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Pang YP. How neocarcerand Octacid4 self-assembles with guests into irreversible noncovalent complexes and what accelerates the assembly. Commun Chem 2022; 5:9. [PMID: 36697791 PMCID: PMC9814096 DOI: 10.1038/s42004-022-00624-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/30/2021] [Indexed: 01/28/2023] Open
Abstract
Cram's supramolecular capsule Octacid4 can irreversibly and noncovalently self-assemble with small-molecule guests at room temperature, but how they self-assemble and what accelerates their assembly remain poorly understood. This article reports 81 distinct Octacid4•guest self-assembly pathways captured in unrestricted, unbiased molecular dynamics simulations. These pathways reveal that the self-assembly was initiated by the guest interaction with the cavity portal exterior of Octacid4 to increase the portal collisions that led to the portal expansion for guest ingress, and completed by the portal contraction caused by the guest docking inside the cavity to impede guest egress. The pathways also reveal that the self-assembly was accelerated by engaging populated host and guest conformations for the exterior interaction to increase the portal collision frequency. These revelations may help explain why the presence of an exterior binding site at the rim of the enzyme active site is a fundamental feature of fast enzymes such as acetylcholinesterase and why small molecules adopt local minimum conformations when binding to proteins. Further, these revelations suggest that irreversible noncovalent complexes with fast assembly rates could be developed-by engaging populated host and guest conformations for the exterior interactions-for materials technology, data storage and processing, molecular sensing and tagging, and drug therapy.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN, USA.
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2
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How does hemoglobin generate such diverse functionality of physiological relevance? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1873-84. [PMID: 23643742 DOI: 10.1016/j.bbapap.2013.04.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 11/24/2022]
Abstract
The absolute values of the O2-affinities (P50, Klow, and Khigh) of hemoglobin (Hb) are regulated neither by changes in the static T-/R-quaternary and associated tertiary structures nor the ligation states. They are pre-determined and regulated by the extrinsic environmental factors such as pH, buffers, and heterotropic effectors. The effect and role of O2 on Hb are reversibly to drive the structural allosteric equilibrium between the T(deoxy)- and R(oxy)-Hb toward R(oxy)-Hb (the structural allostery). R(oxy)-Hb has a higher O2-affinity (Khigh) relative to that (Klow) of the T(deoxy)-Hb (Khigh>Klow) under any fixed environmental conditions. The apparent O2-affinity of Hb is high, as the globin matrix interferes with the dissociation process of O2, forcing the dissociated O2 geminately to re-bind to the heme Fe. This artificially increases [oxy-Hb] and concomitantly decreases [deoxy-Hb], leading to the apparent increases of the O2-affinity of Hb. The effector-linked high-frequency thermal fluctuations of the globin matrix act as a gating mechanism to modulate such physical, energetic, and kinetic barriers to enhance the dissociation process of O2, resulted in increases in [deoxy-Hb] and concomitant decrease in [oxy-Hb], leading to apparent reductions of the O2-affinity of Hb (the entropic allostery). The heme in Hb is simply a low-affinity O2-trap, the coordination structure of which is not altered by static T-/R-quaternary and associated tertiary structural changes of Hb. Thus, heterotrophic effectors are the signal molecule, which acts as a functional link between these two allosteries and generates the diverse functionality of Hb of physiological relevance. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Kang M, Roberts C, Cheng Y, Chang CEA. Gating and Intermolecular Interactions in Ligand-Protein Association: Coarse-Grained Modeling of HIV-1 Protease. J Chem Theory Comput 2011; 7:3438-46. [PMID: 26598172 DOI: 10.1021/ct2004885] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Most biological processes are initiated or mediated by the association of ligands and proteins. This work studies multistep, ligand-protein association processes by Brownian dynamics simulations with coarse-grained models for HIV-1 protease (HIVp) and its neutral ligands. We report the average association times when the ligand concentration is 100 μM. The influence of crowding on the simulated binding time was also studied. HIVp has flexible loops that serve as a gate during the ligand binding processes. It is believed that the flaps are partially closed most of the time in its free state. To accelerate our simulations, we fixed a part of the HIVp and reparameterized our coarse-grained model, using atomistic molecular dynamics simulations, to reproduce the "gating" motions of HIVp. HIVp-ligand interactions changed the gating behavior of HIVp and helped ligands diffuse on HIVp surface to accelerate binding. The structural adjustment of the ligand toward its final stable state was the limiting step in the binding processes, which is highly system dependent. The intermolecular attraction between the ligands and crowder proteins contributes the most to the crowding effects. The results highlight broader implications in recognition pathways under more complex environment that considers molecular dynamics and conformational changes. This work brings insights into ligand-protein associations and is helpful in the design of targeted ligands.
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Affiliation(s)
- Myungshim Kang
- Department of Chemistry, University of California , Riverside, California, United States
| | - Christopher Roberts
- Department of Chemistry, University of California , Riverside, California, United States
| | - Yuhui Cheng
- Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Chia-En A Chang
- Department of Chemistry, University of California , Riverside, California, United States
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4
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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
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5
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Sheu SY. Selectivity principle of the ligand escape process from a two-gate tunnel in myoglobin: molecular dynamics simulation. J Chem Phys 2007; 124:154711. [PMID: 16674255 DOI: 10.1063/1.2185626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We proposed a selectivity principle for the ligand escape process from two fluctuating bottlenecks in a cavity with a multigate inside a myoglobin pocket. Our previous analytical theory proposed a fluctuating bottleneck model for a Brownian particle passing through two gates on a cavity surface of an enzyme protein and has determined the escape rate in terms of the time-dependent gate function and the competition effect. It illustrated that with two (or more than two) gates on a cavity surface the gate modulation, which is controlled by protein fluctuation, dominates the ligand escape pathway. We have performed a molecular dynamics simulation to investigate the selectivity principle of the ligand escape process from two-gate tunnel in myoglobin. The simulation results confirm our theoretical conjecture. It indicates that the escape process is actually entropy driven, and the ligand escape pathway is chosen via the gate modulation. This suggests an interesting intrinsic property, that is, the oxymyoglobin tertiary structure is favorable to the departure of the ligand from one direction rather than through a biased random walk.
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Affiliation(s)
- Sheh-Yi Sheu
- Faculty of Life Sciences and Institute of Genome Sciences, and Structural Biology Program, National Yang-Ming University, Taipei 112, Taiwan.
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6
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Norman AW, Mizwicki MT, Norman DPG. Steroid-hormone rapid actions, membrane receptors and a conformational ensemble model. Nat Rev Drug Discov 2004; 3:27-41. [PMID: 14708019 DOI: 10.1038/nrd1283] [Citation(s) in RCA: 376] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Anthony W Norman
- Department of Biochemistry, University of California, Riverside, California 92521, USA.
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7
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Riley JM, Alkan S, Chen A, Shapiro M, Khan WA, Murphy, WR, Hanson JE. Pyrene-Labeled Poly(aryl ether) Monodendrons: Synthesis, Characterization, Diffusion Coefficients, and Photophysical Studies. Macromolecules 2001. [DOI: 10.1021/ma0007886] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeanne M. Riley
- Department of Chemistry, Seton Hall University, 400 South Orange Avenue, South Orange, New Jersey 07079-2694, and Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901-1398
| | - Sibel Alkan
- Department of Chemistry, Seton Hall University, 400 South Orange Avenue, South Orange, New Jersey 07079-2694, and Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901-1398
| | - Aidi Chen
- Department of Chemistry, Seton Hall University, 400 South Orange Avenue, South Orange, New Jersey 07079-2694, and Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901-1398
| | - Michael Shapiro
- Department of Chemistry, Seton Hall University, 400 South Orange Avenue, South Orange, New Jersey 07079-2694, and Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901-1398
| | - Wajiha A. Khan
- Department of Chemistry, Seton Hall University, 400 South Orange Avenue, South Orange, New Jersey 07079-2694, and Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901-1398
| | - W. Rorer Murphy,
- Department of Chemistry, Seton Hall University, 400 South Orange Avenue, South Orange, New Jersey 07079-2694, and Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901-1398
| | - James E. Hanson
- Department of Chemistry, Seton Hall University, 400 South Orange Avenue, South Orange, New Jersey 07079-2694, and Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901-1398
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Affiliation(s)
- W R Cannon
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Kurzyński M. A synthetic picture of intramolecular dynamics of proteins. Towards a contemporary statistical theory of biochemical processes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1998; 69:23-82. [PMID: 9670774 DOI: 10.1016/s0079-6107(97)00033-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
An increasing body of experimental evidence indicates the slow character of internal dynamics of native proteins. The important consequence of this is that theories of chemical reactions, used hitherto, appear inadequate for description of most biochemical reactions. Construction of a contemporary, truly advanced statistical theory of biochemical processes will need simple but realistic models of microscopic dynamics of biomolecules. In this review, intended to be a contribution towards this direction, three topics are considered. First, an intentionally simplified picture of dynamics of native proteins which emerges from recent investigations is presented. Fast vibrational modes of motion, of periods varying from 10(-14) to 10(-11) s, are contrasted with purely stochastic conformational transitions. Significant evidence is adduced that the relaxation time spectrum of the latter spreads in the whole range from 10(-11) to 10(5) s or longer, and up to 10(-7) s it is practically quasi-continuous. Next, the essential ideas of the theory of reaction rates based on stochastic models of intramolecular dynamics are outlined. Special attention is paid to reactions involving molecules in the initial conformational substrates confirmed to the transition state, which is realized in actual experimental situations. And finally, the two best experimentally justified classes of models of conformational transition dynamics, symbolically referred to as "protein glass" and "protein machine", are described and applied to the interpretation of a few simple biochemical processes, perhaps the most important result reported is the demonstration of the possibility of predominance of the short initial condition-dependent stage of protein involved reactions over the main stage described by the standard kinetics. This initial stage, and not the latter, is expected to be responsible for the coupling of component reactions in the complete enzymatic cycles as well as more complex processes of biological free energy transduction.
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Affiliation(s)
- M Kurzyński
- Institute of Physics, A. Mickiewicz University, Poznań, Poland
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11
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Estimating the effect of protein dynamics on electron transfer to the special pair in the photosynthetic reaction center. Chem Phys Lett 1997. [DOI: 10.1016/s0009-2614(97)00742-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Berezhkovskii AM, Yang DY, Lin SH, Makhnovskii YA, Sheu SY. Smoluchowski-type theory of stochastically gated diffusion-influenced reactions. J Chem Phys 1997. [DOI: 10.1063/1.473722] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Cannon WR, Garrison BJ, Benkovic SJ. Electrostatic Characterization of Enzyme Complexes: Evaluation of the Mechanism of Catalysis of Dihydrofolate Reductase. J Am Chem Soc 1997. [DOI: 10.1021/ja962621r] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- William R. Cannon
- Contribution from 152 Davey Laboratory, Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Barbara J. Garrison
- Contribution from 152 Davey Laboratory, Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Stephen J. Benkovic
- Contribution from 152 Davey Laboratory, Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
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Kurzyński M. Protein machine model of enzymatic reactions gated by enzyme internal dynamics. Biophys Chem 1997; 65:1-28. [PMID: 17029837 DOI: 10.1016/s0301-4622(96)02209-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/1995] [Accepted: 08/01/1996] [Indexed: 11/26/2022]
Abstract
The slow character of conformational transition dynamics in native proteins, recently becoming more and more apparent, makes conventional theories of chemical reactions inapplicable for the description of enzymatic reactions. Any contemporary statistical theory of biochemical processes has to be based on a possibly simple but realistic model of microscopic dynamics of participating biomolecules. In a model considered in this paper the dynamics of enzymatic protein is approximated by a quasi-continuous diffusive motion of its solid-like structural elements relative to each other. The enzymatic reaction is assumed to involve three steps (a covalent tranformation preceded and followed by association-dissociation processes with the substrate and the product), each step being gated by conformational diffusion. In general, the reaction proceeds in three stages: initial, transient and steady-state. Carefully approximated analytical formulae describing the kinetics in each stage are derived. In the limit of the fast internal dynamics of the enzyme, when compared to the local chemical transformations, the initial stage of reaction, dependent on the initial distribution of enzyme conformations, is absent and all the formulae describing the remaining two stages simplify to those provided by the classical theory of Haldane. However, following recent studies, the rule seems to be that it is the conformational dynamics of the enzyme, and not the details of chemical mechanism, that affects the rate of enzymatic reaction. Apart from the possibility of the initial inhomogeneous kinetics, the important result obtained in the limit of slow conformational dynamics is that the kinetic mechanisms of a reaction differ in general between the transient and steady-state stages. Possibilities of carrying out an experimentum crucis directly discrediting the conventional approach are considered.
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Affiliation(s)
- M Kurzyński
- Institute of Physics, A. Mickiewicz University, Umultowska 85, PL-61-614 Poznań, Poland.
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15
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Cannon WR, Singleton SF, Benkovic SJ. A perspective on biological catalysis. NATURE STRUCTURAL BIOLOGY 1996; 3:821-33. [PMID: 8836096 DOI: 10.1038/nsb1096-821] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have analysed enzyme catalysis through a re-examination of the reaction coordinate. The ground state of the enzyme-substrate complex is shown to be related to the transition state through the mean force acting along the reaction path; as such, catalytic strategies cannot be resolved into ground state destabilization versus transition state stabilization. We compare the role of active-site residues in the chemical step with the analogous role played by solvent molecules in the environment of the noncatalysed reaction. We conclude that enzyme catalysis is significantly enhanced by the ability of the enzyme to preorganize the reaction environment. This complementation of the enzyme to the substrate's transition state geometry acts to eliminate the slow components of solvent reorganization required for reactions in aqueous solution. Dramatically strong binding of the transition state geometry is not required.
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Affiliation(s)
- W R Cannon
- Department of Chemistry, Pennsylvania State University, University Park 16802, USA
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16
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Houk KN, Nakamura K, Sheu C, Keating AE. Gating as a control element in constrictive binding and guest release by hemicarcerands. Science 1996; 273:627-9. [PMID: 8662548 DOI: 10.1126/science.273.5275.627] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Theoretical modeling of the dynamics of complexation and decomplexation of guest molecules by container molecules reveals that gating has a critical influence on the ease of formation and stability of host-guest complexes. Hosts equipped with gates can form very stable complexes with a variety of guests under readily achievable conditions. Gating involves conformational processes of the host molecule that alter the size of the portals through which guest molecules pass. "French door" and "sliding door" mechanisms of gate opening are identified.
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Affiliation(s)
- K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569, USA
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17
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Kurzyński M. A model of reversible reaction with slow intramolecular relaxation. J Chem Phys 1994. [DOI: 10.1063/1.468177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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McLendon G, Feitelson J. Electron-transfer reactions of hemoglobin with small molecules: a potential probe of conformational dynamics. Methods Enzymol 1994; 232:86-94. [PMID: 8057887 DOI: 10.1016/0076-6879(94)32045-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- G McLendon
- Department of Chemistry, University of Rochester, New York 14627
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19
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Abstract
Great progress in studies of protein dynamics in the past decade propels an essential alteration in our understanding of the enzymatic catalysis phenomenon. A careful analysis of assumptions made by the hitherto used conventional theory of chemical reactions shows that neither of them is in fact satisfied. One of the reasons is the presence of a slow interconformational dynamics within the protein native state. In consequence, the simple classical statement "enzymes accelerate reactions by decreasing the free energy of activation" represents only half of the truth. Enzymatic reactions actually proceed through 'gates' of relatively low free energy but it is not the process of activated gate crossing that limits the reaction rate, but the process of generally non-activated gate opening, controlled by the conformational relaxation. Possible consequences of this fact are pointed out.
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Affiliation(s)
- M Kurzyński
- Institute of Physics, Adam Mickiewicz University, Poznań, Poland
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Geacintov NE, Brenner HC. The triplet state as a probe of dynamics and structure in biological macromolecules. Photochem Photobiol 1989; 50:841-58. [PMID: 2696992 DOI: 10.1111/j.1751-1097.1989.tb02916.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Case DA. Dynamical simulation of rate constants in protein-ligand interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1988; 52:39-70. [PMID: 3076020 DOI: 10.1016/0079-6107(88)90007-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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