Thirumalai, D. ; Lee, Y. ; Hyeon, C. Ultrasensitivity of water exchange kinetics to the size of metal ion. Journal of the American Chemical Society 2017, 139, 12334-12337. Publisher's Version ultrasensitivity-of-water-exchange-kinetics-to-the-size-of-metal-ion.pdf
Thirumalai, D. ; Suvlu, D. ; Samaratunga, S. ; Rasaiah, J. Thermodynamics of Helix–Coil Transitions of Polyalanine in Open Carbon Nanotubes. The Journal of Physical Chemistry Letters 2017, 8 494-499. Publisher's Version thermodynamics-of-helix-coil-transitions-of-polyalanine-in-open-carbon-nanotubes.pdf
Thirumalai, D. ; Hyeon, C. Ripping RNA by force using Gaussian Network Models. The Journal of Physical Chemistry B 2017, 121, 3515-3522. Publisher's Version ripping-rna-by-force-using-gaussian-network-models.pdf
Thirumalai, D. ; Reddy, G. Collapse precedes folding in denaturant-dependent assembly of ubiquitin. The Journal of Physical Chemistry B 2017, 121, 995-2009. Publisher's Version collapse-precedes-folding-in-denaturant-assembly-of-ubiquitin.pdf
Thirumalai, D. ; Shi, G. Chromatin is stretched but intact when the nucleus is squeezed through constrictions. Biophysical Journal 2017, 112, 411-412. Publisher's Version chromatin-is-stretched-but-intact-when-the-nucleus-is-squeezed-through-constrictions.pdf
Thirumalai, D. ; Chakraborti, S. ; Hinczewski, M. Phenomenological and microscopic theories for catch bonds. Journal of Structural Biology 2017, 197, 50-56. Publisher's Version phenomenological-and-microscopic-theories-for-catch-bonds.pdf
Mugnai, M. L. ; Thirumalai, D. Kinematics of the lever arm swing in myosin VI. Proc Natl Acad Sci U S A 2017, 114, E4389–E4398. DOI:10.1073/pnas.1615708114Abstract

Myosin VI (MVI) is the only known member of the myosin superfamily that, upon dimerization, walks processively toward the pointed end of the actin filament. The leading head of the dimer directs the trailing head forward with a power stroke, a conformational change of the motor domain exaggerated by the lever arm. Using a unique coarse-grained model for the power stroke of a single MVI, we provide the molecular basis for its motility. We show that the power stroke occurs in two major steps. First, the motor domain attains the poststroke conformation without directing the lever arm forward; and second, the lever arm reaches the poststroke orientation by undergoing a rotational diffusion. From the analysis of the trajectories, we discover that the potential that directs the rotating lever arm toward the poststroke conformation is almost flat, implying that the lever arm rotation is mostly uncoupled from the motor domain. Because a backward load comparable to the largest interhead tension in a MVI dimer prevents the rotation of the lever arm, our model suggests that the leading-head lever arm of a MVI dimer is uncoupled, in accord with the inference drawn from polarized total internal reflection fluorescence (polTIRF) experiments. Without any adjustable parameter, our simulations lead to quantitative agreement with polTIRF experiments, which validates the structural insights. Finally, in addition to making testable predictions, we also discuss the implications of our model in explaining the broad step-size distribution of the MVI stepping pattern.

Samanta, H. S. ; Hinczewski, M. ; Thirumalai, D. Optimal information transfer in enzymatic networks: A field theoretic formulation. Phys Rev E 2017, 96, 012406. DOI:10.1103/PhysRevE.96.012406Abstract

Signaling in enzymatic networks is typically triggered by environmental fluctuations, resulting in a series of stochastic chemical reactions, leading to corruption of the signal by noise. For example, information flow is initiated by binding of extracellular ligands to receptors, which is transmitted through a cascade involving kinase-phosphatase stochastic chemical reactions. For a class of such networks, we develop a general field-theoretic approach to calculate the error in signal transmission as a function of an appropriate control variable. Application of the theory to a simple push-pull network, a module in the kinase-phosphatase cascade, recovers the exact results for error in signal transmission previously obtained using umbral calculus [Hinczewski and Thirumalai, Phys. Rev. X 4, 041017 (2014)]. We illustrate the generality of the theory by studying the minimal errors in noise reduction in a reaction cascade with two connected push-pull modules. Such a cascade behaves as an effective three-species network with a pseudointermediate. In this case, optimal information transfer, resulting in the smallest square of the error between the input and output, occurs with a time delay, which is given by the inverse of the decay rate of the pseudointermediate. Surprisingly, in these examples the minimum error computed using simulations that take nonlinearities and discrete nature of molecules into account coincides with the predictions of a linear theory. In contrast, there are substantial deviations between simulations and predictions of the linear theory in error in signal propagation in an enzymatic push-pull network for a certain range of parameters. Inclusion of second-order perturbative corrections shows that differences between simulations and theoretical predictions are minimized. Our study establishes that a field theoretic formulation of stochastic biological signaling offers a systematic way to understand error propagation in networks of arbitrary complexity.

Samanta, H. S. ; Zhuravlev, P. I. ; Hinczewski, M. ; Hori, N. ; Chakrabarti, S. ; Thirumalai, D. Protein collapse is encoded in the folded state architecture. Soft Matter 2017, 13, 3622-3638. DOI:10.1039/C7SM00074JAbstract

Folded states of single domain globular proteins are compact with high packing density. The radius of gyration, Rg, of both the folded and unfolded states increase as Nν where N is the number of amino acids in the protein. The values of the Flory exponent ν are, respectively, ≈⅓ and ≈0.6 in the folded and unfolded states, coinciding with those for homopolymers. However, the extent of compaction of the unfolded state of a protein under low denaturant concentration (collapsibility), conditions favoring the formation of the folded state, is unknown. We develop a theory that uses the contact map of proteins as input to quantitatively assess collapsibility of proteins. Although collapsibility is universal, the propensity to be compact depends on the protein architecture. Application of the theory to over two thousand proteins shows that collapsibility depends not only on N but also on the contact map reflecting the native structure. A major prediction of the theory is that β-sheet proteins are far more collapsible than structures dominated by α-helices. The theory and the accompanying simulations, validating the theoretical predictions, provide insights into the differing conclusions reached using different experimental probes assessing the extent of compaction of proteins. By calculating the criterion for collapsibility as a function of protein length we provide quantitative insights into the reasons why single domain proteins are small and the physical reasons for the origin of multi-domain proteins. Collapsibility of non-coding RNA molecules is similar β-sheet proteins structures adding support to “Compactness Selection Hypothesis”.

Vu, H. T. ; Chakrabarti, S. ; Hinczewski, M. ; Thirumalai, D. Discrete Step Sizes of Molecular Motors Lead to Bimodal Non-Gaussian Velocity Distributions under Force. Phys. Rev. Lett. 2016, 117, 078101. DOI:10.1103/PhysRevLett.117.078101Abstract

Fluctuations in the physical properties of biological machines are inextricably linked to their functions. Distributions of run lengths and velocities of processive molecular motors, like kinesin-1, are accessible through single-molecule techniques, but rigorous theoretical models for these probabilities are lacking. Here, we derive exact analytic results for a kinetic model to predict the resistive force (F)-dependent velocity [P(v)] and run length [P(n)] distribution functions of generic finitely processive molecular motors. Our theory quantitatively explains the zero force kinesin-1 data for both P(n) and P(v) using the detachment rate as the only parameter. In addition, we predict the F dependence of these quantities. At nonzero FP(v) is non-Gaussian and is bimodal with peaks at positive and negative values of v, which is due to the discrete step size of kinesin-1. Although the predictions are based on analyses of kinesin-1 data, our results are general and should hold for any processive motor, which walks on a track by taking discrete steps.

Hinczewski, M. ; Hyeon, C. ; Thirumalai, D. Directly measuring single-molecule heterogeneity using force spectroscopy. Proc Natl Acad Sci U S A 2016, 113, E3852-61.Abstract
One of the most intriguing results of single-molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Although we now have proof of functional heterogeneity in a handful of systems-enzymes, motors, adhesion complexes-identifying and measuring it remains a formidable challenge. Here, we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single-molecule techniques: atomic force microscopy or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This results in a single parameter, quantifying the degree of heterogeneity, and also leads to bounds on the equilibration and conformational interconversion timescales. Surveying 10 published datasets, we find heterogeneity in 5 of them, all with interconversion rates slower than 10 s(-1) Moreover, we identify two systems where additional data at realizable pulling velocities is likely to find a theoretically predicted, but so far unobserved crossover regime between heterogeneous and nonheterogeneous behavior. The significance of this regime is that it will allow far more precise estimates of the slow conformational switching times, one of the least understood aspects of functional heterogeneity.
Liu, Z. ; Reddy, G. ; Thirumalai, D. Folding PDZ2 Domain Using the Molecular Transfer Model. J Phys Chem B 2016. folding-pdz2-domain-using-the-molecular-transfer-model.pdf
Zhuravlev, P. I. ; Hinczewski, M. ; Chakrabarti, S. ; Marqusee, S. ; Thirumalai, D. Force-dependent switch in protein unfolding pathways and transition-state movements. Proc Natl Acad Sci U S A 2016, 113, E715-24.Abstract
Although it is known that single-domain proteins fold and unfold by parallel pathways, demonstration of this expectation has been difficult to establish in experiments. Unfolding rate, [Formula: see text], as a function of force f, obtained in single-molecule pulling experiments on src SH3 domain, exhibits upward curvature on a [Formula: see text] plot. Similar observations were reported for other proteins for the unfolding rate [Formula: see text]. These findings imply unfolding in these single-domain proteins involves a switch in the pathway as f or [Formula: see text] is increased from a low to a high value. We provide a unified theory demonstrating that if [Formula: see text] as a function of a perturbation (f or [Formula: see text]) exhibits upward curvature then the underlying energy landscape must be strongly multidimensional. Using molecular simulations we provide a structural basis for the switch in the pathways and dramatic shifts in the transition-state ensemble (TSE) in src SH3 domain as f is increased. We show that a single-point mutation shifts the upward curvature in [Formula: see text] to a lower force, thus establishing the malleability of the underlying folding landscape. Our theory, applicable to any perturbation that affects the free energy of the protein linearly, readily explains movement in the TSE in a β-sandwich (I27) protein and single-chain monellin as the denaturant concentration is varied. We predict that in the force range accessible in laser optical tweezer experiments there should be a switch in the unfolding pathways in I27 or its mutants.
Goldtzvik, Y. ; Zhang, Z. ; Thirumalai, D. Importance of Hydrodynamic Interactions in the Stepping Kinetics of Kinesin. J Phys Chem B 2016, 120, 2071-5.Abstract
Conventional kinesin walks by a hand-over-hand mechanism on the microtubule (MT) by taking ∼8 nm discrete steps and consumes one ATP molecule per step. The time needed to complete a single step is on the order of 20 μs. We show, using simulations of a coarse-grained model of the complex containing the two motor heads, the MT and the coiled coil, that to obtain quantitative agreement with experiments for the stepping kinetics hydrodynamic interactions (HIs) have to be included. In simulations without hydrodynamic interactions, spanning nearly 20 μs, not a single step was completed in one hundred trajectories. In sharp contrast, nearly 14% of the steps reached the target binding site within 6 μs when HIs were included. Somewhat surprisingly, there are qualitative differences in the diffusion pathways in simulations with and without HI. The extent of movement of the trailing head of kinesin on the MT during the diffusion stage of stepping is considerably greater in simulations with HI than in those without HI. It is likely that inclusion of HI is crucial in the accurate description of motility of other motors as well.
Hinczewski, M. ; Thirumalai, D. Noise Control in Gene Regulatory Networks with Negative Feedback. J Phys Chem B 2016, 120, 6166-77.Abstract
Genes and proteins regulate cellular functions through complex circuits of biochemical reactions. Fluctuations in the components of these regulatory networks result in noise that invariably corrupts the signal, possibly compromising function. Here, we create a practical formalism based on ideas introduced by Wiener and Kolmogorov (WK) for filtering noise in engineered communications systems to quantitatively assess the extent to which noise can be controlled in biological processes involving negative feedback. Application of the theory, which reproduces the previously proven scaling of the lower bound for noise suppression in terms of the number of signaling events, shows that a tetracycline repressor-based negative-regulatory gene circuit behaves as a WK filter. For the class of Hill-like nonlinear regulatory functions, this type of filter provides the optimal reduction in noise. Our theoretical approach can be readily combined with experimental measurements of response functions in a wide variety of genetic circuits, to elucidate the general principles by which biological networks minimize noise.
Chakrabarti, S. ; Hinczewski, M. ; Thirumalai, D. Phenomenological and microscopic theories for catch bonds. J Struct Biol 2016.Abstract
Lifetimes of bound states of protein complexes or biomolecule folded states typically decrease when subject to mechanical force. However, a plethora of biological systems exhibit the counter-intuitive phenomenon of catch bonding, where non-covalent bonds become stronger under externally applied forces. The quest to understand the origin of catch-bond behavior has led to the development of phenomenological and microscopic theories that can quantitatively recapitulate experimental data. Here, we assess the successes and limitations of such theories in explaining experimental data. The most widely applied approach is a phenomenological two-state model, which fits all of the available data on a variety of complexes: actomyosin, kinetochore-microtubule, selectin-ligand, and cadherin-catenin binding to filamentous actin. With a primary focus on the selectin family of cell-adhesion complexes, we discuss the positives and negatives of phenomenological models and the importance of evaluating the physical relevance of fitting parameters. We describe a microscopic theory for selectins, which provides a structural basis for catch bonds and predicts a crucial allosteric role for residues Asn82-Glu88. We emphasize the need for new theories and simulations that can mimic experimental conditions, given the complex response of cell adhesion complexes to force and their potential role in a variety of biological contexts.
Zhuravlev, P. I. ; Hinczewski, M. ; Chakrabarti, S. ; Marqusee, S. ; Thirumalai, D. Reply to Alberti: Are in vitro folding experiments relevant in vivo?. Proc Natl Acad Sci U S A 2016, 113, E3192. reply-to-alberti-are-in-vitro-folding-experiments-relevant-in-vivo.pdf
Hori, N. ; Denesyuk, N. A. ; Thirumalai, D. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension. J Mol Biol 2016, 428, 2847-59. DOI:10.1016/j.jmb.2016.06.002Abstract

Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single-molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed ribosomal frameshifting. Motivated in part by these experiments, we performed simulations using a coarse-grained model of RNA to describe the response of a PK over a range of mechanical forces (fs) and monovalent salt concentrations (Cs). The coarse-grained simulations quantitatively reproduce the multistep thermal melting observed in experiments, thus validating our model. The free energy changes obtained in simulations are in excellent agreement with experiments. By varying f and C, we calculated the phase diagram that shows a sequence of structural transitions, populating distinct intermediate states. As f and C are changed, the stem-loop tertiary interactions rupture first, followed by unfolding of the 3'-end hairpin (I⇌F). Finally, the 5'-end hairpin unravels, producing an extended state (E⇌I). A theoretical analysis of the phase boundaries shows that the critical force for rupture scales as (logCm)(α) with α=1(0.5) for E⇌I (I⇌F) transition. This relation is used to obtain the preferential ion-RNA interaction coefficient, which can be quantitatively measured in single-molecule experiments, as done previously for DNA hairpins. A by-product of our work is the suggestion that the frameshift efficiency is likely determined by the stability of the 5'-end hairpin that the ribosome first encounters during translation.

Thirumalai, D. 48 Design principles governing the motility of myosin motors. J Biomol Struct Dyn 2015, 33 Suppl 1, 33. 48-design-principles-governing-the-motility-of-myosin-motors.pdf
Kang, H. ; Yoon, Y. - G. ; Thirumalai, D. ; Hyeon, C. Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization. Phys Rev Lett 2015, 115, 198102.Abstract
Recent experiments showing scaling of the intrachromosomal contact probability, P(s)∼s(-1) with the genomic distance s, are interpreted to mean a self-similar fractal-like chromosome organization. However, scaling of P(s) varies across organisms, requiring an explanation. We illustrate dynamical arrest in a highly confined space as a discriminating marker for genome organization, by modeling chromosomes inside a nucleus as a homopolymer confined to a sphere of varying sizes. Brownian dynamics simulations show that the chain dynamics slows down as the polymer volume fraction (ϕ) inside the confinement approaches a critical value ϕ(c). The universal value of ϕ(c)(∞)≈0.44 for a sufficiently long polymer (N≫1) allows us to discuss genome dynamics using ϕ as the sole parameter. Our study shows that the onset of glassy dynamics is the reason for the segregated chromosome organization in humans (N≈3×10(9), ϕ≳ϕ(c)(∞)), whereas chromosomes of budding yeast (N≈10(8), ϕ<ϕ(c)(∞)) are equilibrated with no clear signature of such organization.