1
|
Comer J, Aksimentiev A. Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2012; 116:3376-3393. [PMID: 22606364 PMCID: PMC3350822 DOI: 10.1021/jp210641j] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current, and validate this result with all-atom molecular dynamics.
Collapse
Affiliation(s)
- Jeffrey Comer
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
2
|
Carr R, Comer JR, Ginsberg MD, Aksimentiev A. Atoms-to-microns model for small solute transport through sticky nanochannels. LAB ON A CHIP 2011; 11:3766-73. [PMID: 21986816 PMCID: PMC3349904 DOI: 10.1039/c1lc20697d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Modeling the transport of solutes through fluidic systems that have adsorbing surfaces is challenging due to the range of length and time scales involved. The components of such systems typically have dimensions from hundreds of nanometres to microns, whereas adsorption of solutes is sensitive to the atomic-scale structure of the solutes and surfaces. Here, we describe an atomic-resolution Brownian dynamics method for modeling the transport of solutes through sticky nanofluidic channels. Our method can fully recreate the results of all-atom molecular dynamics simulations at a fraction of the computational cost of the latter, which makes simulations of micron-size channels at a millisecond time scale possible without losing information about the atomic-scale features of the system. We demonstrate the capability of our method by simulating the rise and fall of solute concentration in sub-micron-long sticky nanochannels, showing that the atomic-scale features of the channels' surfaces have a dramatic effect on the kinetics of solute transport in and out of the channels. We expect our method to find applications in design and optimization of micro and nanofluidic systems for solute-specific transport and to complement existing approaches to modeling lab-on-a-chip devices by providing atomic scale information at a low computational cost.
Collapse
Affiliation(s)
- Rogan Carr
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, Illinois 61801, USA. Tel: 1 217 333 6495
| | - Jeffrey R. Comer
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, Illinois 61801, USA. Tel: 1 217 333 6495
| | | | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, Illinois 61801, USA. Tel: 1 217 333 6495
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, IL, USA
| |
Collapse
|
3
|
Gopalakrishnan R, Thajudeen T, Hogan CJ. Collision limited reaction rates for arbitrarily shaped particles across the entire diffusive Knudsen number range. J Chem Phys 2011; 135:054302. [DOI: 10.1063/1.3617251] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
4
|
Botti H, Möller MN, Steinmann D, Nauser T, Koppenol WH, Denicola A, Radi R. Distance-dependent diffusion-controlled reaction of •NO and O2•- at chemical equilibrium with ONOO-. J Phys Chem B 2010; 114:16584-93. [PMID: 21067212 DOI: 10.1021/jp105606b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fast reaction of (•)NO and O(2)(•-) to give ONOO(-) has been extensively studied at irreversible conditions, but the reasons for the wide variations in observed forward rate constants (3.8 ≤ k(f) ≤ 20 × 10(9) M(-1) s(-1)) remain unexplained. We characterized the diffusion-dependent aqueous (pH > 12) chemical equilibrium of the form (•)NO + O(2)(•-) = ONOO(-) with respect to its dependence on temperature, viscosity, and [ONOO(-)](eq) by determining [ONOO(-)](eq) and [(•)NO](eq). The equilibrium forward reaction rate constant (k(f)(eq)) has negative activation energy, in contrast to that found under irreversible conditions. In contradiction to the law of mass action, we demonstrate that the equilibrium constant depends on ONOO(-) concentration. Therefore, a wide range of k(f)(eq) values could be derived (7.5-21 × 10(9) M(-1) s(-1)). Of general interest, the variations in k(f) can thus be explained by its dependence on the distance between ONOO(-) particles (sites of generation of (•)NO and O(2)(•-)).
Collapse
Affiliation(s)
- Horacio Botti
- Unidad de Cristalografía de Proteínas, Instituto Pasteur de Montevideo, Montevideo, 11400, Uruguay.
| | | | | | | | | | | | | |
Collapse
|
5
|
Piazza F, Rios PDL, Fanelli D, Bongini L, Skoglund U. Anticooperativity in diffusion-controlled reactions with pairs of anisotropic domains: a model for the antigen–antibody encounter. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 34:899-911. [PMID: 15803329 DOI: 10.1007/s00249-005-0460-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 12/22/2004] [Accepted: 12/23/2005] [Indexed: 10/25/2022]
Abstract
The encounter between anisotropic agents in diffusion-controlled reactions is a topic of very general relevance in chemistry and biology. Here we introduce a simplified model of encounter of an isotropic molecule with a pair of partially reacting agents and apply it to the encounter reaction between an antibody and its antigen. We reduce the problem to the solution of dual series relations, which can be solved iteratively, yielding the exact solution for the encounter rate constant at any desired order of accuracy. We quantify the encounter effectiveness by means of a simple indicator and show that the two binding centers systematically behave in an anti-cooperative fashion. However, we demonstrate that a reduction of the binding active sites allows the composite molecule to recover binding effectiveness, in spite of the overall reduction of the rate constant. In addition, we provide a simple formula that enables one to calculate the anti-cooperativity as a function of the size of the binding site for any values of the separation between the two active lobes and of the antigen size. Finally, some biological implications of our results are discussed.
Collapse
Affiliation(s)
- F Piazza
- Laboratoire de Biophysique Statistique, SB-ITP, Ecole Politechnique Fédérale de Lausanne, BSP-720, 1015 Lausanne, Switzerland.
| | | | | | | | | |
Collapse
|
6
|
Buján-Nuñez MC, López-Quintela MA. Diffusion-controlled reactions in an inhomogeneous medium: Intermediate and high concentration of reagents. J Chem Phys 2002. [DOI: 10.1063/1.1514661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
7
|
Barzykin AV, Seki K, Tachiya M. Kinetics of diffusion-assisted reactions in microheterogeneous systems. Adv Colloid Interface Sci 2001; 89-90:47-140. [PMID: 11215811 DOI: 10.1016/s0001-8686(00)00053-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
This review is focused on the basic theory of diffusion-assisted reactions in microheterogeneous systems, from porous solids to self-organized colloids and biomolecules. Rich kinetic behaviors observed experimentally are explained in a unified fashion using simple concepts of competing distance and time scales of the reaction and the embedding structure. We mainly consider pseudo-first-order reactions, such as luminescence quenching, described by the Smoluchowski type of equation for the reactant pair distribution function with a sink term defined by the reaction mechanism. Microheterogeneity can affect the microscopic rate constant. It also enters the evolution equation through various spatial constraints leading to complicated boundary conditions and, possibly, to the reduction of dimensionality of the diffusion space. The reaction coordinate and diffusive motion along this coordinate are understood in a general way, depending on the problem at hand. Thus, the evolution operator can describe translational and rotational diffusion of molecules in a usual sense, it can be a discrete random walk operator when dealing with hopping of adsorbates in solids, or it can correspond to conformational fluctuations in proteins. Mathematical formulation is universal but physical consequences can be different. Understanding the principal features of reaction kinetics in microheterogeneous systems enables one to extract important structural and dynamical information about the host environments by analyzing suitably designed experiments, it helps building effective strategies for computer simulations, and ultimately opens possibilities for designing systems with controllable reactivity properties.
Collapse
Affiliation(s)
- A V Barzykin
- National Institute of Materials and Chemical Research, Tsukuba, Ibaraki, Japan.
| | | | | |
Collapse
|
8
|
Yang S, Kim J, Lee S. An efficient Brownian dynamics method for calculating the time-dependent rate coefficients of diffusion-influenced reactions. J Chem Phys 1999. [DOI: 10.1063/1.480363] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
9
|
Zhou HX. Theory of the diffusion-influenced substrate binding rate to a buried and gated active site. J Chem Phys 1998. [DOI: 10.1063/1.476255] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
10
|
|
11
|
Zhou HX, Wong KY, Vijayakumar M. Design of fast enzymes by optimizing interaction potential in active site. Proc Natl Acad Sci U S A 1997; 94:12372-7. [PMID: 9356456 PMCID: PMC24950 DOI: 10.1073/pnas.94.23.12372] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The diffusional encounter between substrate and enzyme, and hence catalytic efficiency, can be enhanced by mutating charged residues on the surface of the enzyme. In this paper we present a simple method for screening such mutations. This is based on our earlier result that electrostatic enhancement of the enzyme-substrate binding rate constant can be accounted for just by the interaction potential within the active site. Assuming that catalytic and structural integrity is maintained, the catalytic efficiency can be optimized by surface charge mutations which lead to stronger interaction potential within the active site. Application of the screening method on superoxide dismutase shows that only charge mutations close to the active site will have practical effect on the catalytic efficiency. This rationalizes a large number of findings obtained in previous simulation and experimental studies.
Collapse
Affiliation(s)
- H X Zhou
- Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | | | | |
Collapse
|
12
|
Zhou HX. Theory and Simulation of the Influence of Diffusion in Enzyme-Catalyzed Reactions. J Phys Chem B 1997. [DOI: 10.1021/jp971208i] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
13
|
Zhou HX, Briggs JM, McCammon JA. A 240-Fold Electrostatic Rate-Enhancement for Acetylcholinesterase−Substrate Binding Can Be Predicted by the Potential within the Active Site. J Am Chem Soc 1996. [DOI: 10.1021/ja963134e] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huan-Xiang Zhou
- Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong Departments of Chemistry and Biochemistry and Pharmacology, University of California at San Diego La Jolla, California 92093-0365
| | - James M. Briggs
- Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong Departments of Chemistry and Biochemistry and Pharmacology, University of California at San Diego La Jolla, California 92093-0365
| | - J. Andrew McCammon
- Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay Kowloon, Hong Kong Departments of Chemistry and Biochemistry and Pharmacology, University of California at San Diego La Jolla, California 92093-0365
| |
Collapse
|