Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details.

Integration of experimental and computational approaches to investigate chemical reactions in proteins has proven to be very successful. Experimentally, time-resolved FTIR difference-spectroscopy monitors chemical reactions at atomic detail. To decode detailed structural information encoded in IR spectra, QM/MM calculations are performed. Here, we present a novel method which we call local mode analysis (LMA) for calculating IR spectra and assigning spectral IR-bands on the basis of movements of nuclei and partial charges from just a single QM/MM trajectory. Through LMA the decoding of IR spectra no longer requires several simulations or optimizations. The novel approach correlates the motions of atoms of a single simulation with the corresponding IR bands and provides direct access to the structural information encoded in IR spectra. Either the contributions of a particular atom or atom group to the complete IR spectrum of the molecule are visualized, or an IR-band is selected to visualize the corresponding structural motions. Thus, LMA decodes the detailed information contained in IR spectra and provides an intuitive approach for structural biologists and biochemists. The unique feature of LMA is the bidirectional analysis connecting structural details to spectral features and vice versa spectral features to molecular motions.

Bioinformatic tools uncover the C-terminal strand of Rubisco's large subunit as hot-spot for specificity-enhancing mutations.

Rubisco assumes the double role of accumulating biomass by fixing carbon dioxide to ribulose-1,5-bisphosphate and binding of molecular oxygen to the same substrate. The specificity factor of this mutually competitive activity, defined as the ratio of carboxylation to oxygenation efficiency, varies considerably for reasons which remain obscure. The explanation and the enhancement of specificity are of high theoretical and practical interest. Despite a wealth of structures and experimental findings, the systematic analysis of available data is still at its beginning. Here, we (a) present an analysis of sequences of the large subunit which reliably finds specificity-enhancing mutations and ranks them according to the probability of success. For mutations near the C-terminus, we (b) show by simulations that the positive influence they have on specificity can be explained by the time-window hypothesis.

The kinetics of conformation change as determinant of Rubisco's specificity.

The molecular basis of Rubisco's specificity is investigated in terms of the structure and kinetics of the enzyme. We propose that the rates of the conformational changes (closing/opening) of the binding niche exert a crucial influence on apparent binding rates and the enzyme's specificity. An extended reaction scheme for binding and conformational kinetics is presented and expressed in a mathematical model. The closed conformation, known from X-ray structures, is assumed to be necessary for binding of the gaseous substrates (carbon dioxide and oxygen) and for catalysis. Opening the niche interrupts catalysis and enables a fast exchange of those molecules between the internal cavity and the surrounding solvent. Our model predicts that specificity of Rubisco for CO(2) increases with the rate by which the niche opens. This is due to the fact that binding of the carbon dioxide is faster than oxygen binding, which is hampered by spin inversion. The apparent rate of carbon dioxide binding correlates with the repetition rate of the conformational change, and the rate of oxygen binding with the probability of the closed state.

Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum.

The transitions between the water-equilibrated structures of the GTP and GDP forms of Ha-ras-p21 have been calculated by using the targeted molecular dynamics (TMD) method (Schlitter et al., Mol. Sim. 10:291-309, 1993) both in vacuo and with explicit solvent simulation. These constrained molecular dynamics calculations result in different pathways, depending on the nucleotide bound. Each pathway consists in a sequence of transitions affecting six segments of the protein, four of them forming a hydrophilic cleft around the nucleotide. The transitions are initiated by the removal or introduction of the gamma-phosphate of the nucleotide and proceed sequentially, crossing several low-energy transition states. The movements are transmitted either by direct interactions between the segments or through the nucleotide. The GTP to GDP pathway is initiated by the removal of the nucleotide gamma-phosphate. This gives some space to Gly12, Gly13, and Val14. Their movement is transmitted to the target recognition domain and the switch II region, forcing these segments to adopt another position. In a second step the target recognition domain and the switch II region undergo conformational transitions to reach an intermediate conformation. Finally, there is a relaxation of the target recognition domain to its final state that forces the switch II region to reach its target conformation. The calculated pathways allow the identification of many residues that play an important role in the conformational changes, explain the altered transformation properties of some, and suggest mutations to alter the pathway.

Modelling pathways of alpha-chymotrypsin activation and deactivation.

The conformational change of alpha-chymotrypsin from an inactive, chymotrypsinogen like structure at high pH to an active conformation around pH 8.5 is used here as a model system to generate possible pathways for the transition by use of two different theoretical methods. One method, the 'targeted molecular dynamics' algorithm (TMD) adds a constraint in the direction of the target to a molecular dynamics force field and gives two different paths, one for every direction of the reaction (Schlitter,J., Engels,M., Krüger,P.J., Mol. Graphics (1994) 12, 84-89). The second method, the 'self penalty walk' algorithm (SPW), refines an initially guessed path by minimizing the sum of the energies of its structures (Elber,R. and Karplus,M., Chem. Phys. Lett. (1987) 139, 375-380). Thus, starting from a linear path as a first approximation, it produces a reaction coordinate of the transition. The structures of the TMD and SPW paths are similar only in the beginning while the middle part of the SPW path links the two TMD branches. The activation of alpha-chymotrypsin in the TMD path starts with a movement of loop VII (residues 215-225), pulling on loop VI (residues 186-194). Then the side chain of Met192 turns to the surface and Ile16 approaches Asp194 to form a salt bridge. In the TMD deactivation path, loop VII also moves and pushes loop VI to the protein core. The Met192 side chain adopts three intermediate conformations, till the salt bridge Ile16-Asp194 is broken and loop VI rearranges to its final conformation. In the SPW pathway both the formation of the salt bridge and the movement of Met192 happen simultaneously between two consecutive steps.

Simulation of a complex protein structural change: the T <--> R transition in the insulin hexamer.

The T <--> R transition in the insulin hexamer is an outstanding model for protein structural changes in terms of its extent and complexity: the limiting structures T(6), T(3)R(3) and R(6) have been defined by X-ray crystallography. The transition occurs cooperatively within trimers. It involves displacements of >30 A and a secondary structural rearrangement of 15% of the peptide chain between extended and helical conformations. Experimental data for the transition are plentiful. Theoretical methods to simulate pathways without constraints would never succeed with such substantial transitions. We have developed two approaches, targeted energy minimization (TEM) and targeted molecular dynamics (TMD). Previously successful in simulating the T <--> R transition of the insulin monomer, these procedures are also shown here to be effective in the hexamer. With TMD, more conformational space is explored and pathways are found at 500 kJ/mol lower energy than with TEM. Because the atoms have to meet distance constraints in sum rather than individually, a high degree of conformational freedom and independence is implied. T(6) --> T(3)R(3) and T(3)R(3) --> T(6) pathways do not coincide because the transformation is directed. One subunit enters a dead end pathway in one direction of the TMD simulation, which shows that constraint and freedom are critically balanced. The ensemble of productive pathways represents a plausible corridor for the transition. A video display of the transformations is available.

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions.

Molecular dynamics simulations have proven to be a valuable tool to investigate the dynamic behavior of stable macromolecules at finite temperatures. However, considerable conformational transitions take place during a simulation only accidentally or at exceptionally high temperatures far from the range of experimental conditions. Targeted molecular dynamics (TMD) is a method to induce a conformational change to a known target structure at ordinary temperature by applying a time-dependent, purely geometrical constraint. The transition is enforced independently of the height of energy barriers, while the dynamics of the molecule is only minimally influenced by the constraint. Simulations of decaalanine and insulin show the ability of the method to explore the configurational space for pathways accessible at a given temperature. The transitions studied at insulin comprise unfolding of an alpha-helical portion and, in the reverse direction, refolding from an extended conformation. A possible application of TMD is the search for energy barriers and stable intermediates from rather local changes up to protein denaturation.

The T<-->R structural transition of insulin; pathways suggested by targeted energy minimization.

The transition of insulin between its crystallographically defined states T and R is connected with considerable change even of backbone structure: the N-terminal B chain (residues B1-B8) refolds from extended conformation in T into helical in R, and vice versa. Although hitherto observed only in hexamers the transition of the monomer was adequate for developing and testing the method of 'targeted energy minimization' (TEM), capable of coping with conformational changes of such extent at moderate computational expenditure. The simulation is performed in a predetermined number of steps consisting of two atomic displacements each, one by force in the direction of the target structure, the second by energy minimization releasing the constraint caused in the first. The transition pathway is represented by the string of energy minimized transient structures. Due to the directedness of the algorithm the simulated pathway for R-->T is not the reversal of that for T-->R. It is, therefore, not pretended that the minimum energy pathway was identified. In the T-->R direction the N-terminal B chain first swivels while remaining largely stretched and then winds up extending the pre-existing helix B9-B19. The A chain advances into the space abandoned and withdraws from it in the R-->T simulation. In the latter the extended helix first kinks at B8/B9, and then the B1-B8 segment is unwound and stretched. The helical H-bonds of that segment are formed late in T-->R and are maintained during almost half of R-->T. The AN helix is less stable and more involved in the transitions than helix AC.(ABSTRACT TRUNCATED AT 250 WORDS)

Temperature-jump studies and polarized absorption spectroscopy of methemoglobin-thiocyanate single crystals.

Association equilibria and association kinetics of the thiocyanate binding reaction to methemoglobin in single crystals and solution are studied using temperature-jump technique and polarized absorption spectroscopy. Different kinetic constants are found for the reaction in solution and crystal phase for the alpha- and beta-subunits of the methemoglobin tetramer. The reduction of the reactivity of the alpha- and beta-subunits in crystalline phase is 6-fold and 2.4-fold, respectively, compared to the values found in solution. The intramolecular binding reaction of the N epsilon of the distal histidine E7 which is observed in methemoglobin in solution cannot be detected in single crystals. Our results suggest that crystallization of hemoglobin has little influence on small-scale structural fluctuations which are necessary for ligands to get to the binding sites and large-scale structural motions are suppressed.

Structural fluctuations and conformational entropy in proteins: entropy balance in an intramolecular reaction in methemoglobin.

The reversible intramolecular binding of the distal histidine side chain to the heme iron in methemoglobin is of special interest due to the very large negative reaction entropy which overcompensates the large reaction enthalpy. It may be considered as a prominent example of the ability of proteins (including enzymes) to provide global entropy in a local process. In this work new experiments and model calculations are reported which aim at finding the structural elements contributing to the reaction entropy. Geometrical studies prove the implication of the 20 residue E-helix being shifted by more than 2 A. Vibrational entropies are calculated by a procedure derived from the method of Karplus and Kushik. It turns out that neither the histidine alone nor the complete E-helix contribute more than 15 per cent of the required entropy.

Residual motion of hemoglobin-bound spin labels as a probe for protein dynamics.

The residual motion of spin labels bound to cysteine beta 93 of methemoglobin and oxyhemoglobin has been analyzed as a function of temperature and hydration. The rotational diffusion of the whole protein molecule has been prevented or restricted by crystallization, lyophilization or by high viscosity of the solution. The residual motion of the labels is characterized by an angle of the limited motion cone and their rotational correlation time using computer simulations of the EPR spectra. Two types of motion can be separated due to different correlation times and different dependences on temperature and hydration. One of these motional mechanisms can be shown to be determined by protein fluctuations. Correlation times of these fluctuations decrease from 2 X 10(-8) s at T = 220 K to 10(-9) s at T = 300 K in the samples of high water concentration. Strong correlation between the properties of the hydration shell and these fluctuations are observed.

Rapid energy exchange of enzymes with solvent water by dipolar interaction.

One important problem for the function of proteins, especially enzymes, concerns the exchange of energy with the surrounding medium. In this paper, we study the interaction of vibrational degrees of freedom with the fluctuating water dipole moments. The rates of activation or deactivation attain a maximum at slow frequency vibrations near the water dispersion frequencies, i.e. in the gigahertz region. For medium proteins with molecular weights of approximately 10(4) a.m.u., the rates are estimated to be of the order of magnitude of kBT/h, the frequency factor of the transition state theory. We discuss the connection between energy exchange and reaction rates and show that a rapid energy exchange is at least a necessary condition for enzymatic catalysis.

A statistical mechanical treatment of fatty acyl chain order in phospholipid bilayers and correlation with experimental data. A. Theory.

A theoretical model has been developed in order to describe the organization of acyl chains in phospholipid bilayers. Since the model is intended to reproduce highly quantitative experimental results such as the deuterium magnetic resonance (NMR) data and to supplement the experimental information, all the rotameric degrees of freedom, the excluded volume interactions and the van der Waals interactions have been considered. The model is a direct extension of a generalized van der Waals theory of nematic liquid crystals to flexible molecules. In this picture, the anisotropy of the short-range repulsive forces which are treated by a hard core potential is introduced as the dominant factor governing intrinsic order among the chains. The anisotropy of the attractive forces, which are approximated by a molecular field, plays a somewhat secondary role. The dependence of the energy of interaction on the relative chain conformations is approximated by two order parameters reflecting respectively the 'average shape' of the molecules and the 'average shape' in a 'mean orientation'. The influence of the interactions in the polar region on the lateral chain area is accounted for by an effective lateral pressure. In certain aspects the model has features in common with the Marcelja theory.

A statistical mechanical treatment of fatty acyl chain order in phospholipid bilayers and correlation with experimental data. B. Dipalmitoyl-3-sn-phosphatidylcholine.

In order to help bridge the conceptual gap between experimental data on chains of phospholipid molecules and their microscopic organization, a theoretical model has proposed in a preceding paper. The intentions associated with the new theory were to describe a model able to reproduce accurately the experimental data. This capability is essential to monitor some of the mechanisms behind the physical data. The results presented here show first that, provided a suitable fitting of the phenomenological parameters entailed in the model, the theory indeed gives good agreement with experimental data (2H-NMR, neutron scattering, calorimetry) obtained for a dipalmitoyl-3-sn-phosphatidylcholine bilayer. This property of the model is then specifically used to describe the nature of the perturbing effects of local anaesthetics and cholesterol on the organization of the acyl chains and to correlate these effects with the experimental data. Finally the theoretical model is used to supplement experimental data by describing the acyl chain organization in terms of the most probable spectrum of chain conformations. Predictions are made about the one-, two- and three-dimensional mean spatial characteristics of the acyl chains.