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Kozlov AG, Weiland E, Mittal A, Waldman V, Antony E, Fazio N, Pappu RV, Lohman TM. Intrinsically disordered C-terminal tails of E. coli single-stranded DNA binding protein regulate cooperative binding to single-stranded DNA. J Mol Biol 2015; 427:763-774. [PMID: 25562210 DOI: 10.1016/j.jmb.2014.12.020] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/05/2014] [Accepted: 12/23/2014] [Indexed: 12/27/2022]
Abstract
The homotetrameric Escherichia coli single-stranded DNA binding protein (SSB) plays a central role in DNA replication, repair and recombination. E. coli SSB can bind to long single-stranded DNA (ssDNA) in multiple binding modes using all four subunits [(SSB)65 mode] or only two subunits [(SSB)35 binding mode], with the binding mode preference regulated by salt concentration and SSB binding density. These binding modes display very different ssDNA binding properties with the (SSB)35 mode displaying highly cooperative binding to ssDNA. SSB tetramers also bind an array of partner proteins, recruiting them to their sites of action. This is achieved through interactions with the last 9 amino acids (acidic tip) of the intrinsically disordered linkers (IDLs) within the four C-terminal tails connected to the ssDNA binding domains. Here, we show that the amino acid composition and length of the IDL affects the ssDNA binding mode preferences of SSB protein. Surprisingly, the number of IDLs and the lengths of individual IDLs together with the acidic tip contribute to highly cooperative binding in the (SSB)35 binding mode. Hydrodynamic studies and atomistic simulations suggest that the E. coli SSB IDLs show a preference for forming an ensemble of globular conformations, whereas the IDL from Plasmodium falciparum SSB forms an ensemble of more extended random coils. The more globular conformations correlate with cooperative binding.
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Affiliation(s)
- Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Elizabeth Weiland
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Anuradha Mittal
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Vince Waldman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Edwin Antony
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, USA
| | - Nicole Fazio
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA.
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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Kann ZR, Skinner JL. A scaled-ionic-charge simulation model that reproduces enhanced and suppressed water diffusion in aqueous salt solutions. J Chem Phys 2014; 141:104507. [DOI: 10.1063/1.4894500] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Z. R. Kann
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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53
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Mittal A, Lyle N, Harmon TS, Pappu RV. Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins. J Chem Theory Comput 2014; 10:3550-3562. [PMID: 25136274 PMCID: PMC4132852 DOI: 10.1021/ct5002297] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Indexed: 02/06/2023]
Abstract
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There
is growing interest in the topic of intrinsically disordered
proteins (IDPs). Atomistic Metropolis Monte Carlo (MMC) simulations
based on novel implicit solvation models have yielded useful insights
regarding sequence-ensemble relationships for IDPs modeled as autonomous
units. However, a majority of naturally occurring IDPs are tethered
to ordered domains. Tethering introduces additional energy scales
and this creates the challenge of broken ergodicity for standard MMC
sampling or molecular dynamics that cannot be readily alleviated by
using generalized tempering methods. We have designed, deployed, and
tested our adaptation of the Nested Markov Chain Monte Carlo sampling
algorithm. We refer to our adaptation as Hamiltonian Switch Metropolis
Monte Carlo (HS-MMC) sampling. In this method, transitions out of
energetic traps are enabled by the introduction of an auxiliary Markov
chain that draws conformations for the disordered region from a Boltzmann
distribution that is governed by an alternative potential function
that only includes short-range steric repulsions and conformational
restraints on the ordered domain. We show using multiple, independent
runs that the HS-MMC method yields conformational distributions that
have similar and reproducible statistical properties, which is in
direct contrast to standard MMC for equivalent amounts of sampling.
The method is efficient and can be deployed for simulations of a range
of biologically relevant disordered regions that are tethered to ordered
domains.
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Affiliation(s)
- Anuradha Mittal
- Department of Biomedical Engineering and Center for Biological Systems Engineering and Department of Physics, Washington University in St. Louis One Brookings Drive , Campus Box 1097, St. Louis, Missouri 63130, United States
| | - Nicholas Lyle
- Department of Biomedical Engineering and Center for Biological Systems Engineering and Department of Physics, Washington University in St. Louis One Brookings Drive , Campus Box 1097, St. Louis, Missouri 63130, United States
| | - Tyler S Harmon
- Department of Biomedical Engineering and Center for Biological Systems Engineering and Department of Physics, Washington University in St. Louis One Brookings Drive , Campus Box 1097, St. Louis, Missouri 63130, United States
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering and Department of Physics, Washington University in St. Louis One Brookings Drive , Campus Box 1097, St. Louis, Missouri 63130, United States
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54
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Aragones JL, Rovere M, Vega C, Gallo P. Computer Simulation Study of the Structure of LiCl Aqueous Solutions: Test of Non-Standard Mixing Rules in the Ion Interaction. J Phys Chem B 2014; 118:7680-91. [DOI: 10.1021/jp500937h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Juan L. Aragones
- Dipartimento
di Matematica e Fisica, Università Roma Tre, Via della Vasca
Navale 84, 00146 Roma, Italy
- Departamento
de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Mauro Rovere
- Dipartimento
di Matematica e Fisica, Università Roma Tre, Via della Vasca
Navale 84, 00146 Roma, Italy
| | - Carlos Vega
- Departamento
de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Paola Gallo
- Dipartimento
di Matematica e Fisica, Università Roma Tre, Via della Vasca
Navale 84, 00146 Roma, Italy
- INFN Roma Tre, Via della Vasca
Navale 84, 00146 Roma, Italy
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55
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Lyle N, Das RK, Pappu RV. A quantitative measure for protein conformational heterogeneity. J Chem Phys 2014; 139:121907. [PMID: 24089719 DOI: 10.1063/1.4812791] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Conformational heterogeneity is a defining characteristic of proteins. Intrinsically disordered proteins (IDPs) and denatured state ensembles are extreme manifestations of this heterogeneity. Inferences regarding globule versus coil formation can be drawn from analysis of polymeric properties such as average size, shape, and density fluctuations. Here we introduce a new parameter to quantify the degree of conformational heterogeneity within an ensemble to complement polymeric descriptors. The design of this parameter is guided by the need to distinguish between systems that couple their unfolding-folding transitions with coil-to-globule transitions and those systems that undergo coil-to-globule transitions with no evidence of acquiring a homogeneous ensemble of conformations upon collapse. The approach is as follows: Each conformation in an ensemble is converted into a conformational vector where the elements are inter-residue distances. Similarity between pairs of conformations is quantified using the projection between the corresponding conformational vectors. An ensemble of conformations yields a distribution of pairwise projections, which is converted into a distribution of pairwise conformational dissimilarities. The first moment of this dissimilarity distribution is normalized against the first moment of the distribution obtained by comparing conformations from the ensemble of interest to conformations drawn from a Flory random coil model. The latter sets an upper bound on conformational heterogeneity thus ensuring that the proposed measure for intra-ensemble heterogeneity is properly calibrated and can be used to compare ensembles for different sequences and across different temperatures. The new measure of conformational heterogeneity will be useful in quantitative studies of coupled folding and binding of IDPs and in de novo sequence design efforts that are geared toward controlling the degree of heterogeneity in unbound forms of IDPs.
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Affiliation(s)
- Nicholas Lyle
- Computational and Systems Biology Program, Division of Biology and Biomedical Sciences, Washington University in St. Louis, One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130, USA
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