Accurate Prediction of Antifreeze Protein from Sequences through Natural Language Text Processing and Interpretable Machine Learning Approaches

Antifreeze proteins (AFPs) bind to growing iceplanes owing to their structural complementarity nature, thereby inhibiting the ice-crystal growth by thermal hysteresis. Classification of AFPs from sequence is a difficult task due to their low sequence similarity, and therefore, the usual sequence similarity algorithms, like Blast and PSI-Blast, are not efficient. Here, a method combining n-gram feature vectors and machine learning models to accelerate the identification of potential AFPs from sequences is proposed. All these n-gram features are extracted from the K-mer counting method. The comparative analysis reveals that, among different machine learning models, Xgboost outperforms others in predicting AFPs from sequence when penta-mers are used as a feature vector. When tested on an independent dataset, our method performed better compared to other existing ones with sensitivity of 97.50%, recall of 98.30%, and f1 score of 99.10%. Further, we used the SHAP method, which provides important insight into the functional activity of AFPs

Pairwise Hydrophobicity at Low Temperature: Appearance of a Stable Second Solvent-Separated Minimum with Possible Implication in Cold Denaturation

The hydrophobic effect appears to be a key driving force for many chemical and biological processes, such as protein folding, protein–protein interactions, membrane bilayer self-assembly, and so forth. In this study, we calculated the potential of mean force (PMF) using umbrella sampling technique between different model hydrophobes (methane–methane, cyclobutane–cyclobutane, and between two rodlike hydrophobes) at lower than ambient temperatures (300, 260, and 240 K). We find the appearance of a second solvent-separated minimum at ∼1.0 nm apart from the usual contact and first solvent-separated minimum in the PMF profile of the methane pair at low temperature. In the PMF between both cyclobutane and the rodlike hydrophobe pairs, the second solvent-separated pair (SSSP) becomes even more stable than the first solvent-separated pair (FSSP) at 240 K. Analysis of the water structure shows that, at 240 K, the core water of SSSP for the rodlike hydrophobe pair is more strongly hydrogen bonded and more tetrahedrally oriented than that of the FSSP. Strongly hydrogen-bonded ordered water molecules implicate strong water–water interactions, which are responsible for stabilization of SSSP at low temperature. This weakening of hydrophobic interactions through stabilization of SSSP may play a key role in the cold denaturation of protein

Molecular Insight into the Adsorption of Spruce Budworm Antifreeze Protein to an Ice Surface: A Clathrate-Mediated Recognition Mechanism

The principal mechanism of ice recognition by antifreeze protein (AFP) has been a topic of intense discussion in recent times. Despite many experimental and theoretical studies, the detailed understanding of the process remains elusive. The present work aims to explore the molecular mechanism of ice recognition by an insect AFP from the spruce budworm, <i>sbw</i>AFP. As evident from our simulation, the water dynamics becomes very sluggish around the ice binding surface (IBS) as a result of the combined effect of confinement and ordering induced by the perfectly aligned methyl side chains of threonine residues, the THR ladder. The hydroxyl groups of threonine form strong hydrogen bonds with few of those highly ordered water molecules that are close to the THR ladder, which is the origin of anchored clathrate water at the IBS of <i>sbw</i>AFP. We propose anchored clathrate-mediated basal plane recognition by <i>sbw</i>AFP. The AFP adsorbed on the basal plane through water clathrate framed around the IBS. The surface of the basal plane and anchored clathrate water completes the caging around the threonine residues, which is the origin of the binding plane specificity of <i>sbw</i>AFP. This adsorbed AFP-ice complex undergoes dynamic crossover to a hydrogen-bonded complex within the thermal hysteresis (TH) regime of this particular AFP. The anchored clathrate water becomes part of the newly grown basal front as a result of the geometrical matches between the basal plane and the anchored clathrate water repeat distance. This observation provides a structural rationale for the experimentally observed time-dependent increase in TH activity for insect AFP. Our study proposes clathrate-mediated ice recognition by AFP and elucidates the dynamic events involved during ice binding by the insect AFP

Structural adaptation of the trailing head signals faster ADP release.

<p>(A) Myosin MH domain structure showing the big (red) and small (green) subunits. (B) Nucleotide binding region of the MH domain is shown in terms of P-loop (blue), switch I (red) and switch II (green). (C) RMSD distribution (P(RMSD)) of the small subunit of the MH domain after least square fitting of the big subunit from the leading and trailing head simulations. The RMSD is calculated with respect to the pre-powerstroke MH conformation. Note the larger RMSD for the trailing head indicating substantial structural changes. (D) Distribution of distances between P-loop and switch I (P(d_SWI-Ploop)) for the leading and trailing head simulations. (E) Distribution of distances between P-loop and switch II (P(d_SWII-Ploop)) for the leading and trailing head simulations. (F) Distribution of distances between switch I and switch II (P(d_SWI-SWII)) for the leading and trailing head simulations. A larger distance between switch I and switch II for the trailing head simulation compared to leading head signals faster ADP release.</p

Powerstroke of the myosin motors.

<p>(A) Powerstroke step with the release of P_i. The residues involved in the P_i mediated interactions in terms of p-loop (blue), switch I (red) and switch II (green) are shown. (B) RMSD (with respect to pre-powerstroke crystal structure) distribution for the simulation with P_i mediated interaction. The population of the pre-powerstroke ensemble is higher. (C) RMSD (with respect to pre-powerstroke crystal structure) distribution for the simulation without P_i mediated interactions. Note the inversion of the distribution with phosphate release making post-powerstroke ensemble as the dominant one.</p

Strain regulates the ADP release kinetics of the trailing head.

<p>(A) A schematic representation of myosin dimer showing how P_i release can create strain on the trailing head. This strain arises due to the postponed-powerstroke waiting state of the leading head (left head). (B) Probability distribution of distances between small and big subunits of the MH domain at different level of strain on the trailing head. This distribution shifts towards the larger distances as strain increases, which leads to an increase in ADP release rate with increasing strain.</p

Functional cycle of single- and double-headed myosin.

<p>(A) Sequence of events of the mechanochemical cycle of the single-headed myosin. ATP bound (red) head (i) binds to the actin filament followed by the hydrolysis of ATP. The arm (black line on head) of this actin bound head (ii) in ADP + P_i state (pink) has a pre-powerstroke conformation. Phosphate (P_i) release induces the powerstroke conformational change to the lever arm (iii). Next, ADP (blue) is released from the bound head while keeping the post-powerstroke lever arm conformation (iv). Finally, the empty head (gray) detaches from the actin followed by an ATP intake. The ATP dependent unbound head experiences a repriming event to its stable pre-powerstroke lever arm conformation (v). Note that, state (v) is exactly same as state (i) with an additional stepping towards left and also the nucleotide dependent actin binding affinity information in the middle. (B) The sequence of events of the functional cycle of the double-headed myosin. In state (i), head 1 is in an ATP bound state and head 2 is bound to actin in an ADP state. ATP hydrolysis and subsequent binding to actin by head 1 provide a two-head bound myosin (ii). Head 1 releases phosphate (P_i) to transform into state (iii). In contrary to a single-head myosin, here, after P_i release, head 1 cannot perform powerstroke while head 2 is still bound. The green line shows the expected lever arm conformation of head 1. It is important to note here that the two-head-bound state iii could adopt an alternative conformation with the converters of both heads in a post-powerstroke conformation while the lever arm of the leading/trailing head bends backward/forward. Next, ADP releases from head 2 (iv) and subsequently ATP binds to the empty head. Head 2 now detaches from the actin and head 1 now performs its postponed powerstroke step. Finally, head 2 also perform its spontaneous repriming event to form state (v). Note that, state (v) is exactly same as state (i) with an additional stepping towards the left.</p

Two important conformational states of the mechanical cycle of myosin.

<p>(A) Pre- (PDB 2V26 [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005035#pcbi.1005035.ref034" target="_blank">34</a>]) and post-powerstroke (PDB 2BHK [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005035#pcbi.1005035.ref036" target="_blank">36</a>]) states of the myosin motor showing the motor head (MH) and the converter domains. Note the change in the conformation of the converter domain with respect to the MH in the two conformations. The competing interactions (contacts) between the MH and the converter domains, responsible for stabilizing these two states, are shown by lines. (B) Residue-residue contact map for both the conformations. The two dotted green lines are drawn to separate the contact maps of the MH and the converter domains. In the upper triangle, the post-powerstroke contact map (red) is overlaid upon the pre-powerstroke contact map (blue) to identify the exclusive converter-MH contacts in the pre-powerstroke state (shown by lines in Fig 2A). In contrast, the same data have been overlaid in opposite order (blue upon red) in the lower triangle to extract the exclusive converter-MH contacts in the post-powerstroke state (those interactions are shown by lines in Fig 2A).</p

Correlation between symmetric-asymmetric transition and fluctuation at NT binding region.

<p>(a) Head-stalk contact region and NT binding pocket in Ncd motor are marked on the Ncd structure. (b) Disruption of the head-stalk contact induces disruption of NT binding pocket. Shaded in grey are the anti-correlated signals between the number of head-stalk contacts and the RMSD of NT binding pocket. (c) Different elements of NT binding pocket region in Ncd motor are marked: P-loop (orange), switch I (red) and switch II (yellow). Structural differences of these motifs are compared between the two states. For symmetric state, we use blue color for all elements. Switch I region reveals maximum deformation. (d) RMSD distribution of P-loop, switch I and switch II are shown for both the states. Note the noticeable difference for switch I region.</p

Dynamics between symmetric and asymmetric states of Ncd in solution.

<p>(a) Distribution of the inter-residue distance between E567 of the two monomers calculated from simulation show two peaks corresponding to the symmetric and asymmetric states with representative Ncd structures for each peak position. (b) Two dimensional free energy diagram color-coded in <i>k</i>_B<i>T</i> unit. Energetically possible transitions are between symmetric and one of the two asymmetric states (A or B). (c) Low frequency modes from PCA lend support to the distortion dynamics that drives the Ncd dimer from its symmetric to its asymmetric state. Residue-wise vector represents one of the two low frequency modes.</p