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1.
J Comput Chem ; 30(10): 1545-614, 2009 Jul 30.
Artículo en Inglés | MEDLINE | ID: mdl-19444816

RESUMEN

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.


Asunto(s)
Simulación por Computador , Modelos Químicos , Modelos Moleculares , Teoría Cuántica , Programas Informáticos , Carbohidratos/química , Biología Computacional , Lípidos/química , Ácidos Nucleicos/química , Péptidos/química , Proteínas/química
2.
Science ; 244(4908): 1069-72, 1989 Jun 02.
Artículo en Inglés | MEDLINE | ID: mdl-2727695

RESUMEN

A molecular dynamics simulation method is used to determine the contributions of individual amino acid residues and solvent molecules to free energy changes in proteins. Its application to the hemoglobin interface mutant Asp G1(99) beta----Ala shows that some of the contributions to the difference in the free energy of cooperativity are as large as 60 kilocalories (kcal) per mole. Since the overall free energy change is only -5.5 kcal/mole (versus the experimental value of -3.4 kcal/mole), essential elements of the thermodynamics are hidden in the measured results. By exposing the individual contributions, the free energy simulation provides new insights into the origin of thermodynamic changes in mutant proteins and demonstrates the role of effects beyond those usually considered in structural analyses.


Asunto(s)
Hemoglobinas/genética , Mutación , Alanina , Asparagina , Enlace de Hidrógeno , Sustancias Macromoleculares , Estructura Molecular , Oxihemoglobinas , Relación Estructura-Actividad , Termodinámica
3.
Science ; 229(4713): 571-2, 1985 Aug 09.
Artículo en Inglés | MEDLINE | ID: mdl-3839596

RESUMEN

The internal motions of the double-stranded DNA oligomer (dCdG)3 (dC, deoxycytidylate; dG, deoxyguanylate) in the B and Z forms have been calculated in the harmonic approximation. A complete vibrational analysis has been made, and the resulting normal mode frequencies have been used to evaluate the vibrational entropy of B and Z DNA. The greater flexibility of the B DNA hexamer leads to an entropic stabilization relative to the stiffer Z DNA hexamer of 22 calories per mole per kelvin at 300 K. The calculated value is of the same order as that (21 to 27 calories per mole per kelvin) obtained from nuclear magnetic resonance measurements on the methylated duplexes (m5dCdG)3 and (dCdGm5dCdGdCdG). This result demonstrates the importance of internal motions, which have been neglected in earlier studies of the transition from B to Z DNA, in the stability of different nucleic acid conformers.


Asunto(s)
ADN , Conformación de Ácido Nucleico , Metanol , Oligodesoxirribonucleótidos , Estereoisomerismo , Termodinámica , Vibración
4.
Science ; 252(5009): 1167-71, 1991 May 24.
Artículo en Inglés | MEDLINE | ID: mdl-1709522

RESUMEN

Short peptides that contain the basic region of the HIV-1 Tat protein bind specifically to a bulged region in TAR RNA. A peptide that contained nine arginines (R9) also bound specifically to TAR, and a mutant Tat protein that contained R9 was fully active for transactivation. In contrast, a peptide that contained nine lysines (K9) bound TAR poorly and the corresponding protein gave only marginal activity. By starting with the K9 mutant and replacing lysine residues with arginines, a single arginine was identified that is required for specific binding and transactivation. Ethylation interference experiments suggest that this arginine contacts two adjacent phosphates at the RNA bulge. Model building suggests that the arginine eta nitrogens and the epsilon nitrogen can form specific networks of hydrogen bonds with adjacent pairs of phosphates and that these arrangements are likely to occur near RNA loops and bulges and not within double-stranded A-form RNA. Thus, arginine side chains may be commonly used to recognize specific RNA structures.


Asunto(s)
Arginina , Productos del Gen tat/metabolismo , VIH-1/metabolismo , ARN/metabolismo , Secuencia de Aminoácidos , Secuencia de Bases , Clonación Molecular , Productos del Gen tat/genética , Genes tat , Duplicado del Terminal Largo de VIH/fisiología , VIH-1/genética , Enlace de Hidrógeno , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Datos de Secuencia Molecular , Mutagénesis Insercional , Conformación de Ácido Nucleico , Péptidos/metabolismo , Unión Proteica , ARN/genética , Activación Transcripcional , Productos del Gen tat del Virus de la Inmunodeficiencia Humana
5.
Science ; 282(5393): 1462-7, 1998 Nov 20.
Artículo en Inglés | MEDLINE | ID: mdl-9822371

RESUMEN

Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.


Asunto(s)
Péptidos/química , Conformación Proteica , Ingeniería de Proteínas , Pliegue de Proteína , Proteínas/química , Secuencia de Aminoácidos , Dicroismo Circular , Simulación por Computador , Cristalografía por Rayos X , Dimerización , Enlace de Hidrógeno , Modelos Moleculares , Datos de Secuencia Molecular , Peso Molecular , Mutación , Péptidos/síntesis química , Desnaturalización Proteica , Estructura Secundaria de Proteína , Proteínas/síntesis química , Termodinámica
6.
J Mol Biol ; 238(3): 405-14, 1994 May 06.
Artículo en Inglés | MEDLINE | ID: mdl-8176732

RESUMEN

The association reaction of two molecules to form a single complex must overcome a large entropic barrier due to the loss of translational and rotational degrees of freedom; estimates of the T delta S term are of the order of 30 kcal/mol for proteins. The approach of Chandler and Pratt is used to provide a statistical mechanical formulation for the connection between the gas-phase and solution binding free energies. This makes possible a clear separation of the vibrational contribution to the gas-phase binding enthalpy and entropy from the solvation terms. Further, it suggests that the calculated gas-phase result, should be a good approximation in solution for many systems. To illustrate the formulation, a harmonic dynamics model is used to study the dimerization of insulin. The vibrational entropy increase in the dimer complex, relative to the two separate monomers, is 23 entropy units. This contributes -7.2 kcal/mol to the dimerization free energy. It is not possible to identify a small number of specific dimer modes that give rise to this entropy contribution. Instead, small alterations in the frequencies of many modes below 400 to 600 cm-1 are found to contribute. The relative importance of vibrational and other effects in macromolecule-macromolecule and macromolecule-small molecule associations is discussed.


Asunto(s)
Insulina/química , Sitios de Unión , Insulina/metabolismo , Ligandos , Matemática , Polímeros , Termodinámica
7.
J Mol Biol ; 202(4): 903-8, 1988 Aug 20.
Artículo en Inglés | MEDLINE | ID: mdl-2459399

RESUMEN

The experimental inelastic neutron scattering spectrum of a protein, the bovine pancreatic trypsin inhibitor (BPTI), in a powder sample is presented together with the generalized density of states, G(omega), as a function of the frequency, omega, derived from the scattering data. The experimental results are compared with calculations from two different normal mode analyses of BPTI. One of these, based on an improved model, gives a calculated spectrum and density of states in general agreement with those obtained experimentally; the other, based on an earlier model, shows considerable disagreement. The important improvements in the newer normal mode analysis are the explicit treatment of all atoms (non-polar as well as polar hydrogens are included) and a modified truncation scheme for the long-range electrostatic interactions. The fact that the inelastic neutron scattering measurements can distinguish between the two theoretical models makes clear their utility for the analysis of protein dynamics.


Asunto(s)
Aprotinina , Animales , Bovinos , Neutrones , Dispersión de Radiación
8.
J Mol Biol ; 343(3): 685-701, 2004 Oct 22.
Artículo en Inglés | MEDLINE | ID: mdl-15465055

RESUMEN

Here, we compare an antibody with the highest known engineered affinity (K(d)=270 fM) to its high affinity wild-type (K(d)=700 pM) through thermodynamic, kinetic, structural, and theoretical analyses. The 4M5.3 anti-fluorescein single chain antibody fragment (scFv) contains 14 mutations from the wild-type 4-4-20 scFv and has a 1800-fold increase in fluorescein-binding affinity. The dissociation rate is approximately 16,000 times slower in the mutant; however, this substantial improvement is offset somewhat by the association rate, which is ninefold slower in the mutant. Enthalpic contributions to binding were found by calorimetry to predominate in the differential binding free energy. The crystal structure of the 4M5.3 mutant complexed with antigen was solved to 1.5A resolution and compared with a previously solved structure of an antigen-bound 4-4-20 Fab fragment. Strikingly, the structural comparison shows little difference between the two scFv molecules (backbone RMSD of 0.6A), despite the large difference in affinity. Shape complementarity exhibits a small improvement between the variable light chain and variable heavy chain domains within the antibody, but no significant improvement in shape complementarity of the antibody with the antigen is observed in the mutant over the wild-type. Theoretical modeling calculations show electrostatic contributions to binding account for -1.2 kcal/mol to -3.5 kcal/mol of the binding free energy change, of which -1.1 kcal/mol is directly associated with the mutated residue side-chains. The electrostatic analysis reveals several mechanistic explanations for a portion of the improvement. Collectively, these data provide an example where very high binding affinity is achieved through the cumulative effect of many small structural alterations.


Asunto(s)
Anticuerpos Monoclonales/química , Anticuerpos Monoclonales/metabolismo , Afinidad de Anticuerpos , Modelos Teóricos , Conformación Proteica , Secuencia de Aminoácidos , Anticuerpos Monoclonales/genética , Calorimetría , Cristalografía por Rayos X , Fluoresceína/química , Fluoresceína/metabolismo , Modelos Moleculares , Datos de Secuencia Molecular , Estructura Molecular , Mutación , Unión Proteica , Electricidad Estática , Termodinámica
9.
Protein Sci ; 10(2): 362-77, 2001 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-11266622

RESUMEN

Theoretical and experimental studies have shown that the large desolvation penalty required for polar and charged groups frequently precludes their involvement in electrostatic interactions that contribute strongly to net stability in the folding or binding of proteins in aqueous solution near room temperature. We have previously developed a theoretical framework for computing optimized electrostatic interactions and illustrated use of the algorithm with simplified geometries. Given a receptor and model assumptions, the method computes the ligand-charge distribution that provides the most favorable balance of desolvation and interaction effects on binding. In this paper the method has been extended to treat complexes using actual molecular shapes. The barnase-barstar protein complex was investigated with barnase treated as a target receptor. The atomic point charges of barstar were varied to optimize the electrostatic binding free energy. Barnase and natural barstar form a tight complex (K(d) approximately 10(-14) M) with many charged and polar groups near the interface that make this a particularly relevant system for investigating the role of electrostatic effects on binding. The results show that sets of barstar charges (resulting from optimization with different constraints) can be found that give rise to relatively large predicted improvements in electrostatic binding free energy. Principles for enhancing the effect of electrostatic interactions in molecular binding in aqueous environments are discussed in light of the optima. Our findings suggest that, in general, the enhancements in electrostatic binding free energy resulting from modification of polar and charged groups can be substantial. Moreover, a recently proposed definition of electrostatic complementarity is shown to be a useful tool for examining binding interfaces. Finally, calculational results suggest that wild-type barstar is closer to being affinity optimized than is barnase for their mutual binding, consistent with the known roles of these proteins.


Asunto(s)
Proteínas Bacterianas/química , Ribonucleasas/química , Algoritmos , Proteínas Bacterianas/metabolismo , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/metabolismo , Enlace de Hidrógeno , Concentración de Iones de Hidrógeno , Cinética , Modelos Moleculares , Modelos Estadísticos , Unión Proteica , Conformación Proteica , Estructura Secundaria de Proteína , Ribonucleasas/metabolismo , Temperatura , Termodinámica , Agua/metabolismo
10.
Protein Sci ; 3(2): 211-26, 1994 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-8003958

RESUMEN

The electrostatic contribution to the free energy of folding was calculated for 21 salt bridges in 9 protein X-ray crystal structures using a continuum electrostatic approach with the DELPHI computer-program package. The majority (17) were found to be electrostatically destabilizing; the average free energy change, which is analogous to mutation of salt bridging side chains to hydrophobic isosteres, was calculated to be 3.5 kcal/mol. This is fundamentally different from stability measurements using pKa shifts, which effectively measure the strength of a salt bridge relative to 1 or more charged hydrogen bonds. The calculated effect was due to a large, unfavorable desolvation contribution that was not fully compensated by favorable interactions within the salt bridge and between salt-bridge partners and other polar and charged groups in the folded protein. Some of the salt bridges were studied in further detail to determine the effect of the choice of values for atomic radii, internal protein dielectric constant, and ionic strength used in the calculations. Increased ionic strength resulted in little or no change in calculated stability for 3 of 4 salt bridges over a range of 0.1-0.9 M. The results suggest that mutation of salt bridges, particularly those that are buried, to "hydrophobic bridges" (that pack at least as well as wild type) can result in proteins with increased stability. Due to the large penalty for burying uncompensated ionizable groups, salt bridges could help to limit the number of low free energy conformations of a molecule or complex and thus play a role in determining specificity (i.e., the uniqueness of a protein fold or protein-ligand binding geometry).


Asunto(s)
Cristalografía por Rayos X , Pliegue de Proteína , Estabilidad de Medicamentos , Electroquímica , Enlace de Hidrógeno , Modelos Moleculares , Muramidasa/química , Concentración Osmolar , Programas Informáticos , Termodinámica
11.
Protein Sci ; 8(7): 1381-92, 1999 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-10422826

RESUMEN

The GCN4 leucine zipper is a peptide homodimer that has been the subject of a number of experimental and theoretical investigations into the determinants of affinity and specificity. Here, we utilize this model system to investigate electrostatic effects in protein binding using continuum calculations. A particularly novel feature of the computations made here is that they provide an interaction-by-interaction breakdown of the electrostatic contributions to the free energy of docking that includes changes in the interaction of each functional group with solvent and changes in interactions between all pairs of functional groups on binding. The results show that (1) electrostatic effects disfavor binding by roughly 15 kcal/mol due to desolvation effects that are incompletely compensated in the bound state, (2) while no groups strongly stabilize binding, the groups that are most destabilizing are charged and polar side chains at the interface that have been implicated in determining binding specificity, and (3) attractive intramolecular interactions (e.g., backbone hydrogen bonds) that are enhanced on binding due to reduced solvent screening in the bound state contribute significantly to affinity and are likely to be a general effect in other complexes. A comparison is made between the results obtained in an electrostatic analysis carried out calculationally and simulated results corresponding to idealized data from a scanning mutagenesis experiment. It is shown that scanning experiments provide incomplete information on interactions and, if overinterpreted, tend to overestimate the energetic effect of individual side chains that make attractive interactions. Finally, a comparison is made between the results available from a continuum electrostatic model and from a simpler surface-area dependent solvation model. In this case, although the simpler model neglects certain interactions, on average it performs rather well.


Asunto(s)
Proteínas de Unión al ADN , Proteínas Fúngicas/química , Leucina Zippers , Proteínas Quinasas/química , Proteínas de Saccharomyces cerevisiae , Proteínas Fúngicas/metabolismo , Unión Proteica , Proteínas Quinasas/metabolismo , Solventes , Electricidad Estática , Termodinámica
12.
Protein Sci ; 7(9): 1898-914, 1998 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-9761471

RESUMEN

Theoretical calculations (Hendsch ZS & Tidor B, 1994, Protein Sci 3:211-226) and experiments (Waldburger CD et al., 1995, Nat Struct Biol 2:122-128; Wimley WC et al., 1996, Proc Natl Acad Sci USA 93:2985-2990) suggest that hydrophobic interactions are more stabilizing than salt bridges in protein folding. The lack of apparent stability benefit for many salt bridges requires an alternative explanation for their occurrence within proteins. To examine the effect of salt bridges on protein structure and stability in more detail, we have developed an energy function for simple cubic lattice polymers based on continuum electrostatic calculations of a representative selection of salt bridges found in known protein crystal structures. There are only three types of residues in the model, with charges of -1, 0, or + 1. We have exhaustively enumerated conformational space and significant regions of sequence space for three-dimensional cubic lattice polymers of length 16. The results demonstrate that, while the more highly charged sequences are less stable, the loss of stability is accompanied by a substantial reduction in the degeneracy of the lowest-energy state. Moreover, the reduction in degeneracy is greater due to charges that pair than for lone charges that remain relatively exposed to solvent. We have also explored and illustrated the use of ion-pairing strategies for rational structural design using model lattice studies.


Asunto(s)
Proteínas/química , Sales (Química)/farmacología , Modelos Moleculares , Datos de Secuencia Molecular , Mutación/genética , Conformación Proteica , Electricidad Estática
13.
Protein Sci ; 2(7): 1072-84, 1993 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-8102921

RESUMEN

Combinatorial mutagenesis with an alphabet limited to alanine, glutamic acid, lysine, and threonine was used to probe the role of interactions involving surface residues in stabilizing a short alpha-helical coiled coil. The residues at eight e and g positions in the leucine zipper of the Saccharomyces cerevisiae transcription factor GCN4 were randomized to these four residues in a lambda repressor-leucine zipper fusion protein, resulting in 65,536 possible residue combinations. Roughly three-fourths of these combinations allowed stable coiled-coil formation as assayed by DNA binding by the fusion protein. To understand the basis for the activity differences, functional and non-functional mutants were sequenced and statistical tests were applied to identify structure/function correlations. Helix-forming propensity and favorable intrasubunit and intersubunit charge-charge interactions were positively correlated with activity. These studies suggest that the identities of surface side chains at the e and g positions of coiled coils contribute modestly to stability; by comparison with previous work, however, the e and g positions are far less critical than residues at the a and d positions, which form the hydrophobic core of the dimer interface.


Asunto(s)
Proteínas de Unión al ADN , Proteínas Fúngicas/genética , Leucina Zippers/genética , Proteínas Quinasas/genética , Estructura Secundaria de Proteína , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae/genética , Factores de Transcripción/genética , Secuencia de Aminoácidos , Secuencia de Bases , Escherichia coli/genética , Proteínas Fúngicas/biosíntesis , Variación Genética , Glutamatos/genética , Ácido Glutámico , Glicina/genética , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Conformación Proteica , Proteínas Quinasas/biosíntesis , Proteínas Recombinantes de Fusión/biosíntesis , Proteínas Represoras/biosíntesis , Proteínas Represoras/genética , Estadística como Asunto , Relación Estructura-Actividad , Factores de Transcripción/biosíntesis , Proteínas Virales , Proteínas Reguladoras y Accesorias Virales
14.
Protein Sci ; 7(1): 206-10, 1998 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-9514276

RESUMEN

Recent evidence suggests that the net effect of electrostatics is generally to destabilize protein binding due to large desolvation penalties. A novel method for computing ligand-charge distributions that optimize the tradeoff between ligand desolvation penalty and favorable interactions with a binding site has been applied to a model for barnase. The result is a ligand-charge distribution with a favorable electrostatic contribution to binding due, in part, to ligand point charges whose direct interaction with the binding site is unfavorable, but which make strong intra-molecular interactions that are uncloaked on binding and thus act to lessen the ligand desolvation penalty.


Asunto(s)
Proteínas/química , Electricidad Estática , Proteínas Bacterianas , Sitios de Unión , Ligandos , Modelos Moleculares , Unión Proteica/fisiología , Receptores de Superficie Celular/metabolismo , Ribonucleasas/química
15.
J Biomol Struct Dyn ; 1(1): 231-52, 1983 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-6400872

RESUMEN

The techniques of molecular and harmonic dynamics are used to study the internal mobility of three double-stranded DNA hexamers. A 60 ps molecular dynamics simulation and a normal mode description of d(CpGpCpGpCpG)2 in the B conformation characterize the atomic fluctuations of this structure. A comparison between the two approaches validates the harmonic results at room temperature. Detailed examination of the normal modes indicates that only the low-frequency modes are needed to determine atomic fluctuations. A harmonic analysis is made of d(CpGpCpGpCpG)2 in the Z conformation and of d(TpApTpApTpA)2 in the B conformation using only the low-frequency modes. The atomic fluctuations of the three alternating pyrimidine-purine helices are compared and the dependence on conformation and sequence are discussed. The insights which theoretical calculations can provide for the interpretation of experimental results are explored.


Asunto(s)
Oligodesoxirribonucleótidos , Secuencia de Bases , ADN , Espectroscopía de Resonancia Magnética , Modelos Químicos , Estructura Molecular , Conformación de Ácido Nucleico , Termodinámica
17.
BMC Syst Biol ; 5: 112, 2011 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-21756365

RESUMEN

BACKGROUND: Endothelial permeability is involved in injury, inflammation, diabetes and cancer. It is partly regulated by the thrombin-, histamine-, and VEGF-mediated myosin-light-chain (MLC) activation pathways. While these pathways have been investigated, questions such as temporal effects and the dynamics of multi-mediator regulation remain to be fully studied. Mathematical modeling of these pathways facilitates such studies. Based on the published ordinary differential equation models of the pathway components, we developed an integrated model of thrombin-, histamine-, and VEGF-mediated MLC activation pathways. RESULTS: Our model was validated against experimental data for calcium release and thrombin-, histamine-, and VEGF-mediated MLC activation. The simulated effects of PAR-1, Rho GTPase, ROCK, VEGF and VEGFR2 over-expression on MLC activation, and the collective modulation by thrombin and histamine are consistent with experimental findings. Our model was used to predict enhanced MLC activation by CPI-17 over-expression and by synergistic action of thrombin and VEGF at low mediator levels. These may have impact in endothelial permeability and metastasis in cancer patients with blood coagulation. CONCLUSION: Our model was validated against a number of experimental findings and the observed synergistic effects of low concentrations of thrombin and histamine in mediating the activation of MLC. It can be used to predict the effects of altered pathway components, collective actions of multiple mediators and the potential impact to various diseases. Similar to the published models of other pathways, our model can potentially be used to identify important disease genes through sensitivity analysis of signalling components.


Asunto(s)
Endotelio/citología , Endotelio/metabolismo , Histamina/metabolismo , Modelos Biológicos , Transducción de Señal , Trombina/metabolismo , Factor A de Crecimiento Endotelial Vascular/metabolismo , Animales , Calcio/metabolismo , Calmodulina/metabolismo , Activación Enzimática , Quinasas MAP Reguladas por Señal Extracelular/metabolismo , Regulación de la Expresión Génica , Humanos , Inositol 1,4,5-Trifosfato/metabolismo , Péptidos y Proteínas de Señalización Intracelular , Ratones , Proteínas Musculares/metabolismo , Cadenas Ligeras de Miosina/metabolismo , Quinasa de Cadena Ligera de Miosina/metabolismo , Células 3T3 NIH , Permeabilidad , Fosfoproteínas/metabolismo , Receptor PAR-1/metabolismo , Reproducibilidad de los Resultados , Receptor 2 de Factores de Crecimiento Endotelial Vascular/metabolismo , Proteínas de Unión al GTP rho/metabolismo , Quinasas Asociadas a rho/metabolismo
18.
J Chem Theory Comput ; 5(12): 3260-3278, 2009.
Artículo en Inglés | MEDLINE | ID: mdl-23055839

RESUMEN

We present a partial-differential-equation (PDE)-constrained approach for optimizing a molecule's electrostatic interactions with a target molecule. The approach, which we call reverse-Schur co-optimization, can be more than two orders of magnitude faster than the traditional approach to electrostatic optimization. The efficiency of the co-optimization approach may enhance the value of electrostatic optimization for ligand-design efforts-in such projects, it is often desirable to screen many candidate ligands for their viability, and the optimization of electrostatic interactions can improve ligand binding affinity and specificity. The theoretical basis for electrostatic optimization derives from linear-response theory, most commonly continuum models, and simple assumptions about molecular binding processes. Although the theory has been used successfully to study a wide variety of molecular binding events, its implications have not yet been fully explored, in part due to the computational expense associated with the optimization. The co-optimization algorithm achieves improved performance by solving the optimization and electrostatic simulation problems simultaneously, and is applicable to both unconstrained and constrained optimization problems. Reverse-Schur co-optimization resembles other well-known techniques for solving optimization problems with PDE constraints. Model problems as well as realistic examples validate the reverse-Schur method, and demonstrate that our technique and alternative PDE-constrained methods scale very favorably compared to the standard approach. Regularization, which ordinarily requires an explicit representation of the objective function, can be included using an approximate Hessian calculated using the new BIBEE/P (boundary-integral-based electrostatics estimation by preconditioning) method.

19.
Proteins ; 19(4): 310-23, 1994 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-7984627

RESUMEN

The stability mutant Tyr-26-->Asp was studied in the Cro protein from bacteriophage lambda using free energy molecular dynamics simulations. The mutant was calculated to be more stable than the wild type by 3.0 +/- 1.7 kcal/mol/monomer, in reasonable agreement with experiment (1.4 kcal/mol/monomer). Moreover, the aspartic acid in the mutant was found to form a capping interaction with the amino terminus of the third alpha-helix of Cro. The simulations were analyzed to understand better the source of the stability of this helix-capping interaction and to examine the results in light of previous explanations of stabilizing helix caps--namely, a model of local unsatisfied hydrogen bonds at the helix termini and the helix macrodipole model. Analysis of the simulations shows that the stabilizing effect of this charged helical cap is due both to favorable hydrogen bonds with backbone NH groups at the helix terminus and to favorable electrostatic interactions (but not hydrogen bonds) with their carbonyls (effectively the next row of local dipoles in the helix). However, electrostatic interactions are weak or negligible with backbone dipolar groups in the helix further away from the terminus. Moreover, the importance of other local electrostatic interactions with polar side chains near the helix terminus, which are neglected in most treatments of this effect, are shown to be important. Thus, the results support a model that is intermediate between the two previous explanations: both unsatisfied hydrogen bonds at the helix terminus and other, local preoriented dipolar groups stabilize the helix cap. These findings suggest that similar interactions with preoriented dipolar groups may be important for cooperativity in other charge-dipole interactions and may be employed to advantage for molecular design.


Asunto(s)
Proteínas de Unión al ADN , Estructura Secundaria de Proteína , Proteínas Represoras/química , Ácido Aspártico/genética , Bacteriófago lambda/química , Simulación por Computador , Enlace de Hidrógeno , Modelos Moleculares , Mutación , Proteínas Represoras/genética , Termodinámica , Tirosina/genética , Proteínas Virales , Proteínas Reguladoras y Accesorias Virales , Agua/química
20.
Biochemistry ; 30(13): 3217-28, 1991 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-2009262

RESUMEN

Free energy simulation methods are used to analyze the effects of the mutation Arg 96----His on the stability of T4 lysozyme. The calculated stability change and the lack of significant structural rearrangement in the folded state due to the mutation are in agreement with experimental studies [Kitamura, S., & Sturtevant, J. M. (1989) Biochemistry 28, 3788-3792; Weaver, L. H., et al. (1989) Biochemistry 28, 3793-3797]. By use of thermodynamic integration, the contributions of specific interactions to the free energy change are evaluated. It is shown that a number of contributions that stabilize the wild type or the mutant partially cancel in the overall free energy difference; some of these involve the unfolded state. Comparison of the results with conclusions based on structural and thermodynamic data leads to new insights into the origin of the stability difference between wild-type and mutant proteins. Of particular interest is the importance of the contributions of more distant residues, solvent water, and the covalent linkage of the mutated amino acid. Also, the analysis of the interactions of Arg/His 96 with the C-terminal end of a helix (residues 82-90) makes it clear that the nearby carbonyl groups (Tyr 88 and Asp 89) make the dominant contribution, that the amide groups do not contribute significantly, and that the helix-dipole model is inappropriate for this case.


Asunto(s)
Escherichia coli/enzimología , Muramidasa/metabolismo , Fagos T/enzimología , Arginina , Simulación por Computador , Estabilidad de Enzimas , Histidina , Enlace de Hidrógeno , Matemática , Modelos Moleculares , Modelos Teóricos , Muramidasa/química , Muramidasa/genética , Mutagénesis Sitio-Dirigida , Conformación Proteica , Termodinámica , Difracción de Rayos X
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