101
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Nadig G, Vishveshwara S. Effects of substrate binding on the dynamics of RNase A: Molecular dynamics simulations of UpA bound and native RNase A. Biopolymers 1997. [DOI: 10.1002/(sici)1097-0282(19971015)42:5<505::aid-bip2>3.0.co;2-u] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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102
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Cieplak M, Vishveshwara S, Banavar JR. Cell Dynamics of Model Proteins. PHYSICAL REVIEW LETTERS 1996; 77:3681-3684. [PMID: 10062281 DOI: 10.1103/physrevlett.77.3681] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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103
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Nadig G, Ratnaparkhi GS, Varadarajan R, Vishveshwara S. Dynamics of ribonuclease A and ribonuclease S: computational and experimental studies. Protein Sci 1996; 5:2104-14. [PMID: 8897611 PMCID: PMC2143277 DOI: 10.1002/pro.5560051017] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
RNase S is a complex consisting of two proteolytic fragments of RNase A: the S peptide (residues 1-20) and S protein (residues 21-124). RNase S and RNase A have very similar X-ray structures and enzymatic activities. Previous experiments have shown increased rates of hydrogen exchange and greater sensitivity to tryptic cleavage for RNase S relative to RNase A. It has therefore been asserted that the RNase S complex is considerably more dynamically flexible than RNase A. In the present study we examine the differences in the dynamics of RNase S and RNase A computationally, by MD simulations, and experimentally, using trypsin cleavage as a probe of dynamics. The fluctuations around the average solution structure during the simulation were analyzed by measuring the RMS deviation in coordinates. No significant differences between RNase S and RNase A dynamics were observed in the simulations. We were able to account for the apparent discrepancy between simulation and experiment by a simple model. According to this model, the experimentally observed differences in dynamics can be quantitatively explained by the small amounts of free S peptide and S protein that are present in equilibrium with the RNase S complex. Thus, folded RNase A and the RNase S complex have identical dynamic behavior, despite the presence of a break in polypeptide chain between residues 20 and 21 in the latter molecule. This is in contrast to what has been widely believed for over 30 years about this important fragment complementation system.
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104
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Iyer LK, Vishveshwara S. The stability of transmembrane helices: a molecular dynamics study on the isolated helices of bacteriorhodopsin. Biopolymers 1996; 38:401-21. [PMID: 8906975 DOI: 10.1002/(sici)1097-0282(199603)38:3%3c401::aid-bip12%3e3.0.co;2-f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Bacteriorhodopsin (bR) continues to be a proven testing ground for the study of integral membrane proteins (IMPs). It is important to study the stability of the individual helices of bR, as they are postulated to exist as independently stable transmembrane helices (TMHs) and also for their utility as templates for modeling other IMPs with the postulated seven-helix bundle topology. Toward this purpose, the seven helices of bR have been studied by molecular dynamics simulation in this study. The suitability of using the backbone-dependent rotamer library of side-chain conformations arrived at from the data base of globular protein structures in the case TMHs has been tested by another set of 7 helix simulations with the side-chain orientations taken from this library. The influence of the residue's net charge on the helix stability was examined by simulating the helices III, IV, and VI (from both of the above sets of helices) with zero net charge on the side chains. The results of these 20 simulations demonstrate in general the stability of the isolated helices of bR in conformity with the two-stage hypothesis of IMP folding. However, the helices I, II, V, and VII are more stable than the other three helices. The helical nature of certain regions of III, IV, and VI are influenced by factors such as the net charge and orientation of several residues. It is seen that the residues Arg, Lys, Asp, and Glu (charged residues), and Ser, Thr, Gly, and Pro, play a crucial role in the stability of the helices of bR. The backbone-dependent rotamer library for the side chains is found to be suitable for the study of TMHs in IMP.
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105
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Iyer LK, Vishveshwara S. Threonine mutations in proline helix II of bacteriorhodopsin: a molecular dynamics study. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/0166-1280(95)04326-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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106
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Shobana S, Vishveshwara S. Conformational study of valinomycin: a molecular dynamics approach. Biophys Chem 1996; 57:163-75. [PMID: 17023338 DOI: 10.1016/0301-4622(95)00061-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/1994] [Revised: 12/27/1994] [Accepted: 03/27/1995] [Indexed: 11/25/2022]
Abstract
Valinomycin is a highly flexible cyclic dodecadepsipeptide that transports ions across membranes. Such a flexibility in the conformation is required for its biological function since it has to encounter a variety of environments and liganding state. Exploration of conformational space of this molecule is therefore important and is one of the objectives of the present study that has been carried out by means of high temperature Molecular Dynamics. Further, the stability of the known bracelet-like structure of the uncomplexed valinomycin and the inherent flexibility around this structure has been investigated. The uncomplexed form of valinomycin has been simulated at 75-100 K for 1 ns in order to elucidate the average conformational properties. An alanine-analog of valinomycin has been simulated under identical conditions in order to evaluate the effect of sidechain on the conformational properties, The studies confirm the effect of sidechain on conformational equilibrium.
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107
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Seshadri K, Rao VS, Vishveshwara S. Interaction of substrate uridyl 3',5'-adenosine with ribonuclease A: a molecular dynamics study. Biophys J 1995; 69:2185-94. [PMID: 8599627 PMCID: PMC1236458 DOI: 10.1016/s0006-3495(95)80094-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A wealth of information available from x-ray crystallographic structures of enzyme-ligand complexes makes it possible to study interactions at the molecular level. However, further investigation is needed when i) the binding of the natural substrate must be characterized, because ligands in the stable enzyme-ligand complexes are generally inhibitors or the analogs of substrate and transition state, and when ii) ligand binding is in part poorly characterized. We have investigated these aspects in the binding of substrate uridyl 3',5'-adenosine (UpA) to ribonuclease A (RNase A). Based on the systematically docked RNase A-UpA complex resulting from our previous study, we have undertaken a molecular dynamics simulation of the complex with solvent molecules. The molecular dynamics trajectories of this complex are analyzed to provide structural explanations for varied experimental observations on the ligand binding at the B2 subsite of ribonuclease A. The present study suggests that B2 subsite stabilization can be effected by different active site groups, depending on the substrate conformation. Thus when adenosine ribose pucker is O4'-endo, Gln69 and Glu111 form hydrogen-bonding contacts with adenine base, and when it is C2'-endo, Asn71 is the only amino acid residue in direct contact with this base. The latter observation is in support of previous mutagenesis and kinetics studies. Possible roles for the solvent molecules in the binding subsites are described. Furthermore, the substrate conformation is also examined along the simulation pathway to see if any conformer has the properties of a transition state. This study has also helped us to recognize that small but concerted changes in the conformation of the substrate can result in substrate geometry favorable for 2',3' cyclization. The identified geometry is suitable for intraligand proton transfer between 2'-hydroxyl and phosphate oxygen atom. The possibility of intraligand proton transfer as suggested previously and the mode of transfer before the formation of cyclic intermediate during transphosphorylation are discussed.
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108
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Abstract
The presence of a higher percentage of Proline in the transmembrane helices of transport proteins indicates that they are involved in the function of these integral membrane proteins (IMPs). In many cases, the possible involvement of cis-trans isomerization in function/folding of IMPs has been suggested. The introduction of cis-Pro in an ideal alpha-helix results in a helix-turn-helix motif. A molecular dynamics (MD) simulation is carried out on the sequence ACE-(ALA)10-cis-Pro-(ALA)10-NME with ideal alpha-helical structure to investigate if and how a straight helix can accommodate a cis-Pro. The analysis of the conformations accessed during MD simulation showed that the residues near cis-Pro can adopt alternate conformations other than the right-handed helical conformation such that an almost straight helix is obtained. This may have implications in the involvement of cis-trans isomerization in folding and/or function of IMPs.
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109
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Shrivastava I, Vishveshwara S, Cieplak M, Maritan A, Banavar JR. Lattice model for rapidly folding protein-like heteropolymers. Proc Natl Acad Sci U S A 1995; 92:9206-9. [PMID: 7568102 PMCID: PMC40953 DOI: 10.1073/pnas.92.20.9206] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Protein folding is a relatively fast process considering the astronomical number of conformations in which a protein could find itself. Within the framework of a lattice model, we show that one can design rapidly folding sequences by assigning the strongest attractive couplings to the contacts present in a target native state. Our protein design can be extended to situations with both attractive and repulsive contacts. Frustration is minimized by ensuring that all the native contacts are again strongly attractive. Strikingly, this ensures the inevitability of folding and accelerates the folding process by an order of magnitude. The evolutionary implications of our findings are discussed.
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110
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Ma WJ, Iyer LK, Vishveshwara S, Koplik J, Banavar JR. Molecular-dynamics studies of systems of confined dumbbell molecules. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1995; 51:441-453. [PMID: 9962662 DOI: 10.1103/physreve.51.441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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111
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Seshadri K, Rao VS, Vishveshwara S. Characterization of substrate UpA binding to RNase A--computer modelling and energetics approach. J Biomol Struct Dyn 1994; 12:581-603. [PMID: 7727060 DOI: 10.1080/07391102.1994.10508761] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the past two decades RNase A has been the focus of diverse investigations in order to understand the nature of substrate binding and to know the mechanism of enzyme action. Although this system is reasonably well characterized from the view point of some of the binding sites, the details of interactions in the second base binding (B2) site is insufficient. Further, the nature of ligand-protein interaction is elucidated generally by studies on RNase A-substrate analog complexes (mainly with the help of X-ray crystallography). Hence, the details of interactions at atomic level arising due to substrates are inferred indirectly. In the present paper, the dinucleotide substrate UpA is fitted into the active site of RNase A. Several possible substrate conformations are investigated and the binding modes have been selected based on Contact Criteria. Thus identified RNase A-UpA complexes are energy minimized in coordinate space and are analysed in terms of conformations, energetics and interactions. The best possible ligand conformations for binding to RNase A are identified by experimentally known interactions and by the energetics. Upon binding of UpA to RNase A, the changes associated with protein back bone, side chains in general and at the binding sites in particular are described. Further, the detailed interactions between UpA and RNase A are characterized in terms of hydrogen bonds and energetics. An extensive study has helped in interpreting the diverse results obtained from a number of experiments and also in evaluating the extent of changes the protein and the substrate undergo in order to maximize their interactions.
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112
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Seshadri K, Vishveshwara S, Jain MK. Binding of active site directed ligands to phospholipase A2: Implications on the molecular constraints and catalytic mechanism. J CHEM SCI 1994. [DOI: 10.1007/bf02841925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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113
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Vijayakumar S, Vishveshwara S, Ravishanker G, Beveridge DL. Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation. ACS SYMPOSIUM SERIES 1994. [DOI: 10.1021/bk-1994-0569.ch011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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114
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Vijayakumar S, Vishveshwara S, Ravishanker G, Beveridge DL. Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates. Biophys J 1993; 65:2304-12. [PMID: 8312470 PMCID: PMC1225972 DOI: 10.1016/s0006-3495(93)81288-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structure have been identified in the folding pathway. In the present study, high temperature molecular dynamics simulations have been carried out on the native enzyme in solution. Analysis of these results in terms of root mean square fluctuations in cartesian and [phi, psi] space, backbone dihedral angles and secondary structural hydrogen bonds forms the basis for an investigation of the topology of partially unfolded states of beta-lactamase. A differential stability has been observed for alpha-helices and beta-sheets upon thermal denaturation to putative unfolding intermediates. These observations contribute to an understanding of the folding/unfolding processes of beta-lactamases in particular, and other alpha/beta proteins in general.
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115
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Seshadri K, Balaji PV, Rao VS, Vishveshwara S. Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes. J Biomol Struct Dyn 1993; 11:395-415. [PMID: 8286064 DOI: 10.1080/07391102.1993.10508734] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Different modes of binding of pyrimidine monophosphates 2'-UMP, 3'-UMP, 2'-CMP and 3'-CMP to ribonuclease (RNase) A are studied by energy minimization in torsion angle and subsequently in Cartesian coordinate space. The results are analysed in the light of primary binding sites. The hydrogen bonding pattern brings out roles for amino acids such as Asn44 and Ser123 apart from the well known active site residues viz., His12,Lys41,Thr45 and His119. Amino acid segments 43-45 and 119-121 seem to be guiding the ligand binding by forming a pocket. Many of the active site charged residues display considerable movement upon nucleotide binding.
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116
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Shobana S, Vishveshwara S, Vishveshwara SS. Effect of constraints by threonine on proline containing alpha-helix--a molecular dynamics approach. Biophys Chem 1993; 46:77-89. [PMID: 8443337 DOI: 10.1016/0301-4622(93)87009-l] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Proline plays an important role in the secondary structure of proteins. In the pursuit of understanding its structural role, Proline containing helices with constraints have been studied by employing molecular dynamics (MD) technique. In the present study, the constraint introduced is a threonine residue, whose sidechain has intramolecular hydrogen bond interaction with the backbone oxygen atom. The three systems that have been chosen for characterization are: (1) Ace-(Ala)12-Thr-Pro-(Ala)10-NHMe, (2) Ace-(Ala)13-Pro-Ala-Thr-(Ala)8-NHMe and (3) Ace-(Ala)13-Pro-(Ala)3-Thr-(Ala)6-NHMe. The equilibrium structures and structural transitions have been identified by monitoring the backbone dihedral angles, bend related parameters and the hydrogen bond interactions. The MD averages and root mean square (r.m.s.) fluctuations are compared and discussed. Energy minimization has been carried out on selected MD simulated points in order to analyze the characteristics of different conformations.
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117
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Sankararamakrishnan R, Vishveshwara S. Characterization of proline-containing alpha-helix (helix F model of bacteriorhodopsin) by molecular dynamics studies. Proteins 1993; 15:26-41. [PMID: 8451238 DOI: 10.1002/prot.340150105] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Many of the bilayer spanning segments of membrane transport proteins contain proline residues, and most of them are believed to occur in alpha-helical form. A proline residue in the middle of an alpha-helix is known to produce a bend in the helix, and recent studies have focused on characterizing such a bend at atomic level. In the present case, molecular dynamics (MD) studies are carried out on helix F model of bacteriorhodopsin (BR) Ace-(Ala)7-Trp-(Ala)2-Tyr-Pro-(Ala)2-Trp- (Ala)8-NHMe and compared with Ace-(Ala)7-Trp-(Ala)2-Tyr-(Ala)3-Trp-(Ala)8-NHMe in which the proline is replaced by alanine. The bend in the helix is characterized by structural parameters such as kink angle (alpha), wobble angle (theta), virtual torsion angle (rho), and the hydrogen bond distance d (Op-3 ... Np+1). The average values and the flexibility involved in these parameters are evaluated. The correlation among the bend related parameters are estimated. The equilibrium side chain orientations of tryptophan and tyrosine residues are discussed and compared with those found in the recently proposed model of bacteriorhodopsin. Finally, a detailed characterization of the bend in terms of secondary structures such as alpha I, alpha II and goniometric helices are discussed, which can be useful in the interpretation of the experimental results on the secondary structures of membrane proteins involving the proline residue.
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118
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Seshadri K, Rao VS, Vishveshwara S. Molecular dynamics studies on nucleoside 2',3'-cyclic phosphates. J Biomol Struct Dyn 1992; 9:1253-68. [PMID: 1322144 DOI: 10.1080/07391102.1992.10507990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
2',3'-cyclic nucleotides are intermediates and substrates of Ribonuclease (RNase)-catalysed reactions. The characterization of the equilibrium conformation as well as the flexibility inherent in these molecules helps in understanding the enzymatic action of RNases. The present study explores parameters like phase angle, glycosydic torsion angle and hydrogen bond to find possible interrelationship between them through Molecular Dynamics (MD) simulations on 3'-GMP,3'-UMP, A greater than p, G greater than p, U greater than p, C greater than p, GpA greater than p and UpA greater than p. Interesting results of the effect of cyclisation and other constraints such as hydrogen bond between certain groups on the equilibrium ribose conformation have emerged from this study.
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119
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Sankararamakrishnan R, Vishveshwara S. The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies. J Biomol Struct Dyn 1992; 9:1073-95. [PMID: 1637503 DOI: 10.1080/07391102.1992.10507980] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as--intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96--a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.
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120
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Sankararamakrishnan R, Vishveshwara S. Geometry of proline-containing alpha-helices in proteins. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1992; 39:356-63. [PMID: 1428525 DOI: 10.1111/j.1399-3011.1992.tb01595.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystal structure analysis of proline-containing alpha-helices in proteins has been carried out. High resolution crystal structures were selected from the Protein Data Bank. Apart from the standard internal parameters, some parameters which are specifically related to the bend in the helix due to proline have been developed and analyzed. Finally the position and nature of these helices and their interactions with the rest of the protein have been analyzed.
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121
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Shobana S, Vishveshwara S. Structure of valinomycin by molecular dynamics studies. INDIAN JOURNAL OF BIOCHEMISTRY & BIOPHYSICS 1991; 28:363-8. [PMID: 1812068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Valinomycin is an important ionophore which exhibits a high conformational flexibility. The study of various conformations adopted by this molecule together with the study of flexibility in a given conformation can throw light on the ion transport by the ionophore across the membrane. Molecular dynamics (MD) studies are ideal to characterize the flexibility in different parts of the molecule and can also give an idea of various conformations adopted by the molecule at a given temperature. Hence MD studies at 100K have been carried out on the minimized crystal structure of the molecule to scan the possible conformations in the neighbourhood of the well known 'bracelet' like structure of uncomplexed Valinomycin, Properties, like the flexibility, average values, r.m.s. fluctuations of the various intramolecular hydrogen bonds are discussed. Energy minimization has been carried out on selected MD simulated points to analyze the characteristics of the unique conformation adopted by this molecule at this temperature.
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122
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Sankararamakrishnan R, Sreerama N, Vishveshwara S. Characterization of proline-containing right-handed α-helix by molecular dynamics studies. Biophys Chem 1991; 40:97-108. [PMID: 17014775 DOI: 10.1016/0301-4622(91)85034-n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/1990] [Revised: 10/20/1990] [Accepted: 11/08/1990] [Indexed: 11/28/2022]
Abstract
Proline residues play a special role in shaping the secondary and tertiary structures of proteins. Many of these aspects have been studied in great detail. Current interest lies in elucidating the structure of right-handed alpha-helical fragments which contain proline in the middle of the helix. Such structures play an important role in membrane proteins and in the tight packing of globular proteins. Analysis of several crystal structures and energy minimization using flexible geometry have elucidated the nature of the bend produced by proline in the right-handed alpha-helical structure. Molecular dynamics (MD) simulation studies are ideally suited to characterize rigidity or flexibility in different parts of the molecule and can also give an idea of various conformations of the molecule which can exist at a given temperature. Hence, MD studies on Ace-(Ala)6-Pro-(Ala)3-NHMe have been carried out for 100 ps after equilibration and the resulting trajectories have been analyzed. Information regarding the average values, r.m.s. fluctuations of internal parameters and the time spent in different conformations are discussed. Energy minimization has been carried out on selected MD simulated points in order to analyze the characteristics of different conformations.
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123
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Sankararamakrishnan R, Vishveshwara S. Conformational studies on peptides with proline in the right-handed alpha-helical region. Biopolymers 1990; 30:287-98. [PMID: 2279068 DOI: 10.1002/bip.360300307] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The proline residues in proteins are known to play an important structural role. Recently, the role of a proline residue in the middle of right-handed alpha-helical segments of peptides has been the focus of attention. This role seems to be particularly important in the case of membrane proteins and in the tight packing of globular proteins. In the present study the right-handed alpha-helical region of the Ala-Pro dipeptide and of polypeptides containing this group have been investigated. Crystal structures of proline-containing alpha-helices from some proteins have been analyzed and energy minimization studies on some model fragments containing Ala-Pro in the right-handed alpha-helical conformation have been carried out using flexible geometry. The present calculations indicate that the right-handed alpha-helical region of conformational space is an energetically favored region that can also accommodate Ala-Pro in longer segments of right-handed alpha-helix. This is achieved due to minor variations in some of the internal parameters. Deviations in the backbone parameters of proline in the right-handed alpha-helix lead to a kink of about 23 degrees in the helix axis. These deviations have been characterized and a set of standard values has been suggested for producing such a kink. These values can be used for model building and as starting points for further minimization studies. Previous energy minimization studies have been done using rigid geometry. This may explain why the minimum for Ala-Pro in the right-handed alpha-helical region has not been recognized thus far.
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124
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Sreerama N, Vishveshwara S. Ab initio studies on proton transfer involving Schiff base and related nitrogen compounds. J Mol Struct 1989. [DOI: 10.1016/0022-2860(89)85067-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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125
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Sankara-Ramakrishnan R, Vishveshwara S. A hydrogen bonded chain in bacteriorhodopsin by computer modelling approach. J Biomol Struct Dyn 1989; 7:187-205. [PMID: 2818868 DOI: 10.1080/07391102.1989.10507760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The seven alpha-helical segments of Bacteriorhodopsin (BR) passing through the membrane are investigated for a continuous Hydrogen Bonded Chain (HBC). The study is carried out by computer modelling approach. It is assumed that the seven helices are placed as (AGFEDCB), which has been accepted as the best model by several groups. Helices A, D, E and G are considered to be present in right handed alpha-helical conformation. The inter-orientation of these helices are represented by Eulerian angles alpha, beta and gamma. For the helices B, C and F which contain Proline in the middle, several conformational possibilities were considered. In these cases apart from the Eulerian angles alpha, beta and gamma, the dihedral angles phi p-1 and psi p-1 of the residues that are succeeded by Proline residue in the helical regions were also used in fixing the position of the helices with respect to each other. All these parameters were varied to fit with the top, middle and bottom distances reported by electron diffraction studies. Good fit was obtained for all right handed alpha-helical conformations and also for helices B, C and F with a left handed turn at the residue preceeding proline. Hence two structures were analysed for continuous HBC. Structure I which contained all the seven helices in right handed alpha-helical conformation and Structure II, which had the helices A, D, E and G in right handed conformation and the helices B, C and F in right handed alpha-helical conformation with a left handed turn at the residue preceeding proline. All possible staggered conformations were considered for the side chains and the inter atomic distances were analysed for Hydrogen bonds. It was possible to obtain a continuous chain in both the structures which includes most of the residues found to be important by the experiments. However Lys-216 has to be considered in two different conformations to connect the cytoplasmic side with the extra cellular side. The overall height spanned by HBC is about 25A. The chains obtained by both the structures I and II are analysed in terms of the conformational parameters. It has also been possible to place the retinal in the region as predicted by the experiments. The Tryptophan residues which affect the spectral characteristics can be aligned on either side of the retinal.
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