Invited Review Internal dynamics and protein–matrix coupling in trehalose-coated proteins Lorenzo Cordone a,b, T , Grazia Cottone a,b , Sergio Giuffrida a,b , Gerardo Palazzo c , Giovanni Venturoli b,d , Cristiano Viappiani b,e a Dipartimento di Scienze Fisiche ed Astronomiche, Universita ` di Palermo, Italy b INFM, Italy c Dipartimento di Chimica, Universita ` di Bari, Italy d Laboratorio di Biochimica e Biofisica, Dipartimento di Biologia, Universita ` di Bologna, Italy e Dipartimento di Fisica, Universita ` di Parma, Italy Received 12 October 2004; received in revised form 4 March 2005; accepted 4 March 2005 Available online 15 April 2005 Abstract We review recent studies on the role played by non-liquid, water-containing matrices on the dynamics and structure of embedded proteins. Two proteins were studied, in water–trehalose matrices: a water-soluble protein (carboxy derivative of horse heart myoglobin) and a membrane protein (reaction centre from Rhodobacter sphaeroides ). Several experimental techniques were used: Mfssbauer spectroscopy, elastic neutron scattering, FTIR spectroscopy, CO recombination after flash photolysis in carboxy-myoglobin, kinetic optical absorption spectroscopy following pulsed and continuous photoexcitation in Q B containing or Q B deprived reaction centre from R. sphaeroides . Experimental results, together with the outcome of molecular dynamics simulations, concurred to give a picture of how water-containing matrices control the internal dynamics of the embedded proteins. This occurs, in particular, via the formation of hydrogen bond networks that anchor the protein surface to the surrounding matrix, whose stiffness increases by lowering the sample water content. In the conclusion section, we also briefly speculate on how the protein–matrix interactions observed in our samples may shed light on the protein–solvent coupling also in liquid aqueous solutions. D 2005 Elsevier B.V. All rights reserved. Keywords: Carboxy myoglobin; Trehalose; Water association band; CO stretching band; Flash photolysis; Reaction centre 1. Introduction As it is well known, proteins can assume a very large number of different structures, which are described through a 3N  3 dimension energy landscape, where N is the number of atoms in the protein and of atoms in the surroundings, whose interaction with the protein is not vanishing [1–3]. Such landscape is hierarchically organized in tiers charac- terized by the height of the barrier between the different minima in the given tier, which represent the quasi iso- energetic conformational substates [4]. A simplified cross section through the landscape is sketched in Fig. 1; the particular shape, first proposed by Frauenfelder, emerged from experimental [4–7], theoretical [8] and computer simulation data [9]. In particular, the presence of quasi iso - energetic conformational substates, which determine the tier’s roughness , has been experimentally evidenced by hole burning experiments down to the millikelvin range [10]. This indicates that, even at a very low temperature, motions of protein atoms take place within a non-parabolic potential well, and that interconversion among conformational sub- states of suitable tiers is present at temperatures much lower than the temperature at which the so-called dynamic transition (see below) takes place. In particular, when proteins are embedded in a rigid surrounding as e.g. at 1570-9639/$ - see front matter D 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.bbapap.2005.03.004 T Corresponding author. Dipartimento di Scienze Fisiche ed Astrono- miche, Universita ` di Palermo, Italy. Tel.: +39 0916234215; fax: +39 0916162461. E-mail address: cordone@fisica.unipa.it (L. Cordone). Biochimica et Biophysica Acta 1749 (2005) 252 – 281 http://www.elsevier.com/locate/bba