Molecular Simulations of a Dynamic Protein Complex: Role of Salt-Bridges and Polar Interactions in Configurational Transitions

Ion charge pairs and hydrogen bonds have been extensively studied for their roles in stabilizing protein complexes and in steering the process of protein association. Recently, it has become clear that some protein complexes are dynamic in that they interconvert between several alternate configurations. We have previously characterized one such system: the EphA2:SHIP2 SAM-SAM heterodimer by solution NMR. Here we carried out extensive all-atom molecular-dynamics simulations on a microsecond time-scale starting with different NMR-derived structures for the complex. Transitions are observed between several discernible configurations at average time intervals of 50–100 ns. The domains reorient relative to one another by substantial rotation and a slight shifting of the interfaces. Bifurcated and intermediary salt-bridge and hydrogen-bond interactions play a role in the transitions in a process that can be described as moving along a “monkey-bar”. We notice an increased density of salt bridges near protein interaction surfaces that appear to enable these transitions, also suggesting why the trajectories can become kinetically hindered in regions where fewer of such interactions are possible. In this context, even microsecond molecular-dynamics simulations are not sufficient to sample the energy landscape unless the structures remain close to their experimentally derived low-energy configurations.     

Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations

The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in that it initially involves transitions to surfaces with fewer, less favorable contacts compared with those seen in the fully formed complex.     

Molecular Dynamics Simulations of a Membrane Protein/Amphipol Complex

Amphipathic polymers known as “amphipols” provide a highly stabilizing environment for handling membrane proteins in aqueous solutions. A8-35, an amphipol with a polyacrylate backbone and hydrophobic grafts, has been extensively characterized and widely employed for structural and functional studies of membrane proteins using biochemical and biophysical approaches. Given the sensitivity of membrane proteins to their environment, it is important to examine what effects amphipols may have on the structure and dynamics of the proteins they complex. Here we present the first molecular dynamics study of an amphipol-stabilized membrane protein, using Escherichia coli OmpX as a model. We begin by describing the structure of the complexes formed by supplementing OmpX with increasing amounts of A8-35, in order to determine how the amphipol interacts with the transmembrane and extramembrane surfaces of the protein. We then compare the dynamics of the protein in either A8-35, a detergent, or a lipid bilayer. We find that protein dynamics on all accessible length scales is restrained by A8-35, which provides a basis to understanding some of the stabilizing and functional effects of amphipols that have been experimentally observed.     

Molecular Simulations of Phase Transitions in Pores

Abstract

Methods for simulating phase transitions in narrow pores are reviewed, and the advantages and disadvantages of different techniques are discussed. Examples are given of applications to vapor-liquid, liquid-liquid, melting and freezing, solid-solid and layering transitions. While there has been a considerable body of simulation work on vapor-liquid, wetting and layering transitions for simple fluids and pore geometries, much remains to be done on more complex geometries and network effects, on heterogeneous surfaces, and on liquid-liquid, melting and solid-solid transitions in pores.     

Molecular Dynamics Simulations of a Calmodulin-peptide Complex in Solution

Abstract

We have performed an 4-ns MD simulation of calmodulin complexed with a target peptide in explicit water, under realistic conditions of constant temperature and pressure, in the presence of a physiological concentration of counterions and using Ewald summation to avoid truncation of long-range electrostatic forces. During the simulation the system tended to perform small fluctuations around a structure similar to, but somewhat looser than the starting crystal structure. The calmodulin-peptide complex was quite rigid and did not exhibit any large amplitude domain motions such as previously seen in apo- and calcium-bound calmodulin. We analyzed the calmodulin-peptide interactions by calculating buried surface areas, CHARMM interaction energies and continuum model interaction free energies. In the trajectory, the protein surface area buried by contact with the peptide is 1373 Ų, approximately evenly divided between the calmodulin N-terminal, C-terminal and central linker regions. A majority of this buried surface, 803 ·A², comes from nonpolar residues, in contrast to the protein as a whole, for which the surface is made up of mostly polar and charged groups. Our continuum calculations indicate that the largest favorable contribution to pep- tide binding comes from burial of molecular surface upon complex formation. Electrostatic contributions are favorable but smaller in the trajectory structures, and actually unfavorable for binding in the crystal structure. Since nonpolar groups make up most of buried surface of the protein, our calculations suggest that the hydrophobic effect is the main driving force for binding the helical peptide to calmodulin, consistent with thermodynamic analysis of experimental data. Besides the burial of nonpolar surface area, secondary contributions to peptide binding come from burial of polar surface and electrostatic interactions. In the nonpolar interactions a crucial role is played by the nine methionines of calmodulin. In the electrostatic interactions the negatively charged protein residues and positively charged peptide residues play a dominant role.     

Promotion of Crystal Phase Transitions by Mass-of-cell Control in Molecular Dynamics Simulations: Phase Transitions in Benzene Crystals

Abstract

The promotion of crystal phase transitions in molecular dynamics (MD) simulations was realized by controlling the momentum of the MD cell. It was implemented by increasing the mass or velocity of the MD cell instantaneously during simulations within the framework of the constant-pressure method by Parrinello and Rahman. This method induced phase transitions in benzene crystals which have not been obtained in conventional MD simulations. This method is useful for the global search of stable (and metastable) crystal structures.     

Molecular Dynamics Simulations of DNA-Polycation Complex Formation

Complexes formed from DNA and polycations are of interest because of their potential use in gene therapy; however, there remains a lack of understanding of the structure and formation of DNA-polycation complexes at atomic scale. In this work, molecular dynamics simulations of the DNA duplex d(CGCGAATTCGCG) in the presence of polycation chains are carried out to shed light on the specific atomic interaction that result in complex formation. The structures of complexes formed from DNA with polyethylenimine, which is considered one of the most promising DNA vector candidates, and a second polycation, poly-L-lysine, are compared. After an initial separation of ∼50 Å, the DNA and polycation come together and form a stable complex within 10 ns. The DNA does not undergo any major structural changes on complexation and remains in the B-form. In the formed complex, the charged amine groups of the polycation mainly interact with DNA phosphate groups, with polycation intrusion into the major and minor grooves dependent on the identity and charge state of the polycation. The ability of the polycation to effectively neutralize the charge of the DNA phosphate groups and the resulting influence on the DNA helix interaction are discussed.     

Increasing Protein Stability by Polar Surface Residues: Domain-Wide Consequences of Interactions Within a Loop

We have examined the influence of surface hydrogen bonds on the stability of proteins by studying the effects of mutations of human immunoglobulin light chain variable domain (V_L). In addition to the variants Y27dD, N28F, and T94H of protein κIV Len that were previously described, we characterized mutants M4L, L27cN, L27cQ, and K39T, double mutant M4L/Y27dD, and triple mutant M4L/Y27dD/T94H. The triple mutant had an enhanced thermodynamic stability of 4.2 kcal/mol. We determined the structure of the triple mutant by x-ray diffraction and correlated the changes in stability due to the mutations with changes in the three-dimensional structure. Y27dD mutant had increased stability of Len by 2.7 kcal/mol, a large value for a single mutation. Asp27d present in CDR1 formed hydrogen bonds with the side-chain and main-chain atoms within the loop. In the case of the K39T mutant, which reduces stability by 2 kcal/mol, Lys39 in addition to forming a hydrogen bond with a carbonyl oxygen of a neighboring loop may also favorably influence the surface electrostatics of the molecule. We showed that hydrogen bonds between residues in surface loops can add to the overall stability of the V_L domains. The contribution to stability is further increased if the surface residue makes more than one hydrogen bond or if it forms a hydrogen bond between neighboring turns or loops separated from each other in the amino acid sequence. Based on our experiments we suggest that stabilization of proteins might be systematically accomplished by introducing additional hydrogen bonds on the surface. These substitutions are more straightforward to predict than core-packing interactions and can be selected to avoid affecting the protein’s function.     

Phase Transitions in Coarse-Grained Lipid Bilayers Containing Cholesterol by Molecular Dynamics Simulations

Coarse-grained simulations of model membranes containing mixtures of phospholipid and cholesterol molecules at different concentrations and temperatures have been performed. A random mixing without tendencies for segregation or formation of domains was observed on spatial scales corresponding to a few thousand lipids and timescales up to several microseconds. The gel-to-liquid crystalline phase transition is successively weakened with increasing amounts of cholesterol without disappearing completely even at a concentration of cholesterol as high as 60%. The phase transition temperature increases slightly depending on the cholesterol concentration. The gel phase system undergoes a transition with increasing amounts of cholesterol from a solid-ordered phase into a liquid-ordered one. In the solid phase, the amplitude of the oscillations in the radial distribution function decays algebraically with a prefactor that goes to zero at the solid-liquid transition.     

Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations

Despite recent progress in proteomics most protein complexes are still unknown. Identification of these complexes will help us understand cellular regulatory mechanisms and support development of new drugs. Therefore it is really important to establish detailed information about the composition and the abundance of protein complexes but existing algorithms can only give qualitative predictions. Herein, we propose a new approach based on stochastic simulations of protein complex formation that integrates multi-source data—such as protein abundances, domain-domain interactions and functional annotations—to predict alternative forms of protein complexes together with their abundances. This method, called SiComPre (Simulation based Complex Prediction), achieves better qualitative prediction of yeast and human protein complexes than existing methods and is the first to predict protein complex abundances. Furthermore, we show that SiComPre can be used to predict complexome changes upon drug treatment with the example of bortezomib. SiComPre is the first method to produce quantitative predictions on the abundance of molecular complexes while performing the best qualitative predictions. With new data on tissue specific protein complexes becoming available SiComPre will be able to predict qualitative and quantitative differences in the complexome in various tissue types and under various conditions.     

Plants Actively Avoid State Transitions upon Changes in Light Intensity: Role of Light-Harvesting Complex II Protein Dephosphorylation in High Light

Photosystem II (PSII) core and light-harvesting complex II (LHCII) proteins in plant chloroplasts undergo reversible phosphorylation upon changes in light intensity (being under control of redox-regulated STN7 and STN8 kinases and TAP38/PPH1 and PSII core phosphatases). Shift of plants from growth light to high light results in an increase of PSII core phosphorylation, whereas LHCII phosphorylation concomitantly decreases. Exactly the opposite takes place when plants are shifted to lower light intensity. Despite distinct changes occurring in thylakoid protein phosphorylation upon light intensity changes, the excitation balance between PSII and photosystem I remains unchanged. This differs drastically from the canonical-state transition model induced by artificial states 1 and 2 lights that concomitantly either dephosphorylate or phosphorylate, respectively, both the PSII core and LHCII phosphoproteins. Analysis of the kinase and phosphatase mutants revealed that TAP38/PPH1 phosphatase is crucial in preventing state transition upon increase in light intensity. Indeed, tap38/pph1 mutant revealed strong concomitant phosphorylation of both the PSII core and LHCII proteins upon transfer to high light, thus resembling the wild type under state 2 light. Coordinated function of thylakoid protein kinases and phosphatases is shown to secure balanced excitation energy for both photosystems by preventing state transitions upon changes in light intensity. Moreover, PROTON GRADIENT REGULATION5 (PGR5) is required for proper regulation of thylakoid protein kinases and phosphatases, and the pgr5 mutant mimics phenotypes of tap38/pph1. This shows that there is a close cooperation between the redox- and proton gradient-dependent regulatory mechanisms for proper function of the photosynthetic machinery.Photosynthetic light reactions take place in the chloroplast thylakoid membrane. Primary energy conversion reactions are performed by synchronized function of the two light energy-driven enzymes PSII and PSI. PSII uses excitation energy to split water into electrons and protons. PSII feeds electrons to the intersystem electron transfer chain (ETC) consisting of plastoquinone, cytochrome b₆f, and plastocyanin. PSI oxidizes the ETC in a light-driven reduction of NADP to NADPH. Light energy is collected by the light-harvesting antenna systems in the thylakoid membrane composed of specific pigment-protein complexes (light-harvesting complex I [LHCI] and LHCII). The majority of the light-absorbing pigments are bound to LHCII trimers that can serve the light harvesting of both photosystems (Galka et al., 2012; Kouřil et al., 2013; Wientjes et al., 2013b). Energy distribution from LHCII is regulated by protein phosphorylation (Bennett, 1979; Bennett et al., 1980; Allen et al., 1981) under control of the STN7 and STN8 kinases (Depège et al., 2003; Bellafiore et al., 2005; Bonardi et al., 2005; Vainonen et al., 2005) and the TAP38/PPH1 and Photosystem II Core Phosphatase (PBCP) phosphatases (Pribil et al., 2010; Shapiguzov et al., 2010; Samol et al., 2012). LHCII trimers are composed of LHCB1, LHCB2, and LHCB3 proteins, and in addition to reversible phosphorylation of LHCB1 and LHCB2, the protein composition of the LHCII trimers also affects the energy distribution from the light-harvesting system to photosystems (Damkjaer et al., 2009; Pietrzykowska et al., 2014). Most of the LHCII trimers are located in the PSII-rich grana membranes and PSII- and PSI-rich grana margins of the thylakoid membrane, and only a minor fraction resides in PSI- and ATP synthase-rich stroma lamellae (Tikkanen et al., 2008b; Suorsa et al., 2014). Both photosystems bind a small amount of LHCII trimers in biochemically isolatable PSII-LHCII and PSI-LHCII complexes (Pesaresi et al., 2009; Järvi et al., 2011; Caffarri et al., 2014). The large portion of the LHCII, however, does not form isolatable complexes with PSII or PSI, and therefore, it separates as free LHCII trimers upon biochemical fractionation of the thylakoid membrane by Suc gradient centrifugation or in native gel analyses (Caffarri et al., 2009; Järvi et al., 2011), the amount being dependent on the thylakoid isolation method. Nonetheless, in vivo, this major LHCII antenna fraction serves the light-harvesting function. This is based on the fact that fluorescence from free LHCII, peaking at 680 nm in 77-K fluorescence emission spectra, can only be detected when the energy transfer properties of the thylakoid membrane are disturbed by detergents (Grieco et al., 2015).Regulation of excitation energy distribution from LHCII to PSII and PSI has, for decades, been linked to LHCII phosphorylation and state transitions (Bennett, 1979; Bennett et al., 1980; Allen et al., 1981). It has been explained that a fraction of LHCII gets phosphorylated and migrates from PSII to PSI, which can be evidenced as increase in PSI cross section and was assigned as transition to state 2 (for review, see Allen, 2003; Rochaix et al., 2012). The LHCII proteins are, however, phosphorylated all over the thylakoid membrane (i.e. in the PSII- and LHCII-rich grana core) in grana margins containing PSII, LHCII, and PSI as well as in PSI-rich stroma lamellae also harboring PSII-LHCII, LHCII, and PSI-LHCII complexes in minor amounts (Tikkanen et al., 2008b; Grieco et al., 2012; Leoni et al., 2013; Wientjes et al., 2013a)—making the canonical-state transition theory inadequate to explain the physiological role of reversible LHCII phosphorylation (Tikkanen and Aro, 2014). Moreover, the traditional-state transition model is based on lateral segregation of PSII-LHCII and PSI-LHCI to different thylakoid domains. It, however, seems likely that PSII and PSI are energetically connected through a shared light-harvesting system composed of LHCII trimers (Grieco et al., 2015), and there is efficient excitation energy transfer between the two photosystems (Yokono et al., 2015). Nevertheless, it is clear that LHCII phosphorylation is a prerequisite to form an isolatable PSI-LHCII complex called the state transition complex (Pesaresi et al., 2009; Järvi et al., 2011). Existence of a minor state transition complex, however, does not explain why LHCII is phosphorylated all over the thylakoid membrane and how the energy transfer is regulated from the majority of LHCII antenna that is shared between PSII and PSI but does not form isolatable complexes with them (Grieco et al., 2015).Plants grown under any steady-state white light condition show the following characteristics of the thylakoid membrane: PSII core and LHCII phosphoproteins are moderately phosphorylated, phosphorylation takes place all over the thylakoid membrane, and the PSI-LHCII state transition complex is present (Järvi et al., 2011; Grieco et al., 2012; Wientjes et al., 2013b). Upon changes in the light intensity, the relative phosphorylation level between PSII core and LHCII phosphoproteins drastically changes (Rintamäki et al., 1997, 2000) in the timescale of 5 to 30 min. When light intensity increases, the PSII core protein phosphorylation increases, whereas the level of LHCII phosphorylation decreases. On the contrary, a decrease in light intensity decreases the phosphorylation level of PSII core proteins but strongly increases the phosphorylation of the LHCII proteins (Rintamäki et al., 1997, 2000). The presence and absence of the PSI-LHCII state transition complex correlate with LHCII phosphorylation (similar to the state transitions; Pesaresi et al., 2009; Wientjes et al., 2013b). Despite all of these changes in thylakoid protein phosphorylation, the relative excitation of PSII and PSI (i.e. the absorption cross section of PSII and PSI measured by 77-K fluorescence) remains nearly unchanged upon changes in white-light intensity (i.e. no state transitions can be observed despite massive differences in LHCII protein phosphorylation; Tikkanen et al., 2010).The existence of the opposing behaviors of PSII core and LHCII protein phosphorylation, as described above, has been known for more than 15 years (Rintamäki et al., 1997, 2000), but the physiological significance of this phenomenon has remained elusive. It is known that PSII core protein phosphorylation in high light (HL) facilitates the unpacking of PSII-LHCII complexes required for proper processing of the damaged PSII centers and thus, prevents oxidative damage of the photosynthetic machinery (Tikkanen et al., 2008a; Fristedt et al., 2009; Goral et al., 2010; Kirchhoff et al., 2011). It is also known that the damaged PSII core protein D1 needs to be dephosphorylated before its proteolytic degradation upon PSII turnover (Koivuniemi et al., 1995). There is, however, no coherent understanding available to explain why LHCII proteins are dephosphorylated upon exposure of plants to HL and PSII core proteins are dephosphorylated upon exposure to low light (LL).The above-described light quantity-dependent control of thylakoid protein phosphorylation drastically differs from the light quality-dependent protein phosphorylation (Tikkanen et al., 2010). State transitions are generally investigated by using different light qualities, preferentially exciting either PSI or PSII. State 1 light favors PSI excitation, leading to oxidation of the ETC and dephosphorylation of both the PSII core and LHCII proteins. State 2 light, in turn, preferentially excites PSII, leading to reduction of ETC and strong concomitant phosphorylation of both the PSII core and LHCII proteins (Haldrup et al., 2001). Shifts between states 1 and 2 lights induce state transitions, mechanisms that change the excitation between PSII and PSI (Murata and Sugahara, 1969; Murata, 2009). Similar to shifts between state lights, the shifts between LL and HL intensity also change the phosphorylation of the PSII core and LHCII proteins (Rintamäki et al., 1997, 2000). Importantly, the white-light intensity-induced changes in thylakoid protein phosphorylation do not change the excitation energy distribution between the two photosystems (Tikkanen et al., 2010). Despite this fundamental difference between the light quantity- and light quality-induced thylakoid protein phosphorylations, a common feature for both mechanisms is a strict requirement of LHCII phosphorylation for formation of the PSI-LHCII complex. However, it is worth noting that LHCII phosphorylation under state 2 light is not enough to induce the state 2 transition but that the P-LHCII docking proteins in the PSI complex are required (Lunde et al., 2000; Jensen et al., 2004; Zhang and Scheller, 2004; Leoni et al., 2013).Thylakoid protein phosphorylation is a dynamic redox-regulated process dependent on the interplay between two kinases (STN7 and STN8; Depège et al., 2003; Bellafiore et al., 2005; Bonardi et al., 2005; Vainonen et al., 2005) and two phosphatases (TAP38/PPH1 and PBCP; Pribil et al., 2010; Shapiguzov et al., 2010; Samol et al., 2012). Concerning the redox regulation mechanisms in vivo, only the LHCII kinase (STN7) has so far been thoroughly studied (Vener et al., 1997; Rintamäki et al., 2000; Lemeille et al., 2009). The STN7 kinase is considered as the LHCII kinase, and indeed, it phosphorylates the LHCB1 and LHCB2 proteins (Bellafiore et al., 2005; Bonardi et al., 2005; Tikkanen et al., 2006). In addition to this, STN7 takes part in the phosphorylation of PSII core proteins (Vainonen et al., 2005), especially in LL (Tikkanen et al., 2008b, 2010). The STN8 kinase is required for phosphorylation of PSII core proteins in HL but does not significantly participate in phosphorylation of LHCII (Bellafiore et al., 2005; Bonardi et al., 2005; Vainonen et al., 2005; Tikkanen et al., 2010). It has been shown that, in traditional state 1 condition, which oxidizes the ETC, the dephosphorylation of LHCII is dependent on TAP38/PPH1 phosphatase (Pribil et al., 2010; Shapiguzov et al., 2010), whereas the PSII core protein dephosphorylation is dependent on the PBCP phosphatase (Samol et al., 2012). However, it remains unresolved whether and how the TAP38/PPH1 and PBCP phosphatases are involved in the light intensity-dependent regulation of thylakoid protein phosphorylation typical for natural environments.Here, we have used the two kinase (stn7 and stn8) and the two phosphatase (tap38/pph1and pbcp) mutants of Arabidopsis (Arabidopsis thaliana) to elucidate the individual roles of these enzymes in reversible thylakoid protein phosphorylation and distribution of excitation energy between PSII and PSI upon changes in light intensity. It is shown that the TAP38/PPH1-dependent, redox-regulated LHCII dephosphorylation is the key component to maintain excitation balance between PSII and PSI upon increase in light intensity, which at the same time, induces strong phosphorylation of the PSII core proteins. Collectively, reversible but opposite phosphorylation and dephosphorylation of the PSII core and LHCII proteins upon increase or decrease in light intensity are shown to be crucial for maintenance of even distribution of excitation energy to both photosystems, thus preventing state transitions. Moreover, evidence is provided indicating that the pH gradient across the thylakoid membrane is yet another important component in regulation of the distribution of excitation energy to PSII and PSI, possibly by affecting the regulation of thylakoid kinases and phosphatases.     

The Role of Solvent Interactions in Protein Conformatio

Abstract

For many years, the ease with which the pH of enzyme reactions could be varied has led to innumerable reports of the pH-dependence of the kinetic parameters of such reactions. These studies have been provided with a veneer of respectability by suggestions that they allow deductions to be made about the nature of the ionizing groups upon which the catalytic activity of the enzyme depends. It is the purpose of this article to summarize some of the reasons why a large proportion of pH-dependence studies yields little information about the real pK_a-values of ionizing groups in enzymes, and still less about the identity of these groups.     

Assembly and Kinetic Folding Pathways of a Tetrameric β-Sheet Complex: Molecular Dynamics Simulations on Simplified Off-Lattice Protein Models

We have performed discontinuous molecular dynamic simulations of the assembly and folding kinetics of a tetrameric β-sheet complex that contains four identical four-stranded antiparallel β-sheet peptides. The potential used in the simulation is a hybrid Go-type potential characterized by the bias gap parameter g, an artificial measure of a model protein's preference for its native state, and the intermolecular contact parameter η, which measures the ratio of intermolecular to intramolecular native attractions. The formation of the β-sheet complex and its equilibrium properties strongly depend on the size of the intermolecular contact parameter η. The ordered β-sheet complex in the folded state and nonaligned β-sheets or tangled chains in the misfolded state are distinguished by measuring the squared radius of gyration and the fraction of native contacts Q. The folding yield for the folded state is high at intermediate values of η, but is low at both small and large values of η. The folded state at small η is liquid-like, but is solid-like at both intermediate and large η. The misfolded state at small η contains nonaligned β-sheets and tangled chains with poor secondary structure at large η. Various folding pathways via dimeric and trimeric intermediates are observed, depending on η. Comparison with experimental results on protein aggregation indicates that intermediate η values are most appropriate for modeling fibril formation and small η values are most appropriate for modeling the formation of amorphous aggregates.     

Elastic Interactions of Photosynthetic Reaction Center Proteins Affecting Phase Transitions and Protein Distributions

Reaction-center proteins of Rhodopseudomonas Sphaeroides reconstituted into phosphatidylcholine vesicles shift and broaden the fluid-gel transition of the lipid bilayer. The amount of broadening and temperature shift of the transition depend both on protein concentration and on lipid chain length. In particular, the direction of the transition temperature shift is very sensitive to lipid chain length. Electron micrographs show homogeneous protein distribution on the fluid surface whereas the solid phase contains protein aggregates the type depending on chain length. The results can qualitatively be understood in the framework of a mattress model of lipid/protein interactions in membranes.     

蛋白质与极性配体复合物的绝对结合自由能计算

介绍了用分子动力学模拟与热力学积分法相结合,模拟蛋白质与配体的绝对结合自由能的方法.通过分子转换法,使蛋白质分子（包括水分子）与配体小分子之间的相互作用逐渐减弱 （或增强）至完全消失（或完全出现）. 运用体约束方法,计算了配体与受体结合后平动、转动自由度的丧失即熵效应所引起的自由能变化.以胰蛋白酶双突变体（D189G/G226D）与极性配体苯甲脒为例,研究了蛋白质活性部位与极性配体的相互作用对结合自由能的影响,该复合物绝对结合自由能的模拟结果(－15.5 kJ/mol)与实验值(－10.5 kJ/mol)相近.     

Crystal Structure of the cGMP-dependent Protein Kinase II Leucine Zipper and Rab11b Protein Complex Reveals Molecular Details of G-kinase-specific Interactions

cGMP-dependent protein kinase (PKG)-interacting proteins (GKIPs) mediate cellular targeting of PKG isoforms by interacting with their leucine zipper (LZ) domains. These interactions prevent aberrant signaling cross-talk between different PKG isotypes. To gain detailed insight into isotype-specific GKIP recognition by PKG, we analyzed the type II PKG leucine zipper domain and found that residues 40–83 dimerized and specifically interacted with Rab11b. Next, we determined a crystal structure of the PKG II LZ-Rab11b complex. The PKG II LZ domain presents a mostly nonpolar surface onto which Rab11b docks, through van der Waals interactions. Contact surfaces in Rab11b are found in switch I and II, interswitch, and the β1/N-terminal regions. This binding surface dramatically differs from that seen in the Rab11 family of interacting protein complex structures. Structural comparison with PKG Iα and Iβ LZs combined with mutagenic analysis reveals that GKIP recognition is mediated through surface charge interactions.     

Dynamic Fluctuations of Protein-Carbohydrate Interactions Promote Protein Aggregation

Protein-carbohydrate interactions are important for glycoprotein structure and function. Antibodies of the IgG class, with increasing significance as therapeutics, are glycosylated at a conserved site in the constant Fc region. We hypothesized that disruption of protein-carbohydrate interactions in the glycosylated domain of antibodies leads to the exposure of aggregation-prone motifs. Aggregation is one of the main problems in protein-based therapeutics because of immunogenicity concerns and decreased efficacy. To explore the significance of intramolecular interactions between aromatic amino acids and carbohydrates in the IgG glycosylated domain, we utilized computer simulations, fluorescence analysis, and site-directed mutagenesis. We find that the surface exposure of one aromatic amino acid increases due to dynamic fluctuations. Moreover, protein-carbohydrate interactions decrease upon stress, while protein-protein and carbohydrate-carbohydrate interactions increase. Substitution of the carbohydrate-interacting aromatic amino acids with non-aromatic residues leads to a significantly lower stability than wild type, and to compromised binding to Fc receptors. Our results support a mechanism for antibody aggregation via decreased protein-carbohydrate interactions, leading to the exposure of aggregation-prone regions, and to aggregation.