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Functions of biological macromolecules, including enzyme catalysis, allostery, and ligand recognition, in some circumstances can be rate-limited by dynamic processes that couple nonproductive and productive conformations. 1,2 Delineating the amplitudes, rates, and mechanisms of these motions is necessary to explicate biological function. 3-5 This paper describes a modified protondetected 15 N Carr-Purcell-Meiboom-Gill 6,7 (CPMG) spin-echo pulse sequence that overcomes the disadvantages associated with pulsing rates comparable to the one-bond J NH scalar coupling constant. The new experiment permits measurement of chemical or conformational exchange time constants from approximately 0.5 to 5 ms. This range of time scales fills an important gap between microsecond time scales that are accessible by the offresonance rotating-frame experiment 8,9 and millisecond time scales that are accessible by the zz-exchange experiment. [10][11][12] Conformational or chemical kinetic processes that transfer a nuclear spin between sites with different magnetic environments contribute to the adiabatic decay of transverse magnetization. The phenomenological transverse relaxation rate constant measured in a CPMG experiment, R 2 (τ cp ), is given by:in which τ cp is the delay between pulses in the spin-echo pulse train; R in and R anti are the transverse relaxation rate constants for in-phase and antiphase coherences averaged over the populations of each chemical or conformational state, respectively; 0 e e 1 reflects the averaging between in-phase and antiphase coherences due to evolution under the scalar coupling Hamiltonian during τ cp ; 13-15 and R ex is the rate constant for damping due to exchange between sites. For two exchanging sites 16 in which Φ ex ) (ω 1 -ω 2 ) 2 p 1 p 2 ; and p i and ω i are the populations and Larmor frequencies for the nuclear spin in site i; and τ ex is the reduced lifetime of the exchanging sites.In principle, exchange kinetics can be determined by fitting eqs 1 and 2 to R 2 (τ cp ) data obtained for different values of τ cp ; however, both and R ex depend on τ cp , which renders the analysis intractable. This difficulty is circumvented if τ cp is limited to small values (<1/(4J NH )), because ≈ 1. 17 In this case, only fast exchange processes can be studied, and the resulting high radio frequency duty cycle poses a significant drawback compared with the off-resonance rotating-frame experiment. 8,9 Broadband proton decoupling during τ cp prevents evolution of in-phase into antiphase magnetization and makes ) 1; however, decoupling interferes with spin-echo formation and accentuates the decay of transverse magnetization. 14,15,18 In the approach adopted herein, the rate constants for in-phase and antiphase coherences are averaged explicitly during the CPMG sequence to render ) 0.5 for all τ cp . Application of the experiment to basic pancreatic trypsin inhibitor (BPTI) confirms the effectiveness of the proposed averaging procedure for values of τ cp as large as 2/J NH .The modified CPMG pulse sequenc...

Protein allosteric pathways are investigated in the imidazole glycerol phosphate synthase heterodimer in an effort to elucidate how the effector (PRFAR,formimino]-5-aminoimidazole-4-carboxamide ribonucleotide) activates glutaminase catalysis at a distance of 25 Å from the glutamine-binding site. We apply solution NMR techniques and community analysis of dynamical networks, based on mutual information of correlated protein motions in the active and inactive enzymes. We find evidence that the allosteric pathways in the PRFAR bound enzyme involve conserved residues that correlate motion of the PRFAR binding loop to motion at the protein-protein interface, and ultimately at the glutaminase active site. The imidazole glycerol phosphate synthase bienzyme is an important branch point for the histidine and nucleotide biosynthetic pathways and represents a potential therapeutic target against microbes. The proposed allosteric mechanism and the underlying allosteric pathways provide fundamental insights for the design of new allosteric drugs and/or alternative herbicides.glutamine hydrolysis | protein networks | generalized correlation analysis | network theory A llostery is a fundamental property that allows for the regulation of function and dynamic adaptability of enzymes and proteins. Allosteric enzymes contain at least two distant binding sites, including the active site responsible for catalytic activity, which binds the substrate, and the allosteric site, which binds the effector and initiates the allosteric signal propagation to the active site. In V-type systems, substrate binding is not affected by the presence of the effector but if the effector is not bound, the allosteric protein is usually catalytically inactive (or poorly active), indicating that the effector binding is coupled to the kinetic and/or thermodynamic parameters of the biochemical reaction in the active site. Allosteric information transfer can range from large, enthalpically driven conformational changes to purely entropically driven motions or a combination of both enthalpic and entropic effects, but in each case the kinetic parameters of the catalyzed reaction at the substrate binding site are altered. At the heart of allosterism there is intramolecular thermodynamic coupling over long distances (>10 Å), between the active and allosteric sites. An important challenge for fundamental studies is the elucidation of the allosteric pathways that connect the two ligand-binding sites.In this work, we combine community network analysis based on molecular dynamics (MD) simulations and NMR studies of protein motion based on relaxation dispersion techniques and chemical shift titrations experiments to provide an atomistic description of allostery in the V-type allosteric enzyme imidazole glycerol phosphate synthase (IGPS) from the thermophile Thermotoga maritima (Fig. 1). IGPS is a tightly associated heterodimeric enzyme in which each monomer enzyme catalyzes a different reaction (1-3). The 23 kDa HisH enzyme is a member of the glutamine amidotransferas...

The static magnetic field dependence of chemical exchange linebroadening in NMR spectroscopy is investigated theoretically and experimentally. Two-site exchange (A / B) is considered with site A more highly populated than site B (p a > p b ), a shift difference between sites equal to ∆ω, and an exchange rate constant given by k ex . The exchange contribution to the transverse relaxation rate constant for the more highly populated site is denoted R ex . The dependence of R ex on the static magnetic field strength is characterized by a scaling parameter R ) d ln R ex /d ln ∆ω, in which 0 e R e 2 for p a > 0.7. The value of R depends on the NMR chemical shift time scale for the exchange process: for slow exchange (k ex /∆ω < 1), 0 e R < 1; for intermediate exchange (k ex /∆ω ) 1), R ) 1; and for fast exchange (k ex /∆ω > 1), 1 < R e 2. Consequently, the static magnetic field dependence of R ex defines the chemical shift time scale for an exchange process even if the populations are so highly skewed (p a . p b ) that the minor resonance is not observable in the slow exchange limit. The theoretical results are verified by measuring 15 N transverse relaxation rate constants at static magnetic fields of 11.7 and 14.1 T and temperatures of 300 and 313 K for the protein basic pancreatic trypsin inhibitor. At each combination of static magnetic field and temperature, the rate constants were measured using Carr-Purcell-Meiboom-Gill and Hahn echo techniques with spin-echo delays ranging from 1.0 to 64.5 ms. 15 N resonances for residues in the region of the Cys14-Cys38 disulfide bond are broadened due to chemical exchange. Values of R obtained from the relaxation rate constants range from 0.26 ( 0.17 for Arg39 at 300 K to 1.96 ( 0.25 for Cys38 at 313 K. For Cys38 and Arg39, the two residues most strongly affected by chemical exchange, values of k ex were determined to be 380 ( 70 s -1 and 530 ( 90 s -1 at 300 K and 1300 ( 290 s -1 and 1370 ( 160 s -1 at 313 K by global analysis of the relaxation rate constants. The scaling parameters R indicate that chemical exchange for most residues in basic pancreatic trypsin inhibitor does not satisfy k ex /∆ω . 1. Consequently, the assumption of fast-limit quadratic scaling of exchange broadening in proteins and other macromolecules may be incorrect, even if a single broadened resonance is observed for a nuclear spin. The theoretical results for the static magnetic field dependence of chemical exchange broadening in NMR spectroscopy are applicable to other nuclei and to other techniques for measuring chemical exchange linebroadening.