information analysis identifies specific intradomain interactions that correlate strongly to transition kinetics, supporting observations from previous chimera experiments. While our results underscore the role of internal domain properties in determining the kinetics of open/close transition in apo AK, no evidence is observed for any significant degree of local unfolding during the transition. These observations about AK have general implications to our view of conformational states, transition pathways, and time scales of conformational changes in proteins. The key features and time scales of observed transition pathways are robust and similar from simulations using two popular fixed charge force fields.