**6. References**


ligand photo-release may be associated with the repositioning of the IHP molecule within the Hb central cavity. Based on a molecular dynamics simulation of IHP binding sides in south polar skua deoxyHb, an IHP migration pathway connecting the binding site at the interface between the -chains and the second binding site located between the β-chains was proposed suggesting that IHP interactions with Hb are dynamic and involve numerous positively charged residues situated along the central cavity (Riccio et al., 2001). Therefore, CO photo-release may trigger relocation of IHP within the central cavity resulting in larger exposure of IHP phosphate groups and/or charged amino acid

The photoacoustic data for the ligand photo-dissociation from Mb shows that the structural volume changes associated with the O2 diffusion from the Mb active site are similar to those determined previously for CO in agreement with the crystallographic data. On the other hand, the time constant for O2 escape from the distal pocket to the surrounding solvent is two to three time faster than that for CO suggesting a distinct migration pathway for diatomic ligands in Mb. Our PAC study also indicates that IHP binding to Hb-CO complex alters the volume and enthalpy changes associated with the CO photo-dissociation from the heme iron indicating that the transition between the fully ligated (CO)4Hb and partially ligated (CO)3Hb complex is associated with the reorientation of IHP molecule within the

This work was supported by J. & E. Biomedical Research Program (Florida Department of

Angeloni, L.&Feis, A. (2003). Protein relaxation in the photodissociation of myoglobin-CO

Ascenzi, P., Bertollini, A., Santucci, R., Amiconi, G., Coletta, M., Desideri, A., Giardina, B.,

Belogortseva, N., Rubio, M., Terrell, W.&Miksovska, J. (2007). The contribution of heme

Bossa, C., Anselmi, M., Roccatano, D., Amadei, A., Vallone, B., Brunori, M.&Di Nola, A.

Polizio, F.&Scatena, R. (1993). Cooperative effect of inositol hexakisphosphate, bezafibrate, and clofibric acid on the spectroscopic properties of the nitric oxide derivative of ferrous human hemoglobin. *J. Inorg. Biochem.,* 50, 4, pp. 263-272, 0162-

propionate groups to the conformational dynamics associated with CO photodissociation from horse heart myoglobin. *J. Inorg. Biochem.,* 101, 7, pp. 977-986,

(2004). Extended Molecular Dynamics Simulation of the Carbon Monoxide Migration in Sperm Whale Myoglobin. *Biophys. J.,* 86, 6, pp. 3855-3862, 0006-3495

complexes. *Photochem. Photobiol. Sci,* 2, 7, pp. 730-740, 1474-905X

residues and concomitant electrostriction of solvent molecules.

central cavity and/ or charged amino acid residues interacting with IHP.

Health) and National Science Foundation (MCB 1021831).

**4. Conclusion** 

**5. Acknowledgement** 

**6. References** 

0134

0162-0134


Time Resolved Thermodynamics Associated with Diatomic Ligand Dissociation from Globins 317

Saffran, W. A.&Gibson, Q. H. (1977). Photodissociation of ligands from heme and heme

Savino, C., Miele, A. E., Draghi, F., Johnson, K. A., Sciara, G., Brunori, M.&Vallone, B. (2009).

Shibayama, N., Miura, S., Tame, J. R. H., Yonetani, T.&Park, S.-Y. (2002). Crystal Structure of

Silva, M. M., Rogers, P. H.&Arnone, A. (1992). A third quaternary structure of human hemoglobin A at 1.7-A resolution. *J. Biol. Chem.,* 267, 24, pp. 17248-17256, Song, X.-j., Simplaceanu, V., Ho, N. T.&Ho, C. (2008). Effector-Induced Structural

Šrajer, V., Ren, Z., Teng, T.-Y., Schmidt, M., Ursby, T., Bourgeois, D., Pradervand, C.,

Tsuneshige, A., Park, S.&Yonetani, T. (2002). Heterotropic effectors control the hemoglobin

Unno, M., Ishimori, K.&Morishima, I. (1990). High-pressure laser photolysis study of

and T-state hemoglobins. *Biochemistry,* 29, 44, pp. 10199-10205, 0006-2960 Vetromile, C. M., Miksovska, J.&Larsen, R. W. (2011). Time resolved thermodynamics

channels versus gated ligand release. *Biochim. Biophys. Acta,* pp. 1570-9639 Walda, K. N., Liu, X. Y., Sharma, V. S.&Magde, D. (1994). Geminate recombination of diatomic ligands CO, O2, NO with myoglobin *Biochemistry,* 33, pp. 2198-2209, Westrick, J. A.&Peters, K. S. (1990). A photoacoustic calorimetric study of horse myoglobin.

Westrick, J. A., Peters, K. S., Ropp, J. D.&Sligar, S. G. (1990). Role of the arginine-45 salt

Yang, F.&Phillips Jr, G. N. (1996). Crystal Structures of CO-, Deoxy- and Met-myoglobins at

Ye, X., Demidov, A.&Champion, P. M. (2002). Measurements of the Photodissociation

Various pH Values. *J. Mol. Biol.,* 256, 4, pp. 762-774, 0022-2836

photoacoustic calorimetry. *Biochemistry,* 29, 28, pp. 6741-6746, 0006-2960 Wilson, J., Phillips, K.&Luisi, B. (1996). The Crystal Structure of Horse

of Hemoglobin. *Biochemistry,* 47, 17, pp. 4907-4915, 0006-2960

allostery. *Biophys. Chem.,* 98, 1-2, pp. 49-63, 0301-4622

*Biophys. Chem.,* 37, 1-3, pp. 73-79, 0301-4622

pp. 743-756, 0022-2836

7955-7958,

pp. 1097-1107, 1097-0282

13815, 0006-2960

*Biol. Chem.,* 277, 41, pp. 38791-38796,

proteins. Effect of temperature and organic phosphate. *J. Biol. Chem.,* 252, 22, pp.

Pattern of cavities in globins: The case of human hemoglobin. *Biopolymers,* 91, 12,

Horse Carbonmonoxyhemoglobin-Bezafibrate Complex at 1.55-Å Resolution. *J.* 

Fluctuation Regulates the Ligand Affinity of an Allosteric Protein: Binding of Inositol Hexaphosphate Has Distinct Dynamic Consequences for the T and R States

Schildkamp, W., Wulff, M.&Moffat, K. (2001). Protein Conformational Relaxation and Ligand Migration in Myoglobin: A Nanosecond to Millisecond Molecular Movie from Time-Resolved Laue X-ray Diffraction†. *Biochemistry,* 40, 46, pp. 13802-

function by interacting with its T and R states--a new view on the principle of

hemoproteins. Effects of pressure on carbon monoxide binding dynamics for R-

associated with ligand photorelease in heme peroxidases and globins: Open access

bridge in ligand dissociation from sperm whale carboxymyoglobin as probed by

Deoxyhaemoglobin Trapped in the High-affinity (R) State. *J. Mol. Biol.,* 264, 4,

Quantum Yields of MbNO and MbO2 and the Vibrational Relaxation of the Six-Coordinate Heme Species. *J. Am. Chem. Soc.,* 124, 20, pp. 5914-5924, 0002-7863


Marden, M. C., Bohn, B., Kister, J.&Poyart, C. (1990). Effectors of hemoglobin. Separation of allosteric and affinity factors. *Biophys. J.,* 57, 3, pp. 397-403, 0006-3495 Miksovska, J.&Larsen, R. W. (2003). Structure-function relationships in metalloproteins.

Miksovska, J., Norstrom, J.&Larsen, R. W. (2005). Thermodynamic profiles for CO

Milani, M., Nardini, M., Pesce, A., Mastrangelo, E.&Bolognesi, M. (2008). Hemoprotein timeresolved X-ray crystallography. *IUBMB Life,* 60, 3, pp. 154-158, 1521-6551 Miller, L. M., Patel, M.&Chance, M. R. (1996). Identification of Conformational

Mills, F. C., Ackers, G. K., Gaud, H. T.&Gill, S. J. (1979). Thermodynamic studies on

Mouawad, L., Maréchal, J.-D.&Perahia, D. (2005). Internal cavities and ligand passageways

Mueser, T. C., Rogers, P. H.&Arnone, A. (2000). Interface sliding as illustrated by the

Olson, J. S., Soman, J.&Phillips, G. N. (2007). Ligand pathways in myoglobin: A review of trp

Park, S.-Y., Yokoyama, T., Shibayama, N., Shiro, Y.&Tame, J. R. H. (2006). 1.25 Å Resolution

Peters, K. S., Watson, T.&Logan, T. (1992). Photoacoustic calorimetry study of human carboxyhemoglobin. *J. Am. Chem. Soc.,* 114, 11, pp. 4276-4278, 0002-7863 Petrich, J. W., Poyart, C.&Martin, J. L. (1988). Photophysics and reactivity of heme proteins:

Phillips, S. E. V.&Schoenborn, B. P. (1981). Neutron diffraction reveals oxygen-histidine

Projahn, H. D., Dreher, C.&Van Eldik, R. (1990). Effect of pressure on the formation and

Riccio, A., Tamburrini, M., Giardina, B.&di Prisco, G. (2001). Molecular Dynamics Analysis

cavity mutations. *IUBMB Life,* 59, 8-9, pp. 552-562, 1521-6551

hydrogen bond in oxymyoglobin. *Nature,* 292, 5818, pp. 81-82,

profile analysis. *J. Am. Chem. Soc.,* 112, 1, pp. 17-22, 0002-7863

photodissociation from heme model compounds: effect of proximal ligands. *Inorg* 

Substates in Oxymyoglobin through the pH-Dependence of the Low-Temperature Photoproduct Yield. *J. Am. Chem. Soc.,* 118, 19, pp. 4511-4517,

ligand binding and subunit association of human hemoglobins. Enthalpies of binding O2 and CO to subunit chains of hemoglobin A. *J. Biol. Chem.,* 254, 8, pp.

in human hemoglobin characterized by molecular dynamics simulations. *Biochim.* 

multiple quaternary structures of liganded hemoglobin. *Biochemistry,* 39, 50, pp.

Crystal Structures of Human Haemoglobin in the Oxy, Deoxy and Carbonmonoxy

a femtosecond absorption study of hemoglobin, myoglobin, and protoheme.

deoxygenation kinetics of oxymyoglobin. Mechanistic information from a volume

of a Second Phosphate Site in the Hemoglobins of the Seabird, South Polar Skua. Is There a Site-Site Migratory Mechanism along the Central Cavity? *Biophys. J.,* 81, 4,

*Methods Enzymol,* 360, pp. 302-329, 0076-6879

*Biophys. Acta,* 1724, 3, pp. 385-393, 0304-4165

Forms. *J. Mol. Biol.,* 360, 3, pp. 690-701, 0022-2836

*Biochemistry,* 27, 11, pp. 4049-4060, 0006-2960

*Chem,* 44, 4, pp. 1006-1014, 0020-1669

0002-7863

2875-2880,

15353-15364, 0006-2960

pp. 1938-1946, 0006-3495


**12** 

*1Russia 2Denmark* 

**Some Applications of Thermodynamics** 

Eugene A. Silow1, Andrey V. Mokry1 and Sven E. Jørgensen2

*2Chair of Environmental Chemistry, Copenhagen University,* 

*1Institute of Biology, UNESCO Chair of Water Resources, Irkutsk State University,* 

Now ecologists feel necessary to construct the theoretical building of system ecology, to break strong reductionistic tradition of ecology and to include the use of thermodynamics in a new holistic approach to study ecosystems, their structure, functioning and natural history. We tried to present here the current state of thermodynamic view on ecosystems. The first law of thermodynamics proclaims constancy of the total energy of isolated system for all changes, taking place in this system: energy cannot be created or destroyed. According to the second law of thermodynamics in isolated system entropy is always increasing or remaining constant. All processes in the Universe are oriented to the equilibrium state. Nevertheless, biological systems, and, consequently, ecological systems create order from disorder, they create and support chemical and physical non-equilibrium

In this chapter the general overview of ecosystem as thermodynamic system is given and the concept of Eco-Exergy is introduced. The use of this concept in ecology is demonstrated to be very fruitful. To make it easy for other researchers to use the Eco-Exergy the procedure of exergy evaluation for ecosystems is followed with special attention to dimensions used. The main applications of exergy in modern ecology are reviewed with special focus on practical use of Eco-Exergy, exergy index, and structural exergy for real ecosystem

Another application of irreversible thermodynamics (Prigogine's inventions) is discussed. The theory of hypercycles, developed for cycles of autocatalytic reactions and widely accepted in biochemistry and molecular biology can also be applied for ecological systems. The model of conjugated hypercycles, applied to ecological systems explains many aspects of their non-linear dynamics and can be used for analysis of oscillating processes in

Ecosystem is an open system. It supports structure and functioning due to external energy input. Usually ecosystem consume solar energy in the form of relatively short-wave radiation (visible light), though we know some ecosystems (e.g., at great depth in ocean)

**1. Introduction** 

state – the basis they live on.

ecological systems.

assessment and estimation of their health and disturbance.

**2. Ecosystem as thermodynamic system** 

**for Ecological Systems** 

Yonetani, T., Park, S. I., Tsuneshige, A., Imai, K.&Kanaori, K. (2002). Global allostery model of hemoglobin. Modulation of O(2) affinity, cooperativity, and Bohr effect by heterotropic allosteric effectors. *J. Biol. Chem.,* 277, 37, pp. 34508-34520, 0021-9258
