PHD thesis National University of Singapore Cao zhiwei Chapter Introduction 1.1 Protein motion and dynamics vs. protein function Protein motions and dynamics are involved in a variety of biological processes in living organisms. Though in some of these processes the static structure of a protein determines its function (e.g. collagen in tissues or α-keratin in hair), protein motions and dynamics are crucial in others cases. Examples are metabolism, transport and synthesis of biomolecules etc. In fact, all dynamic biological processes can find the origin in protein motions and dynamics. Muscle contraction, for example, is based on the combined motion of actin and myosin. Other examples are the molecular motors kinesin and F1-ATPase. Motion and dynamics also play important roles in many other proteins whose primary function is not mobility itself. Conformational change is actually essential to the function of many transport proteins, enzymes, and those proteins involved in signal transduction, immune protection or gene expression[1]. It has been noticed that the biological function of most of the globular proteins often includes an interaction with one or more different molecules on appropriate occasions, such as small ligand, substrate, peptide, a fragment of nucleic acids, even another protein. In many enzymes, conformational changes serve to enclose the substrate, thereby PHD thesis National University of Singapore Cao zhiwei preventing its release from the protein and ideally positioning it for the protein to perform its function, as in lysozyme. For example, immunoglobulins are highly flexible in order to be able to interact with a large range of ligands. Generally, functional interactions of flexible ligands with protein binding sites often require conformational adjustments in both the binding ligands and the host protein. The structural changes in some proteins regulate the interaction between ligands and protein through induced fit and allosteric effects [2,3] The “induced fit” theory by Koshland [4] proposed that the original structure of active site in enzymes does not fit substrate exactly, but the presence of the substrate induces structure changes in the active site to fit for substrate binding. It is expected that each intermediate step of the whole cycle of enzyme catalysis requires the enzyme molecule, especially the active site region, to be in a specific conformation different from another. Allosteric effect is found in a special class of proteins, so-called allosteric proteins. Substrate binding to one subunit of these multimeric proteins triggers conformational changes in proteins which alters the substrate affinity of the other subunits, thereby sharpening the switching response of these proteins [5,6]. Moreover, the importance of motion and dynamics to protein function has been further confirmed by various experimental studies. Two major sources of evidence come from Xray crystallographic analysis and Nuclear Magnetic Resonance (NMR). One example from X-ray analysis is myoglobin. In order to capture, bind and release oxygen (O2) freely, myoglobin has been found to have more mobile character toward the periphery of the molecule although the core surrounding of its heme group is compact [7]. A similar X- PHD thesis National University of Singapore Cao zhiwei ray analysis of lysozyme has produced the intriguing observation that the enzyme’s active site cleft undergoes an ~1 Å closure upon substrate binding [8]. On the other hand, NMR study revealed that several sub-states often exit for one protein or enzyme. These sub-states, which each have slightly different atomic arrangements, randomly interconvert at rates that increase with increasing temperature [9]. Instead of being stationary at fixed positions, the atoms in a protein molecule are rather in a state of constant motion. The “static” view of a protein structure from X-ray analysis is at best a representation of its average structure. The atoms in each protein molecule exhibit sizable high-frequency fluctuations about this average. The atomic fluctuation affects various bond interactions in proteins, especially those relatively weaker noncovalent interactions. For example, hydrogen bonds break when the partner atoms fluctuate out of a certain limit of distance, while alternative hydrogen bonds reform if the new partners come closer. Hydrogen bonds keep breaking and reforming during protein motion which gives protein molecule extra dynamic features. In summary, proteins are constantly changing the details of their conformation. Therefore any attempt to understand the function of proteins requires a scientific investigation of protein motion and dynamics. 1.2 Structure basis for protein motion and dynamics The motions of the atoms in a protein tend to share certain characteristics that can be explained in terms of the basic structure of proteins. Each protein is made up of a specific number of small units, the amino acids. Each of the 20 different amino acids is characterized by a side chain, a distinctive chemical group that ranges in complexity from PHD thesis National University of Singapore Cao zhiwei a hydrogen atom in the simplest amino acid, glycine, to elaborate rings of atoms in the most complex amino acid, tryptophan. The side chain of each amino acid can vary not only in size and shape, but also in charge, reactivity and ability of forming hydrogen bonds. Proteins are commonly consisting of from 50 to more than 500 amino acids, which corresponds to some 500 to 5,000 non-hydrogen atoms. The precise sequence of amino acids determines the average structure and other properties of the protein. In particular, the balance of the attractive and repulsive forces between the individual atoms of which the protein are composed causes the peptide to fold in a characteristic way essential to its motions and its functions. In a protein, the amino acids are linked together into a polypeptide chain by peptide bond, as being indicated in Fig 1.1. The peptide bond itself is rigid, because it is involved into tautomerization that gives it considerable double bond character, as Fig 1.2 shows. However, there are many other strong bonds in the main chain of the polypeptide free to twist. For instance, the N-C and C-C bonds relatively are free to rotate. These rotations are represented by the torsion angles phi (φ) and psi (ψ), respectively (shown in Fig 1.3). Phi and psi can vary to certain extent within the Ramanchandran Plots as Fig 1.4 shows [10]. This allows the protein to potentially adopt many different conformations. Therefore, the twisting, or bond rotation, allows one part of the polypeptide chain to move with respect to another. As the polypeptide chain twists and turns, its various side chains move with it. The side chains themselves have rotatable bonds which imparts additional flexibility. Fig 1.5 shows the rotatable bonds in peptide. PHD thesis National University of Singapore Cao zhiwei The flexibility of the polypeptide backbone and of the side chains is what enables each protein to fold into its characteristic native, or average, structure. These sites also facilitate the fluctuations of protein atoms around their average positions. Even in the folded protein, however, the thermal energy corresponding to the atomic velocities at room temperature is sufficient to allow twisting motions. Fig 1.1 Peptide bond of amino acids. The rectangle line is the part of the peptide bond. PHD thesis National University of Singapore Cao zhiwei Fig 1.2 Tautomerization of peptide bond Fig 1.3 Torsion angles in the main chain of protein. φ and ψ are free to rotate. PHD thesis National University of Singapore Cao zhiwei Fig 1.4: The Ramachandran plot. In the above diagram the white areas are sterically disallowed regions for all amino acids except glycine which lacks a side chain. The red regions correspond to conformations where there are no steric clashes, i.e. these are the allowed regions namely the alpha-helical and beta-sheet conformations. The yellow areas show the allowed regions if slightly shorter van der Waals radi are used in the calculation, i.e. the atoms are allowed to come a little closer together. PHD thesis National University of Singapore Cao zhiwei Fig 1.5 Sites of flexibility, rotatable bonds in peptide chain. The drawing depicts only the principal atoms of a polypeptide chain. The backbone of the chain (black bonds) consists of carbon and nitrogen atoms; the linkage called peptide bonds is rigid, whereas the intervening bonds allow rotations (curved arrows). The side chains shown in detail also contain rotatable bonds. PHD thesis National University of Singapore Cao zhiwei 1.3 Classification of protein motion Protein motion involves a wide variety of conformational change ranging from very subtle, local fluctuations to large, global movements. These may be motions of individual atoms, groups of atoms, or whole section of the molecule. Generally they can be classified into three broad categories for convenience according to their coherence, displacement amplitude and time-scale, as shown in Table 1A [11]. Methods used to study them are given in the table. Table 1A: Types of motions found in protein Motion Atomic fluctuations Spatial displacement (Å) 0.01 to Characteristic time (second) 10-15 to 10-11 Energy source kB T Collective motions 0.01 to >5 10-12 to 10-3 kB T Triggered conformational change 0.5 to >10 10-9 to 103 Inter-action Method of observation Computer simulation, X-ray diffraction NMR, fluorescence, hydrogen exchange, simulation, X-ray X-ray, spectroscopy The first category contains atomic fluctuations, such as individual atom vibrations. These motions are random, very fast, but rarely cover more than 0.5 Å. The time scale of these motions is in the order of picoseconds or less, and therefore it is usual to observe them by vibrational spectroscopy and to model them by molecular dynamics. X-ray diffraction can give information on the spatial distribution of atomic fluctuations though an analysis of the spreading of atomic electron density produced by such motion. The energy for these motions comes from the kinetic energy inherent in the proteins as a PHD thesis National University of Singapore Cao zhiwei function of temperature. They are normally driven by collisions with solvent molecules or by random collision with neighboring atoms in the protein. Although many of them individually may not be important for protein functions, they contain information that is of considerable significance. There may be a correlated directional character to the activesite fluctuations that play a role in enzyme catalysis. Furthermore, the small amplitude fluctuations are essential to all other motions in proteins. They serve as the “lubricant” which makes it possible for large-scale protein motions to happen on a physiological time scale. The second category contains collective motions, such as the movements of groups of atoms that are covalently linked in such a way that the group moves as a unit. Noncovalently interacting groups of atoms may also move collectively. The size of the group ranges from a few atoms to many hundreds of atoms, or even entire structural domains, as in the case of the flexible Fc portion of immunoglobulins [12]. There are two types of rapid collective motion: those that occur infrequently (like internal aromatic ringflips), and those that occur with high probability (many collective motions of small groups of neighboring atoms, bonded or nonbonded, are in the pico-second time regime.) Collective motions can also be very slow, as local unfolding of a polypeptide segments. The energy for collective motions also derives from the thermal energy inherent in a protein as a function of temperature. The time scale of collective motions (from picoseconds to nanoseconds or slower) allows some of them to be studied by techniques such as NMR and fluorescence spectroscopy. 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Cao Zhiwei, Zhang Heyun, Zhang Taiping etc. Purification of TPO-like protein from partially purified HEK cell fulture medium Journel of Nanjing University: Natural Science, 34, 83-88(1998). 2. Z. W. Cao, Y. Z. Chen Hydrogen bond disruption probability in proteins by a modified self-consistent harmonic approach Biopolymers,58, 319-328 (2001). 3. Y. Z. Chen, X. L. Gu, and Z. W. Cao, Can an optimization/scoring procedure in ligand-protein docking be employed to probe drug-resistant mutations in proteins? J. Mol. Graph. Mod.,19, 560-570 (2001). 4. Z. W. Cao, X. Chen and Y. Z. Chen. Correlation between Normal Modes in The 20-200cm-1 Frequency Range and Localized Torsion Motions Related to Certain Collective Motions in Proteins. J. Mol. Graph. Mod. 21,309-319. (2003). 5. Z. L. Ji, L. Z. Sun, X. Chen, C. J. Zheng, L. X. Yao, L. Y. Han, Z.W. Cao, J. F. Wang, W. K. Yeo, C.Z. Cai, and Y. Z. Chen. Internet Resources for Proteins Associated with Drug Therapeutic Effects, Adverse Reactions, and ADME. Drug Discovery Today Accepted(2003). 162 [...]... protein motions often has a combination of both motions, i.e., hinges in one part of the protein and shearing interfaces elsewhere Nevertheless, many protein large-scale collective motions can be described as occurring predominantly by a hinge or a shear mechanism, or none of them In the smaller intra-domain protein motions, hinge and shear mechanism are also involved in the collective motion, when individual... and direct results on protein motions In MD modeling, insights into molecular flexibility and activity are sought by numerically following molecular configurations in time according to Newton’s law of motions [18,19,20] One of the main tasks in MD simulation is to derive and analyze the overwhelming amount of trajectory that describes the time-dependant changes in atomic coordinates Several kinds of. .. various motions are summarized below Items Shear mechanism Hinged mechanism Well-packed interfaces MAINTAINED, throughout NOT MAINTAINED; rather motions created, burying surface Motion at interface Parallel to plane of interface Perpendicular to interface (shear) Mainchain packing Constrained by close packing Free to kink at hinge Mainchain torsions Small changes in many torsion angles Large changes in. .. permissive single bonds in main chain [11] Comparing with the short-time relatively small amplitude motions, the substantial displacement of this class of localized collective motions occur over longer time intervals, 11 PHD thesis National University of Singapore Cao zhiwei and result in concomitant displacements of the different fragments of protein, like domain or intra-domain motion in biological... developed and widely applied in studying protein collective motions and dynamics in the past decades Protein motion can be derived from atomic interactions based on knowledge of the structural fluctuations that occur as a result of thermal motion Such fluctuations can be obtained in various ways, such as molecular dynamics, harmonic dynamics, and stochastic dynamics, and others Molecular Dynamics (MD)... angles 1.4.1 Feature of hinge domain motion The most basic motion of a protein is a few large changes in main-chain torsion angles in the localized region, i.e., at flexible inter-domain linker regions The deformation of an extended strand is the simplest hinge motion because its only constraint is that the torsion angles of the strand remain in the allowed regions of the Ramachandran diagram Consequently,... summarized in Fig 1.6 and Table 1B According to analysis from Gerstein, motions of close packed segments of polypeptide can be divided into those that are perpendicular to an interface and those that are parallel Generally, hinge motions produce a motion perpendicular to the plane of an interface, so that the interface exists in one conformation but not in the other, as in the opening and closing of a book... Features of functionally important collective motions in protein Relatively large inter- or intra-domain movements provide spectacular examples of collective motions, and thus have been under extensive investigation because of their important functional roles They normally occur in proteins with half-rigid domains, or constrained sub-domains, or functional groups, linked by short flexible linker regions,... demanding Molecular mechanics is based on a rather simple model of molecular interactions within a system with contributions from processes such as bond stretching, bond angle bending, rotation of torsion angle and other interactions For convenince to describe the model we first divide these underlying forces in proteins into consideration of covalent interactions (namely bonds stretching, angle bending... thesis National University of Singapore Cao zhiwei Most of the standard amino acids found in proteins have uncharged side chain groups However, there are a number of basic residues which are positively charged at normal pH as in Lysine and Argine (Fig 2.7) : Fig 2.7 Charges of Arginine and Lysine In addition, histidine is normally charged at neutral pH (the charge normally residing on the delta carbon . functional interactions of flexible ligands with protein binding sites often require conformational adjustments in both the binding ligands and the host protein. The structural changes in some proteins. real protein motions often has a combination of both motions, i.e., hinges in one part of the protein and shearing interfaces elsewhere. Nevertheless, many protein large-scale collective motions. understand the function of proteins requires a scientific investigation of protein motion and dynamics. 1.2 Structure basis for protein motion and dynamics The motions of the atoms in a