Dataset Information

A Unified Walking Model for Dimeric Motor Proteins.

ABSTRACT: Dimeric motor proteins, kinesin-1, cytoplasmic dynein-1, and myosin-V, move stepwise along microtubules and actin filaments with a regular step size. The motors take backward as well as forward steps. The step ratio r and dwell time ?, which are the ratio of the number of backward steps to the number of forward steps and the time between consecutive steps, respectively, were observed to change with the load. To understand the movement of motor proteins, we constructed a unified and simple mathematical model to explain the load dependencies of r and of ? measured for the above three types of motors quantitatively. Our model consists of three states, and the forward and backward steps are represented by the cycles of transitions visiting different pairs of states among the three, implying that a backward step is not the reversal of a forward step. Each of r and ? is given by a simple expression containing two exponential functions. The experimental data for r and ? for dynein available in the literature are not sufficient for a quantitative analysis, which is in contrast to those for kinesin and myosin-V. We reanalyze the data to obtain r and ? of native dynein to make up the insufficient data to fit them to the model. Our model successfully describes the behavior of r and ? for all of the motors in a wide range of loads from large assisting loads to superstall loads.

SUBMITTER: Sasaki K

PROVIDER: S-EPMC6303276 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Publications

A Unified Walking Model for Dimeric Motor Proteins.

Sasaki Kazuo K Kaya Motoshi M Higuchi Hideo H

Biophysical journal 20181016 10

Dimeric motor proteins, kinesin-1, cytoplasmic dynein-1, and myosin-V, move stepwise along microtubules and actin filaments with a regular step size. The motors take backward as well as forward steps. The step ratio r and dwell time τ, which are the ratio of the number of backward steps to the number of forward steps and the time between consecutive steps, respectively, were observed to change with the load. To understand the movement of motor proteins, we constructed a unified and simple mathem ...[more]

PMID: 30396511

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Project description:The concept of hydrophobicity is critical to our understanding of the principles of membrane protein (MP) folding, structure, and function. In the last decades, several groups have derived hydrophobicity scales using both experimental and statistical methods that are optimized to mimic certain natural phenomena as closely as possible. The present work adds to this toolset the first knowledge-based scale that unifies the characteristics of both alpha-helical and beta-barrel multispan MPs. This unified hydrophobicity scale (UHS) distinguishes between amino acid preference for solution, transition, and trans-membrane states. The scale represents average hydrophobicity values of amino acids in folded proteins, irrespective of their secondary structure type. We furthermore present the first knowledge-based hydrophobicity scale for mammalian alpha-helical MPs (mammalian hydrophobicity scale--MHS). Both scales are particularly useful for computational protein structure elucidation, for example as input for machine learning techniques, such as secondary structure or trans-membrane span prediction, or as reference energies for protein structure prediction or protein design. The knowledge-based UHS shows a striking similarity to a recent experimental hydrophobicity scale introduced by Hessa and coworkers (Hessa T et al., Nature 2007;450:U1026-U1032). Convergence of two very different approaches onto similar hydrophobicity values consolidates the major differences between experimental and knowledge-based scales observed in earlier studies. Moreover, the UHS scale represents an accurate absolute free energy measure for folded, multispan MPs--a feature that is absent from many existing scales. The utility of the UHS was demonstrated by analyzing a series of diverse MPs. It is further shown that the UHS outperforms nine established hydrophobicity scales in predicting trans-membrane spans along the protein sequence. The accuracy of the present hydrophobicity scale profits from the doubling of the number of integral MPs in the PDB over the past four years. The UHS paves the way for an increased accuracy in the prediction of trans-membrane spans.

Dataset Information

A Unified Walking Model for Dimeric Motor Proteins.

Publications

A Unified Walking Model for Dimeric Motor Proteins.

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