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Biomedical subjects

K Schulten

Publications and source records attributed to K Schulten.

At least 19 recordsLinked to original sources
PubMed2003

Forced detachment of the CD2-CD58 complex.

The force-induced detachment of the adhesion protein complex CD2-CD58 was studied by steered molecular dynamics simulations. The forced detachment of CD2 and CD58 shows that the system can respond to an external force by two mechanisms, which depend on the loading rate. At the rapid loading rates of 70 and 35 pN/ps (pulling speeds of 1 and 0.5 A/ps) the two proteins unfold before they separate, whereas at slower loading rates of 7 and 3.5 pN/ps (pulling speeds of 0.1 and 0.05 A/ps), the proteins separate before the domains can unfold. When subjected to a constant force of 400 pN, the two proteins separated without significant structural distortion. These findings suggest that protein unfolding is not coupled to the adhesive function of CD2 and CD58. The simulations further confirm that salt bridges primarily determine the tensile strength of the protein-to-protein bond, and that the order of salt bridge rupture depends mainly on the position of the bond, relative to the line of action of the applied force. Salt bridges close to this line break first. The importance of each of the salt bridges for adhesion, determined from the simulations, correlates closely with their role in cell-to-cell adhesion and equilibrium binding determined by site-directed mutagenesis experiments.

Binding Sites↗
PubMed2002

The role of intersection topography in bond selectivity of cis-trans photoisomerization.

Ab initio methods are used to characterize the ground and first excited state of the chromophore in the rhodopsin family of proteins: retinal protonated Schiff base. Retinal protonated Schiff base has five double bonds capable of undergoing isomerization. Upon absorption of light, the chromophore isomerizes and the character of the photoproducts (e.g., 13-cis and 11-cis) depends on the environment, protein vs. solution. Our ab initio calculations show that, in the absence of any specific interactions with the environment (e.g., discrete ordered charges in a protein), energetic considerations cannot explain the observed bond selectivity. We instead attribute the origin of bond selectivity to the shape (topography) of the potential energy surfaces in the vicinity of points of true degeneracy (conical intersections) between the ground and first excited electronic states. This provides a molecular example where a competition between two distinct but nearly isoenergetic photochemical reaction pathways is resolved by a topographical difference between two conical intersections.

Biophysical Phenomena↗
PubMed2001

Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer.

The aquaporin-1 water channel was modeled in a palmitoyl-oleoyl-phosphatidyl-choline lipid bilayer, by means of molecular dynamics simulations. Interaction of the protein with the membrane and inter-monomer interactions were analyzed. Structural features of the channel important for its biological function, including the Asn-Pro-Ala (NPA) motifs, and the diffusion of water molecules into the channels, were investigated. Simulations revealed the formation of single file water inside the channels for certain relative positions of the NPA motifs.

Aquaporin 1↗
PubMed2001

Comparison of the early stages of forced unfolding for fibronectin type III modules.

The structural changes accompanying stretch-induced early unfolding events were investigated for the four type III fibronectin (FN-III) modules, FN-III(7), FN-III(8), FN-III(9), and FN-III(10) by using steered molecular dynamics. Simulations revealed that two main energy barriers, I and II, have to be overcome to initiate unraveling of FN-III's tertiary structure. In crossing the first barrier, the two opposing beta-sheets of FN-III are rotated against each other such that the beta-strands of both beta-sheets align parallel to the force vector (aligned state). All further events in the unfolding pathway proceed from this intermediate state. A second energy barrier has to be overcome to break the first major cluster of hydrogen bonds between adjacent beta-strands. Simulations revealed that the height of barrier I varied significantly among the four modules studied, being largest for FN-III(7) and lowest for FN-III(10), whereas the height of barrier II showed little variation. Key residues affecting the mechanical stability of FN-III modules were identified. These results suggest that FN-III modules can be prestretched into an intermediate state with only minor changes to their tertiary structures. FN-III(10), for example, extends 12 A from the native "twisted" to the intermediate aligned state, and an additional 10 A from the aligned state to further unfolding where the first beta-strand is peeled away. The implications of the existence of intermediate states regarding the elasticity of fibrillar fibers and the stretch-induced exposure of cryptic sites are discussed.

Amino Acid Sequence↗
PubMed2001

Phylogenetic analysis of metabolic pathways.

The information provided by completely sequenced genomes can yield insights into the multi-level organization of organisms and their evolution. At the lowest level of molecular organization individual enzymes are formed, often through assembly of multiple polypeptides. At a higher level, sets of enzymes group into metabolic networks. Much has been learned about the relationship of species from phylogenetic trees comparing individual enzymes. In this article we extend conventional phylogenetic analysis of individual enzymes in different organisms to the organisms' metabolic networks. For this purpose we suggest a method that combines sequence information with information about the underlying reaction networks. A distance between pathways is defined as incorporating distances between substrates and distances between corresponding enzymes. The new analysis is applied to electron-transfer and amino acid biosynthesis networks yielding a more comprehensive understanding of similarities and differences between organisms.

Animals↗
PubMed2001

Simulated refolding of stretched titin immunoglobulin domains.

Steered molecular dynamics (SMD) is used to investigate forced unfolding and spontaneous refolding of immunoglobulin I27, a domain of the muscle protein titin. Previous SMD simulations revealed the events leading to stretch-induced unfolding of I27, the rupture of hydrogen bonds bridging beta-strands A and B, and those bridging beta-strands A' and G, the latter rupture occurring at an extension of approximately 15 A and preceding the complete unfolding. Simulations are now used to study the refolding of partially unfolded I27 domains. The results reveal that stretched domains with ruptured interstrand hydrogen bonds shrink along the extension direction. Two types of refolding patterns are recognized: for separated beta-strands A' and G, in most simulations five of the six hydrogen bonds between A' and G stably reformed in 2 ns, whereas for separated beta-strands A and B hydrogen bonds seldom reformed in eight 2-ns simulations. The mechanical stability of the partially refolded intermediates has been tested by re-stretching.

Connectin↗
PubMed2001

Structural determinants of MscL gating studied by molecular dynamics simulations.

The mechanosensitive channel of large conductance (MscL) in prokaryotes plays a crucial role in exocytosis as well as in the response to osmotic downshock. The channel can be gated by tension in the membrane bilayer. The determination of functionally important residues in MscL, patch-clamp studies of pressure-conductance relationships, and the recently elucidated crystal structure of MscL from Mycobacterium tuberculosis have guided the search for the mechanism of MscL gating. Here, we present a molecular dynamics study of the MscL protein embedded in a fully hydrated POPC bilayer. Simulations totaling 3 ns in length were carried out under conditions of constant temperature and pressure using periodic boundary conditions and full electrostatics. The protein remained in the closed state corresponding to the crystal structure, as evidenced by its impermeability to water. Analysis of equilibrium fluctuations showed that the protein was least mobile in the narrowest part of the channel. The gating process was investigated through simulations of the bare protein under conditions of constant surface tension. Under a range of conditions, the transmembrane helices flattened as the pore widened. Implications for the gating mechanism in light of these and experimental results are discussed.

Computer Simulation↗
PubMed2001

Steered molecular dynamics and mechanical functions of proteins.

Atomic force microscopy of single molecules, steered molecular dynamics and the theory of stochastic processes have established a new field that investigates mechanical functions of proteins, such as ligand-receptor binding/unbinding and elasticity of muscle proteins during stretching. The combination of these methods yields information on the energy landscape that controls mechanical function and on the force-bearing components of proteins, as well as on the underlying physical mechanisms.

Avidin↗
PubMed2001

The mechanism of glycerol conduction in aquaglyceroporins.

BACKGROUND: The E. coli glycerol facilitator, GlpF, selectively conducts glycerol and water, excluding ions and charged solutes. The detailed mechanism of the glycerol conduction and its relationship to the characteristic secondary structure of aquaporins and to the NPA motifs in the center of the channel are unknown. RESULTS: Molecular dynamics simulations of GlpF reveal spontaneous glycerol and water conduction driven, on a nanosecond timescale, by thermal fluctuations. The bidirectional conduction, guided and facilitated by the secondary structure, is characterized by breakage and formation of hydrogen bonds for which water and glycerol compete. The conduction involves only very minor changes in the protein structure, and cooperativity between the GlpF monomers is not evident. The two conserved NPA motifs are strictly linked together by several stable hydrogen bonds and their asparagine side chains form hydrogen bonds with the substrates passing the channel in single file. CONCLUSIONS: A complete conduction of glycerol through the GlpF was deduced from molecular dynamics simulations, and key residues facilitating the conduction were identified. The nonhelical parts of the two half-membrane-spanning segments expose carbonyl groups towards the channel interior, establishing a curve-linear pathway. The conformational stability of the NPA motifs is important in the conduction and critical for selectivity. Water and glycerol compete in a random manner for hydrogen bonding sites in the protein, and their translocations in single file are correlated. The suggested conduction mechanism should apply to the whole family.

Amino Acid Motifs↗
PubMed2001

Steered molecular dynamics investigations of protein function.

Molecular recognition and mechanical properties of proteins govern molecular processes in the cell that can cause disease and can be targeted for drug design. Single molecule measurement techniques have greatly advanced knowledge but cannot resolve enough detail to be interpreted in terms of protein structure. We seek to complement the observations through so-called Steered Molecular Dynamics (SMD) simulations that link directly to experiments and provide atomic-level descriptions of the underlying events. Such a research program has been initiated in our group and has involved, for example, studies of elastic properties of immunoglobulin and fibronectin domains as well as the binding of biotin and avidin. In this article we explain the SMD method and suggest how it can be applied to the function of three systems that are the focus of modern molecular biology research: force transduction by the muscle protein titin and extracellular matrix protein fibronectin, recognition of antibody-antigene pairs, and ion selective conductivity of the K+ channel.

Antigen-Antibody Reactions↗
PubMed2000

Computer modeling of force-induced titin domain unfolding.

Titin, a 1 micron long protein found in striated muscle myofibrils, possesses unique elastic and extensibility properties, and is largely composed of a PEVK region and beta-sandwich immunoglobulin (Ig) and fibronectin type III (FnIII) domains. The extensibility behavior of titin has been shown in atomic force microscope and optical tweezer experiments to partially depend on the reversible unfolding of individual Ig and FnIII domains. We performed steered molecular dynamics simulations to stretch single titin Ig domains in solution with pulling speeds of 0.1-1.0 A/ps, and FnIII domains with a pulling speed of 0.5 A/ps. Resulting force-extension profiles exhibit a single dominant peak for each domain unfolding, consistent with the experimentally observed sequential, as opposed to concerted, unfolding of Ig and FnIII domains under external stretching forces. The force peaks can be attributed to an initial burst of a set of backbone hydrogen bonds connected to the domains' terminal beta-strands. Constant force stretching simulations, applying 500-1000 pN of force, were performed on Ig domains. The resulting domain extensions are halted at an initial extension of 10 A until the set of all six hydrogen bonds connecting terminal beta-strands break simultaneously. This behavior is accounted for by a barrier separating folded and unfolded states, the shape of which is consistent with AFM and chemical denaturation data.

Amino Acid Sequence↗
PubMed2000

The key event in force-induced unfolding of Titin's immunoglobulin domains.

Steered molecular dynamics simulation of force-induced titin immunoglobulin domain I27 unfolding led to the discovery of a significant potential energy barrier at an extension of approximately 14 A on the unfolding pathway that protects the domain against stretching. Previous simulations showed that this barrier is due to the concurrent breaking of six interstrand hydrogen bonds (H-bonds) between beta-strands A' and G that is preceded by the breaking of two to three hydrogen bonds between strands A and B, the latter leading to an unfolding intermediate. The simulation results are supported by Angstrom-resolution atomic force microscopy data. Here we perform a structural and energetic analysis of the H-bonds breaking. It is confirmed that H-bonds between strands A and B break rapidly. However, the breaking of the H-bond between strands A' and G needs to be assisted by fluctuations of water molecules. In nanosecond simulations, water molecules are found to repeatedly interact with the protein backbone atoms, weakening individual interstrand H-bonds until all six A'-G H-bonds break simultaneously under the influence of external stretching forces. Only when those bonds are broken can the generic unfolding take place, which involves hydrophobic interactions of the protein core and exerts weaker resistance against stretching than the key event.

Amino Acid Sequence↗
PubMed2000

Excitation transfer in the peridinin-chlorophyll-protein of Amphidinium carterae.

Peridinin-chlorophyll-protein (PCP) is a unique light-harvesting protein that uses carotenoids as its primary light-absorbers. This paper theoretically investigates excitation transfer between carotenoids and chlorophylls in PCP of the dinoflagellate Amphidinium carterae. Calculations based on a description of the electronic states of the participating chromophores and on the atomic level structure of PCP seek to identify the mechanism and pathways of singlet excitation flow. After light absorption the optically allowed states of peridinins share their electronic excitation in excitonic fashion, but are not coupled strongly to chlorophyll residues in PCP. Instead, a gateway to chlorophyll Q(y) excitations is furnished through a low-lying optically forbidden excited state, populated through internal conversion. Carbonyl group and non-hydrogen side groups of peridinin are instrumental in achieving the respective coupling to chlorophyll. Triplet excitation transfer to peridinins, mediated by electron exchange, is found to efficiently protect chlorophylls against photo-oxidation.

Animals↗
PubMed2000

Calculations suggest a pathway for the transverse diffusion of a hydrophobic peptide across a lipid bilayer.

Alamethicin is a hydrophobic antibiotic peptide 20 amino acids in length. It is predominantly helical and partitions into lipid bilayers mostly in transmembrane orientations. The rate of the peptide transverse diffusion (flip-flop) in palmitoyl-oleyl-phosphatidylcholine vesicles has been measured recently and the results suggest that it involves an energy barrier, presumably due to the free energy of transfer of the peptide termini across the bilayer. We used continuum-solvent model calculations, the known x-ray crystal structure of alamethicin and a simplified representation of the lipid bilayer as a slab of low dielectric constant to calculate the flip-flop rate. We assumed that the lipids adjust rapidly to each configuration of alamethicin in the bilayer because their motions are significantly faster than the average peptide flip-flop time. Thus, we considered the process as a sequence of discrete peptide-membrane configurations, representing critical steps in the diffusion, and estimated the transmembrane flip-flop rate from the calculated free energy of the system in each configuration. Our calculations indicate that the simplest possible pathway, i.e., the rotation of the helix around the bilayer midplane, involving the simultaneous burial of the two termini in the membrane, is energetically unfavorable. The most plausible alternative is a two-step process, comprised of a rotation of alamethicin around its C-terminus residue from the initial transmembrane orientation to a surface orientation, followed by a rotation around the N-terminus residue from the surface to the final reversed transmembrane orientation. This process involves the burial of one terminus at a time and is much more likely than the rotation of the helix around the bilayer midplane. Our calculations give flip-flop rates of approximately 10(-7)/s for this pathway, in accord with the measured value of 1.7 x 10(-6)/s.

Alamethicin↗
PubMed2000

Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin.

The planarity of the polyene chain of the retinal chromophore in bacteriorhodopsin is studied using molecular dynamics simulation techniques and applying different force-field parameters and starting crystal structures. The largest deviations from a planar structure are observed for the C(13)==C(14) and C(15)==N(16) double bonds in the retinal Schiff base structure. The other dihedral angles along the polyene chain of the chromophore, although having lower torsional barriers in some cases, do not significantly deviate from the planar structure. The results of the simulations of different mutants of the pigment show that, among the studied amino acids of the binding pocket, the side chain of Trp-86 has the largest impact on the planarity of retinal, and the mutation of this amino acid to alanine leads to chromophore planarity. Deletion of the methyl C(20), removal of a water molecule hydrogen-bonded to H(15), or mutation of other amino acids to alanine did not show any significant influence on the distortion of the chromophore. The results from the present study suggest the importance of the bulky residue of Trp-86 in the isomerization process, in both ground and excited states of the chromophore, and in fine-tuning of the pK(a) of the retinal protonated Schiff base in bacteriorhodopsin. The dark adaptation of the pigment and the last step of the bacteriorhodopsin photocycle imply low barriers against the rotation of the double bonds in the Schiff base region. The twisted double bonds found in the present study are consistent with the proposed mechanism of these ground state isomerization events.

Algorithms↗
PubMed2000

A model for photoreceptor-based magnetoreception in birds.

A large variety of animals has the ability to sense the geomagnetic field and utilize it as a source of directional (compass) information. It is not known by which biophysical mechanism this magnetoreception is achieved. We investigate the possibility that magnetoreception involves radical-pair processes that are governed by anisotropic hyperfine coupling between (unpaired) electron and nuclear spins. We will show theoretically that fields of geomagnetic field strength and weaker can produce significantly different reaction yields for different alignments of the radical pairs with the magnetic field. As a model for a magnetic sensory organ we propose a system of radical pairs being 1) orientationally ordered in a molecular substrate and 2) exhibiting changes in the reaction yields that affect the visual transduction pathway. We evaluate three-dimensional visual modulation patterns that can arise from the influence of the geomagnetic field on radical-pair systems. The variations of these patterns with orientation and field strength can furnish the magnetic compass ability of birds with the same characteristics as observed in behavioral experiments. We propose that the recently discovered photoreceptor cryptochrome is part of the magnetoreception system and suggest further studies to prove or disprove this hypothesis.

Animals↗
PubMed2000

Insulin-like growth factor system components in hyperparathyroidism and renal osteodystrophy.

BACKGROUND: The insulin-like growth factor (IGF) system plays a key role in regulation of bone formation. In patients with renal osteodystrophy, an elevation of some IGF binding proteins (IGFBPs) has been described, but there is no study measuring serum levels of both IGF-I and IGF-II as well as IGFBP-1 to -6 in different forms of renal osteodystrophy and hyperparathyroidism. METHODS: In a cross-sectional study, we investigated 319 patients with mild (N = 29), moderate (N = 48), preuremic (N = 37), and end-stage renal failure (ESRF; N = 205). The ESRF group was treated by hemodialysis (HD; N = 148), peritoneal dialysis (PD; N = 27), or renal transplantation (RTX; N = 30). As controls without renal failure, we recruited age-matched healthy subjects (N = 87) and patients with primary hyperparathyroidism (pHPT; N = 25). Serum levels of total and free IGF-I, IGF-II, IGFBP-1 to -6, and biochemical bone markers including intact parathyroid hormone (PTH), bone alkaline phosphatase (B-ALP), and osteocalcin (OSC) were measured by specific immunometric assays. IGF system components and bone markers were correlated with clinical and bone histologic findings. Mean values +/- SEM are given. RESULTS: With declining renal function a significant increase was measured for IGFBP-1 (range 7- to 14-fold), IGFBP-2 (3- to 8-fold), IGFBP-3 (1.5- to 3-fold), IGFBP-4 (3- to 19-fold), and IGFBP-6 (8- to 25-fold), whereas IGFBP-5 levels tended to decrease (1.3- to 1. 6-fold). In contrast, serum levels of IGF-I, free IGF-I, and IGF-II remained constant in most patients. Compared with renal failure patients, pHPT patients showed a similar decline in IGFBP-5 levels and less elevated levels of IGFBP-1 (3.5-fold), IGFBP-2 (2-fold), IGFBP-3 (1.2-fold), and IGFBP-6 (4-fold) but no elevation of IGFBP-4 levels. In all subjects, free and total IGF-I levels showed significant negative correlations with IGFBP-1, IGFBP-2, and IGFBP-4 (that is, inhibitory IGF system components) and significant positive correlations with IGFBP-3 and IGFBP-5 (that is, stimulatory IGF system components). A positive correlation was observed between IGF-II and IGFBP-6. ESRF patients with mixed uremic bone disease and histologic evidence for osteopenia revealed significantly (P < 0.05) higher levels of IGFBP-2 and IGFBP-4 but lower IGFBP-5 levels. Histologic parameters of bone formation showed significant positive correlations with serum levels of IGF-I, IGF-II, and IGFBP-5. In contrast, IGFBP-2 and IGFBP-4 correlated positively with indices of bone loss. Moreover, dialysis patients with low bone turnover (N = 24) showed significantly (P < 0.05) lower levels of IGFBP-5, PTH, B-ALP, and OSC than patients with high bone turnover. CONCLUSION: Patients with primary and secondary hyperparathyroidism showed lower levels of the putative stimulatory IGFBP-5 but higher levels of IGFBP-1, -2, -3, and -6, whereas total IGF-I and IGF-II levels were not or only moderately increased. The marked increase in serum levels of IGFBP-4 appeared to be characteristic for chronic renal failure. IGFBP-5 correlated with biochemical markers and histologic indices of bone formation in renal osteodystrophy patients and was not influenced by renal function. Therefore, IGFBP-5 may gain significance as a serological marker for osteopenia and low bone turnover in long-term dialysis patients.

Adult↗