Proton magnetic resonance studies of ribose dinucleoside monophosphates in aqueous solution. II. Nature of the base-stacking interaction in adenylyl-(3' .far. 5')-cytidine and cytidylyl-(3' .far. 5')adenosine

Bangerter, Benedict W.; Chan, Sunney I.

doi:10.1021/ja01042a039

Cited by 83 publications

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“…At any concentration of C, however small, a quantity of the dimer will always be present, so any measured value of ai for a nucleus in C can never be equal to 6,. In NMR studies of dimerisation [6] [7], 6, has been determined by manual extrapolation of 6, us.…”

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confidence: 99%

Estimation of Dimerisation Constants from Complexatin‐Induced Displacements of ¹H‐NMR Chemical Shifts: Dimerisation of Caffeine

Horman

Dreux

1984

Helvetica Chimica Acta

110

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SummaryThe determination of the dimerisation constant (KD) for the weak self-association of a compound C in dilute solution according to the equilibrium, 2Cz+C, is described. The method uses chemical shifts measured on a series of solutions of C at different concentrations: the optimum K D is defined by a linear regression best-f& procedure, which simultaneously determines optimum values for 6, and d s o for 6,, the intrinsic chemical shifts for nuclei in the monomer and dimer species. 'The dimerisation of caffeine in D,O is used as a model to demonstrate the working of the method and the quality of results obtained. The most probable value of K D for caffeine at 30.5" is found in the range 5.5-6.0 kg solution.mol-', and the enthalpy and entropy of dimerisation are found to be A H e = -15.1 kJ.mol-l and ASe = -35.3 J."C-'.mol-', respectively. The influence of small errors in 6, on the confidence limits of KD is discussed.Weak complexes are important in molecular biology and in pharmacology €or interpreting biomechanisms and modes of drug action [I]. Methods to date for determining association constants ( K ) of weak molecular complexes as defined in Eqn. 1 and 2 have often been approximate, and there have been many reports of anomalous results[2]. We have recently described a method for estimating KAB values as defined in Eqn. I from complexation-induced displacements of NMR line positions in equimolar solutions of the reactants A and B [3]. We report here an improved version of that method and show how it can be applied to study dimerisation according to Eqn.2. Relative to our earlier method, our present approach shows the following advantages: it is about 20 times faster in calculation time, it uses standard linear least-squares statistical methodology, it can be implemented on a relatively modest programmable desk calculator, and it permits the ready estimation of error limits for complex parameters. Further, it retains our rigorous mathematical treatment of the law of mass action equation; this we feel is important for the estimation of complex parameters which can be validly compared from one complex to another.NMR has often been exploited to determine association constants (KAB) for weak bimolecular complexes forming according to Eqn

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confidence: 99%

Estimation of Dimerisation Constants from Complexatin‐Induced Displacements of ¹H‐NMR Chemical Shifts: Dimerisation of Caffeine

Horman

Dreux

1984

Helvetica Chimica Acta

110

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“…The putative redox linkage could occur only during the second half of the turnover cycle when the final two electrons are passed to the activated dioxygen, i.e., when the peroxide and the oxyferryl intermediates are presumably formed (67). The redox potentials of these dioxygen intermediates are of the order of 1 volt, which is approximately 700-800 mV higher than the intrinsic redox potentials of the cytochrome a 3 and Cu B without the dioxygen bound (105).…”

Section: Wwwannualreviewsorg • Adventures With Molecular Machinesmentioning

confidence: 99%

“…The protein was thought to contain two iron heme As and two copper ions (4). The hemes were called cytochrome a and cytochrome a 3 , and the copper ions were called Cu A and Cu B . It was established that the enzyme participated in dioxygen reduction and was thus the terminal enzyme in the respiratory chain of mitochondria.…”

Section: The Era Of Membrane Proteins Cytochrome C Oxidase: a Redox-lmentioning

confidence: 99%

“…Ligand structures of (a) Cu A , (b) cytochrome a and cytochrome a 3 , and (c) cytochrome a 3 and Cu B in bovine cytochrome c oxidase.…”

Section: Figurementioning

confidence: 99%

“…In this model, both Cu A and the dioxygen-activated cytochrome a 3 and Cu B are involved in the redox linkage. The primary electron donor that initiates the process is cytochrome c, which is denoted by c. D denotes the electron donor for the electron transfer coupled to the proton pump (i.e., the input linkage site), and A represents the peroxide or oxyferryl dioxygen intermediate (electron acceptor) (i.e., the output linkage site).…”

Section: Figurementioning

confidence: 99%

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A Physical Chemist's Expedition to Explore the World of Membrane Proteins

Chan

2009

Annu. Rev. Biophys.

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NMR of base-stacking interactions in nucleic acids in solution, dynamic structure of bilayer membranes, membrane biophysics, metal cofactor structure and function, redox linkage and proton pumping in cytochrome c oxidase, methane hydroxylation by the particulate methane monooxygenase, early kinetic events in protein folding AbstractDespite growing up amid humble surroundings, I ended up receiving an excellent education at the University of California at Berkeley and postdoctoral training at Harvard. My academic career at Caltech was shaped by serendipity, inspirational colleagues, and a stimulating research environment, as well as smart, motivated students and postdocs who were willing to join my search for molecular understanding of complex biological systems. From chemical physics I allowed my research to evolve, beginning with the application of NMR to investigate the base stacking of nucleic acid bases in solution, the dynamic structure of membranes, and culminating with the use of various forms of spectroscopy to elucidate the structure and function of membrane proteins and the early kinetic events in protein folding. The journey was a biased random walk driven by my own intellectual curiosity and instincts and by the pace at which I learned biochemistry from my students and postdocs, my colleagues, and the literature and through osmosis during seminars and scientific meetings.

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Oligonucleotide interactions. IV. Conformational differences between deoxy‐ and ribodinucleoside phosphates

1970

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synopsisThe circular dichroism spectra of all 16 ribodinucleoside phosphates containing the bwes adenine, uracil, cytosine, and guanine have been measured at room temperature and neutral pH. These results are compared with the circular dichroism spectra of the corresponding deoxy compounds. From the optical properties it is clear that the geometry of the basestacked conformation of ribo compounds must differ substantially from that of deoxy compounds. Because of this, it is not possible to draw firm conclusions about the relative extent of stacking in most ribo and deoxy compounds. The optical rotatory dispersion of about a dozen deoxy and ribodinucleoside phosphates has been studied as a function of temperature. These results confirmed the conclusions drawn earlier from measurements at a single temperature. Several dinucleoside phosphates containing a 2' + 5' phosphodiester bond have also been examined. These compounds have a substantial degree of base stacking at room temperature. The geometry of the stacked conformation is different from that of either the normal ribo dimer or the deoxy dimer. The role of the 2'-hydroxyl group in stabilizing base stacked geomet,ries has been examined by studies on C-2'-O-methyl-pC. This compound has optical properties almost identical to those of CpC. This suggests that t,he effect of the 2' hydroxyl is felt indirectly through its perturbation of the geometry of the sugar ring rather than directly by Iiydrogc~i bonding. It is not possible at present t.o identify precise conformational difierciices anioiig cleoxy-, ribo-and 2'+ 5' ribodiiiucleoside phosphatw.

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Proton magnetic resonance studies of ribose dinucleoside monophosphates in aqueous solution. II. Nature of the base-stacking interaction in adenylyl-(3' .far. 5')-cytidine and cytidylyl-(3' .far. 5')adenosine

Cited by 83 publications

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Estimation of Dimerisation Constants from Complexatin‐Induced Displacements of ¹H‐NMR Chemical Shifts: Dimerisation of Caffeine

Estimation of Dimerisation Constants from Complexatin‐Induced Displacements of ¹H‐NMR Chemical Shifts: Dimerisation of Caffeine

A Physical Chemist's Expedition to Explore the World of Membrane Proteins

Oligonucleotide interactions. IV. Conformational differences between deoxy‐ and ribodinucleoside phosphates

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Proton magnetic resonance studies of ribose dinucleoside monophosphates in aqueous solution. II. Nature of the base-stacking interaction in adenylyl-(3' .far. 5')-cytidine and cytidylyl-(3' .far. 5')adenosine

Cited by 83 publications

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Estimation of Dimerisation Constants from Complexatin‐Induced Displacements of 1H‐NMR Chemical Shifts: Dimerisation of Caffeine

Estimation of Dimerisation Constants from Complexatin‐Induced Displacements of 1H‐NMR Chemical Shifts: Dimerisation of Caffeine

A Physical Chemist's Expedition to Explore the World of Membrane Proteins

Oligonucleotide interactions. IV. Conformational differences between deoxy‐ and ribodinucleoside phosphates

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Estimation of Dimerisation Constants from Complexatin‐Induced Displacements of ¹H‐NMR Chemical Shifts: Dimerisation of Caffeine

Estimation of Dimerisation Constants from Complexatin‐Induced Displacements of ¹H‐NMR Chemical Shifts: Dimerisation of Caffeine