Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins

Hwang, Wonmuk,Karplus, Martin National Academy of Sciences 2019 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.116 No.40

<P>Two mechanisms have been proposed for the function of motor proteins: The power stroke and the Brownian ratchet. The former refers to generation of a large downhill free energy gradient over which the motor protein moves nearly irreversibly in making a step, whereas the latter refers to biasing or rectifying the diffusive motion of the motor. Both mechanisms require input of free energy, which generally involves the processing of an ATP (adenosine 5′-triphosphate) molecule. Recent advances in experiments that reveal the details of the stepping motion of motor proteins, together with computer simulations of atomistic structures, have provided greater insights into the mechanisms. Here, we compare the various models of the power stroke and the Brownian ratchet that have been proposed. The 2 mechanisms are not mutually exclusive, and various motor proteins employ them to different extents to perform their biological function. As examples, we discuss linear motor proteins Kinesin-1 and myosin-V, and the rotary motor F<SUB>1</SUB>-ATPase, all of which involve a power stroke as the essential element of their stepping mechanism.</P>

Nucleotide-dependent control of internal strains in ring-shaped AAA+ motors.

Hwang, Wonmuk,Lang, Matthew J SPRINGER SCIENCE + BUSINESS MEDIA 2013 Cellular and molecular bioengineering Vol.6 No.1

<P>The AAA+ (ATPase Associated with various cellular Activities) machinery represents an extremely successful and widely used design plan for biological motors. Recently found crystal structures are beginning to reveal nucleotide-dependent conformational changes in the canonical hexameric rings of the AAA+ motors. However, the physical mechanism by which ATP binding on one subunit allosterically propagates across the entire ring remains to be found. Here we analyze and compare structural organization of three ring-shaped AAA+ motors, ClpX, HslU, and dynein. By constructing multimers using subunits of identical conformations, we find that individual subunits locally possess helical geometries with varying pitch, radius, chirality, and symmetry number. These results suggest that binding of an ATP to a subunit imposes conformational constraint that must be accommodated by more flexible nucleotide-free subunits to relieve mechanical strain on the ring. Local deformation of the ring contour and subsequent propagation of strains may be a general strategy that AAA+ motors adopt to generate force while achieving functional diversity.</P>

Kinetic Signature of Fractal-like Filament Networks Formed by Orientational Linear Epitaxy

Hwang, Wonmuk,Eryilmaz, Esma American Physical Society 2014 Physical review letters Vol.113 No.2

<P>We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.</P>

Effect of Methylation on Local Mechanics and Hydration Structure of DNA

Teng, Xiaojing,Hwang, Wonmuk Published for the Biophysical Society by the Rocke 2018 Biophysical journal Vol.114 No.8

<P><B>Abstract</B></P> <P>Cytosine methylation affects mechanical properties of DNA and potentially alters the hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not well understood, and we address this via all-atom molecular dynamics simulations. We find that the stiffness of the methylated dinucleotide step changes marginally, whereas the neighboring steps become stiffer. Stiffening is further enhanced for consecutively methylated steps, providing a mechanistic origin for the effect of hypermethylation. Steric interactions between the added methyl groups and the nonpolar groups of the neighboring nucleotides are responsible for the stiffening in most cases. By constructing hydration maps, we found that methylation also alters the surface hydration structure in distinct ways. Its resistance to deformation may contribute to the stiffening of DNA for deformational modes lacking steric interactions. These results highlight the sequence- and deformational-mode-dependent effects of cytosine methylation.</P>

Chain Registry and Load-Dependent Conformational Dynamics of Collagen

Teng, Xiaojing,Hwang, Wonmuk American Chemical Society 2014 Biomacromolecules Vol.15 No.8

<P/><P>Degradation of fibrillar collagen is critical for tissue maintenance. Yet, understanding collagen catabolism has been challenging partly due to a lack of atomistic picture for its load-dependent conformational dynamics, as both mechanical load and local unfolding of collagen affect its cleavage by matrix metalloproteinase (MMP). We use molecular dynamics simulation to find the most cleavage-prone arrangement of α chains in a collagen triple helix and find amino acids that modulate stability of the MMP cleavage domain depending on the chain registry within the molecule. The native-like state is mechanically inhomogeneous, where the cleavage site interfaces a stiff region and a locally unfolded and flexible region along the molecule. In contrast, a triple helix made of the stable glycine-proline-hydroxyproline motif is uniformly flexible and is dynamically stabilized by short-lived, low-occupancy hydrogen bonds. These results provide an atomistic basis for the mechanics, conformation, and stability of collagen that affect catabolism.</P>

Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross- <i>β</i> Spine

Park, Jiyong,Kahng, Byungnam,Hwang, Wonmuk Public Library of Science 2009 PLoS computational biology Vol.5 No.9

<▼1><P>At the core of amyloid fibrils is the cross-<I>β</I> spine, a long tape of <I>β</I>-sheets formed by the constituent proteins. Recent high-resolution x-ray studies show that the unit of this filamentous structure is a <I>β</I>-sheet bilayer with side chains within the bilayer forming a tightly interdigitating “steric zipper” interface. However, for a given peptide, different bilayer patterns are possible, and no quantitative explanation exists regarding which pattern is selected or under what condition there can be more than one pattern observed, exhibiting molecular polymorphism. We address the structural selection mechanism by performing molecular dynamics simulations to calculate the free energy of incorporating a peptide monomer into a <I>β</I>-sheet bilayer. We test filaments formed by several types of peptides including GNNQQNY, NNQQ, VEALYL, KLVFFAE and STVIIE, and find that the patterns with the lowest binding free energy correspond to available atomistic structures with high accuracy. Molecular polymorphism, as exhibited by NNQQ, is likely because there are more than one most stable structures whose binding free energies differ by less than the thermal energy. Detailed analysis of individual energy terms reveals that these short peptides are not strained nor do they lose much conformational entropy upon incorporating into a <I>β</I>-sheet bilayer. The selection of a bilayer pattern is determined mainly by the van der Waals and hydrophobic forces as a quantitative measure of shape complementarity among side chains between the <I>β</I>-sheets. The requirement for self-complementary steric zipper formation supports that amyloid fibrils form more easily among similar or same sequences, and it also makes parallel <I>β</I>-sheets generally preferred over anti-parallel ones. But the presence of charged side chains appears to kinetically drive anti-parallel <I>β</I>-sheets to form at early stages of assembly, after which the bilayer formation is likely driven by energetics.</P></▼1><▼2><P><B>Author Summary</B></P><P>Accumulation of amyloid fibrils is a salient feature of various protein misfolding diseases. Recent advances in precision experiments have begun to reveal their atomistic structures. Quantitative elucidation of how the observed structures are selected over other possible filament patterns would provide much insight into the formation and properties of amyloid fibrils. Using computer simulations and structural modeling, we demonstrate that the most stable filament pattern corresponds to the experimentally observed structure, and molecular polymorphism, selection of two or more patterns, is possible when there are more than one most stable structures. Ability to predict the structure allows for more detailed analysis, so that, for example, we can identify the most important residue for stabilizing the structure that could be therapeutically targeted. Our analysis will be useful for comparing different amyloid structures formed by the same protein or when delineating roles of different intermolecular forces in filament formation.</P></▼2>

Role of mechanical flow for actin network organization

Kang, Byungjun,Jo, Seunghan,Baek, Jonghyeok,Nakamura, Fumihiko,Hwang, Wonmuk,Lee, Hyungsuk Elsevier 2019 ACTA BIOMATERIALIA Vol.90 No.-

<P><B>Abstract</B></P> <P>The major cytoskeletal protein actin forms complex networks to provide structural support and perform vital functions in cells. <I>In vitro</I> studies have revealed that the structure of the higher-order actin network is determined primarily by the type of actin binding protein (ABP). By comparison, there are far fewer studies about the role of the mechanical environment for the organization of the actin network. In particular, the duration over which cells reorganize their shape in response to functional demands is relatively short compared to the <I>in vitro</I> protein polymerization time, suggesting that such changes can influence the actin network formation. We hypothesize that mechanical flows in the cytoplasm generated by exogenous and endogenous stimulation play a key role in the spatiotemporal regulation of the actin architecture. To mimic cytoplasmic streaming, we generated a circulating flow using surface acoustic wave in a microfluidic channel and investigated its effect on the formation of networks by actin and ABPs. We found that the mechanical flow affected the orientation and thickness of actin bundles, depending on the type and concentration of ABPs. Our computational model shows that the extent of alignment and thickness of actin bundle are determined by the balance between flow-induced drag forces and the tendency of ABPs to crosslink actin filaments at given angles. These results suggest that local intracellular flows can affect the assembly dynamics and morphology of the actin cytoskeleton.</P> <P><B>Statement of Significance</B></P> <P>Spatiotemporal regulation of actin cytoskeleton structure is essential in many cellular functions. It has been shown that mechanical cues including an applied force and geometric boundary can alter the structural characteristics of actin network. However, even though the cytoplasm accounts for a large portion of the cell volume, the effect of the cytoplasmic streaming flow produced during cell dynamics on actin network organization has not been reported. In this study, we demonstrated that the mechanical flow exerted during actin network organization play an important role in determining the orientation and dimension of actin bundle network. Our result will be beneficial in understanding the mechanism of the actin network reorganization occurred during physiological and pathological processes.</P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Molecular Mechanisms of Tight Binding through Fuzzy Interactions

Shen, Qingliang,Shi, Jie,Zeng, Danyun,Zhao, Baoyu,Li, Pingwei,Hwang, Wonmuk,Cho, Jae-Hyun Elsevier 2018 Biophysical journal Vol.114 No.6

<P><B>Abstract</B></P> <P>Many intrinsically disordered proteins (IDPs) form fuzzy complexes upon binding to their targets. Although many IDPs are weakly bound in fuzzy complexes, some IDPs form high-affinity complexes. One example is the nonstructural protein 1 (NS1) of the 1918 Spanish influenza A virus, which hijacks cellular CRKII through the strong binding affinity (K<SUB>d</SUB> ∼10 nM) of its proline-rich motif (PRM<SUP>NS1</SUP>) to the N-terminal Src-homology 3 domain of CRKII. However, its molecular mechanism remains elusive. Here, we examine the interplay between structural disorder of a bound PRM<SUP>NS1</SUP> and its long-range electrostatic interactions. Using x-ray crystallography and NMR spectroscopy, we found that PRM<SUP>NS1</SUP> retains substantial conformational flexibility in the bound state. Moreover, molecular dynamics simulations showed that structural disorder of the bound PRM<SUP>NS1</SUP> increases the number of electrostatic interactions and decreases the mean distances between the positively charged residues in PRM<SUP>NS1</SUP> and the acidic residues in the N-terminal Src-homology 3 domain. These results are analyzed using a polyelectrostatic model. Our results provide an insight into the molecular recognition mechanism for a high-affinity fuzzy complex.</P>

Electric field-induced reversible trapping of microtubules along metallic glass microwire electrodes

Kim, Kyongwan,Sikora, Auré,lien,Nakayama, Koji S.,Umetsu, Mitsuo,Hwang, Wonmuk,Teizer, Winfried American Institute of Physics 2015 JOURNAL OF APPLIED PHYSICS - Vol.117 No.14

Behavior of Kinesin Driven Quantum Dots Trapped in a Microtubule Loop

Sikora, Auré,lien,Canova, Filippo Federici,Kim, Kyongwan,Nakazawa, Hikaru,Umetsu, Mitsuo,Kumagai, Izumi,Adschiri, Tadafumi,Hwang, Wonmuk,Teizer, Winfried AMERICAN CHEMICAL SOCIETY 2015 ACS NANO Vol.9 No.11