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Scheraga HA, Rackovsky S. Dynamic and conformational switching in proteins. Biopolymers 2020; 112:e23411. [PMID: 33270217 DOI: 10.1002/bip.23411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 11/06/2022]
Abstract
Using bioinformatic methods for treating protein dynamics, developed in earlier work, we study the relationship between sequence mobility and dynamics in proteins. It is shown that sequence mobility drives a transition between two dynamic regimes in proteins, and that the specific details of this transition differ qualitatively between α-helical proteins and those in other structural classes. We examine the possibility that conformational switching is related to dynamic switching, by considering a specific system of sequences which exhibit the switching phenomenon. It is shown that a relationship between dynamic and conformational switching is entirely plausible.
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Affiliation(s)
- H A Scheraga
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York, USA
| | - S Rackovsky
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York, USA.,Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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2
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Scheraga HA, Rackovsky S. Sequence-specific dynamic information in proteins. Proteins 2019; 87:799-804. [PMID: 31134683 DOI: 10.1002/prot.25747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/10/2019] [Accepted: 05/22/2019] [Indexed: 11/05/2022]
Abstract
We examine the local and global properties of the average B-factor, 〈B〉, as a residue-specific indicator of protein dynamic characteristics. It has been shown that values of 〈B〉 for the 20 amino acids differ in a statistically significant manner, and that, while strongly determined by the static physical properties of amino acids, they also encode averaged information about the influence of global fold on single-residue dynamics. Therefore, complete sequences of amino acids also encode fold-related global dynamic information, in addition to the local information that arises from static physical properties. We show that the relative magnitudes of these two contributions can be determined using Fourier methods, which represent the global properties of the sequences. It has also been shown that the behavior of Fourier components of 〈B〉 differs, with very high statistical significance, between structural groups, and that this information is not available from a comparable analysis of static amino acid properties.
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Affiliation(s)
- H A Scheraga
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York
| | - S Rackovsky
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York
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Chinchio M, Czaplewski C, Liwo A, Ołdziej S, Scheraga HA. Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field. J Chem Theory Comput 2015; 3:1236-48. [PMID: 26633198 DOI: 10.1021/ct7000842] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many proteins contain disulfide bonds that are usually essential for maintaining function and a stable structure. Several algorithms attempt to predict the arrangement of disulfide bonds in the context of protein structure prediction, but none can simulate the entire process of oxidative folding, including dynamic formation and breaking of disulfide bonds. In this work, a potential function developed to model disulfide bonds is coupled with the united-residue (UNRES) force field, and used in both canonical and replica exchange molecular dynamics simulations to produce complete oxidative folding pathways. The potential function is obtained by introducing a transition barrier that separates the bonded and nonbonded states of the half-cystine residues. Tests on several helical proteins show that improved predictions are obtained when dynamic disulfide-bond formation and breaking are considered. The effect of the disulfide bonds on the folding kinetics is also investigated, particularly their role in stabilizing folding intermediates, resulting in slower folding.
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Affiliation(s)
- M Chinchio
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
| | - C Czaplewski
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
| | - A Liwo
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
| | - S Ołdziej
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
| | - H A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
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Burgess AW, Ponnuswamy PK, Scheraga HA. Analysis of Conformations of Amino Acid Residues and Prediction of Backbone Topography in Proteins. Isr J Chem 2013. [DOI: 10.1002/ijch.197400022] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Lam AR, Rodriguez JJ, Rojas A, Scheraga HA, Mukamel S. Tracking the mechanism of fibril assembly by simulated two-dimensional ultraviolet spectroscopy. J Phys Chem A 2013; 117:342-50. [PMID: 23214934 DOI: 10.1021/jp3101267] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of plaque deposits in the human brain. The main component of these plaques consists of highly ordered structures called amyloid fibrils, formed by the amyloid β-peptide (Aβ). The mechanism connecting Aβ and AD is yet undetermined. In a previous study, a coarse-grained united-residue model and molecular dynamics simulations were used to model the growth mechanism of Aβ amyloid fibrils. On the basis of these simulations, a dock/lock mechanism was proposed, in which Aβ fibrils grow by adding monomers at either end of an amyloid fibril template. To examine the structures in the early time-scale formation and growth of amyloid fibrils, simulated two-dimensional ultraviolet spectroscopy is used. These early structures are monitored in the far ultraviolet regime (λ = 190-250 nm) in which the computed signals originate from the backbone nπ* and ππ* transitions. These signals show distinct cross-peak patterns that can be used, in combination with molecular dynamics, to monitor local dynamics and conformational changes in the secondary structure of Aβ-peptides. The protein geometry-correlated chiral xxxy signal and the non-chiral combined signal xyxy-xyyx were found to be sensitive to, and in agreement with, a dock/lock pathway.
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Affiliation(s)
- A R Lam
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697-2025, USA.
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Affiliation(s)
- S Rackovsky
- Dept of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine of NYU, One Gustave L Levy Place, New York, NY 10029, USA.
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Abstract
Silk-like proteins are a topic of long-standing scientific interest and recently are being considered for such uses as high performance fibers [1] and enzyme-immobilizing substrates [2]. The structure of silk (in particular, the metastable silk I form) is critical in understanding the formation and processing of these materials.Computations provide a useful tool for the detailed modeling of the structures of fibrous proteins. Conformational energy calculations on representative model polypeptides have been used successfully to elucidate the structure of collagen [3]. We have applied this method to the study of the crystalline region of Bombvx mori silk fibroin [4].
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Scott RA, Vanderkooi G, Tuttle RW, Shames PM, Scheraga HA. Minimization of polypeptide energy, iii. Application of a rapid energy minimization technique to the calculation of preliminary structures of gramicidin-s. Proc Natl Acad Sci U S A 2010; 58:2204-11. [PMID: 16591582 PMCID: PMC223821 DOI: 10.1073/pnas.58.6.2204] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- R A Scott
- DEPARTMENT OF CHEMISTRY, CORNELL UNIVERSITY, ITHACA, NEW YORK
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Rackovsky S, Scheraga HA. Intermolecular anti-parallel beta sheet: Comparison of predicted and observed conformations of gramicidin S. Proc Natl Acad Sci U S A 2010; 77:6965-7. [PMID: 16592928 PMCID: PMC350420 DOI: 10.1073/pnas.77.12.6965] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A recently determined x-ray structure of the hydrated gramicidin S-urea complex is compared with a structure predicted by conformational energy minimization. It is shown that the two structures are in good general agreement, including the prediction of a hydrogen bond between the side-chain amino group of ornithine and the backbone carbonyl of phenylalanine. This agreement demonstrates the power of empirical potential energy methods in conformational analysis and illustrates one method for solution of the multiple-minimum problem for small peptides. It is noted that, in the crystal, gramicidin S is a dimer that forms an intermolecular antiparallel four-stranded beta sheet and that differences between the predicted and x-ray structures can be explained by this intermolecular interaction. The residual conformational asymmetry of the x-ray structure is shown to be due to the formation of the complex with urea.
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Affiliation(s)
- S Rackovsky
- Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853
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Meirovitch H, Scheraga HA. Introduction of short-range restrictions in a protein-folding algorithm involving a long-range geometrical restriction and short-, medium-, and long-range interactions. Proc Natl Acad Sci U S A 2010; 78:6584-7. [PMID: 16593113 PMCID: PMC349092 DOI: 10.1073/pnas.78.11.6584] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A protein-folding algorithm, based on short-range and geometrical long-range restrictions, is applied to bovine pancreatic trypsin inhibitor (BPTI). These restrictions are used to define a starting conformation, SI, by means of a space-filling model of the protein, whose energy is then minimized. The long-range restriction is the imposition of the native spatial geometric arrangement of the loops (SGAL) formed by the disulfide bonds. The short-range restrictions are applied as follows: the (varphi, psi) map of each residue is divided into six regions (corresponding to the right- and left-handed alpha-helical, extended, right- and left-handed bridge, and coil states) and the individual residues are placed in the states of the native structure [although not in conformations with the correct values of (varphi, psi)]. Minimization of the energy of SI leads to a structure, SF, with a root-mean-square deviation of 4.4 A from NI, a previously energy-optimized version of the x-ray structure. SF is closer to the native structure than is the structure RF, which was obtained previously by imposing only the correct SGAL as a restriction. The energy of SF is much lower than that of RF but still larger than the energy of NF (the energy-refined x-ray structure).
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Affiliation(s)
- H Meirovitch
- Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853
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11
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Fitzwater S, Scheraga HA. Combined-information protein structure refinement: Potential energy-constrained real-space method for refinement with limited diffraction data. Proc Natl Acad Sci U S A 2010; 79:2133-7. [PMID: 16593175 PMCID: PMC346140 DOI: 10.1073/pnas.79.6.2133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A potential energy-constrained real-space refinement method designed for use with x-ray diffraction data of low to moderate resolution has been developed. The number of adjustable parameters is severely restricted to ensure a reasonable ratio of data to parameters. Only dihedral angles are allowed to vary; bond lengths and bond angles are fixed at physically reasonable values. The structure of bovine pancreatic trypsin inhibitor was refined by using this method with data to only 2.5-A resolution. Both the R-factor and the electron-density map improved throughout the refinement, and the final structure was a satisfactory approximation to the 1.5-A structure.
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Affiliation(s)
- S Fitzwater
- Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853
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Abstract
Raman spectra of several compounds containing the CS-SC moiety were obtained (in the solid phase) from 450-800 cm(-1) to investigate the S-S and C-S stretching behavior. The S-S stretching frequency varied linearly with the CS-SC dihedral angle (obtained from either x-ray or neutron diffraction or ultraviolet absorption) for compounds whose CC-SS dihedral angles were not very different. The ratio of the intensities of the S-S and C-S stretching bands exhibited no recognizable correlation with either the CS-SC dihedral angle or the CSS bond angle, probably because this ratio is sensitive to the crystalline environment. The linear dependence of the S-S stretching frequency on dihedral angle leads to a dihedral angle for the plant hormone, malformin A, that is in excellent agreement with that estimated from the longest wavelength CS-SC ultraviolet absorption band.
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Affiliation(s)
- H E Van Wart
- Department of Chemistry, Cornell University, Ithaca, New York 14850
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Gibson KD, Scheraga HA. Minimization of polypeptide energy, vi. Systematic searches for low-energy conformations of deca-L-alanine and the octapeptide loop of ribonuclease. Proc Natl Acad Sci U S A 2010; 63:9-15. [PMID: 16591753 PMCID: PMC534039 DOI: 10.1073/pnas.63.1.9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A succession of apparent local energy minima, in which the energies decrease successively, have been located for deca-L-alanine and the octapeptide loop of ribonuclease. The lowest energy minima were approximately 40 kcal/mole lower than the highest ones. The results suggest that the computational methods used here might be of considerable use in searching for the global energy minimum of larger polypeptides.
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Affiliation(s)
- K D Gibson
- DEPARTMENT OF CHEMISTRY, CORNELL UNIVERSITY
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Abstract
The x-ray structure of rubredoxin has been refined by energy minimization. The computed structure is constrained to have standard bond lengths, bond angles, and planar trans peptide groups. Also, since most of the steric overlaps have been relieved, it has a very low energy. As judged by the root mean square (RMS) deviation of the computed coordinates from those of the x-ray structure, the two are very similar. The reliability index R for the computed structure (determined from the structure factors for the calculated conformation) is 0.37, which is comparable to that for other proteins.
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Affiliation(s)
- D Rasse
- Department of Chemistry, Cornell University, Ithaca, New York 14850
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Shipman LL, Burgess AW, Scheraga HA. A new approach to empirical intermolecular and conformational potential energy functions. I. Description of model and derivation of parameters. Proc Natl Acad Sci U S A 2010; 72:543-7. [PMID: 16592221 PMCID: PMC432349 DOI: 10.1073/pnas.72.2.543] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An empirical potential energy function based on the interactions of the electrons and nuclei in molecules has been developed and tested. The potential energy of interaction is approximated by the sum of the coulombic interactions between all point charge centers (electrons and nuclei), an exponential repulsion to represent electron-electron overlap repulsion, and an R(-6) (R = distance) attraction to simulate dispersion and other attractive energies between the heavy atom fragments of the molecules. The parameters of the potential energy function have been determined from experimental gas-phase and crystal data.The results indicate that both intramolecular and intermolecular interaction energies can be treated with the same set of parameters. In comparison to other empirical interaction potentials now in use, there are fewer independent parameters, there is no need for intrinsic torsional potentials to obtain the correct rotational barriers, and there is no need for special hydrogen bonding functions to account for the directionality and energetics of hydrogen bonding.
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Affiliation(s)
- L L Shipman
- Department of Chemistry, Cornell University, Ithaca, New York 14853
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Momany FA, Vanderkooi G, Scheraga HA. The determination of intermolecular potentials from crystal data, I. General theory and application to crystalline benzene at several temperatures. Proc Natl Acad Sci U S A 2010; 61:429-36. [PMID: 16591700 PMCID: PMC225176 DOI: 10.1073/pnas.61.2.429] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- F A Momany
- DEPARTMENT OF CHEMISTRY, CORNELL UNIVERSITY, ITHACA, NEW YORK
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Gabel D, Rasse D, Scheraga HA. Search for low-energy conformations of a neurotoxic protein by means of predictive rules, tests for hard-sphere overlaps, and energy minimization. Int J Pept Protein Res 2009; 8:237-52. [PMID: 945247 DOI: 10.1111/j.1399-3011.1976.tb02500.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A method to obtain models for the three-dimensional structure of the neurotoxin alpha from Naja nigricollis from its amino acid sequence is explored here. Empirical predictive rules were used to estimate the positions of helices, extended structures and bends; advantage was taken of the availability of 14 homologous sequences for the neurotoxins in an attempt to increase the reliability of these predictions. Unassigned residues were allowed to take up several possible conformations determined from the frequencies of occurrence of each type of conformation of that residue in x-ray structures of many proteins. The conformational space of the molecule was explored initially by testing for hard-sphere overlaps and approximate closure of disulfide loops with the aid of a computer; this procedure yielded a limited number of conformations, whose conformational energies were then determined and minimized by optimizing the backbone and side-chain dihedral angles of each residue. Five compact conformations with low energy were found for this neurotoxin. The procedure used here provides an illustration as to how empirical protein algorithms may be used to limit the conformational space, in which energy minimization has to be carried out.
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Platzer KE, Momany FA, Scheraga HA. Conformational energy calculations of enzyme-substrate interactions. I. Computation of preferred conformations of some substrates of -chymotrypsin. Int J Pept Protein Res 2009; 4:187-200. [PMID: 5077595 DOI: 10.1111/j.1399-3011.1972.tb03419.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Platzer KE, Momany FA, Scheraga HA. Conformational energy calculations of enzyme-substrate interactions. II. Computation of the binding energy for substrates in the active site of -chymotrypsin. Int J Pept Protein Res 2009; 4:201-19. [PMID: 5077596 DOI: 10.1111/j.1399-3011.1972.tb03420.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Ponnuswamy PK, McGuire RF, Scheraga HA. Refinement of the molecular structure of actinomycin D by energy minimization. Int J Pept Protein Res 2009; 5:73-84. [PMID: 4763361 DOI: 10.1111/j.1399-3011.1973.tb02321.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Leung HJ, Xu G, Narayan M, Scheraga HA. Impact of an easily reducible disulfide bond on the oxidative folding rate of multi-disulfide-containing proteins. ACTA ACUST UNITED AC 2008; 65:47-54. [PMID: 15686534 DOI: 10.1111/j.1399-3011.2004.00189.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The burial of native disulfide bonds, formed within stable structure in the regeneration of multi-disulfide-containing proteins from their fully reduced states, is a key step in the folding process, as the burial greatly accelerates the oxidative folding rate of the protein by sequestering the native disulfide bonds from thiol-disulfide exchange reactions. Nevertheless, several proteins retain solvent-exposed disulfide bonds in their native structures. Here, we have examined the impact of an easily reducible native disulfide bond on the oxidative folding rate of a protein. Our studies reveal that the susceptibility of the (40-95) disulfide bond of Y92G bovine pancreatic ribonuclease A (RNase A) to reduction results in a reduced rate of oxidative regeneration, compared with wild-type RNase A. In the native state of RNase A, Tyr 92 lies atop its (40-95) disulfide bond, effectively shielding this bond from the reducing agent, thereby promoting protein oxidative regeneration. Our work sheds light on the unique contribution of a local structural element in promoting the oxidative folding of a multi-disulfide-containing protein.
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Affiliation(s)
- H J Leung
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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Day GM, Motherwell WDS, Ammon HL, Boerrigter SXM, Della Valle RG, Venuti E, Dzyabchenko A, Dunitz JD, Schweizer B, van Eijck BP, Erk P, Facelli JC, Bazterra VE, Ferraro MB, Hofmann DWM, Leusen FJJ, Liang C, Pantelides CC, Karamertzanis PG, Price SL, Lewis TC, Nowell H, Torrisi A, Scheraga HA, Arnautova YA, Schmidt MU, Verwer P. A third blind test of crystal structure prediction. Acta Crystallogr B Struct Sci 2005; 61:511-27. [PMID: 16186652 DOI: 10.1107/s0108768105016563] [Citation(s) in RCA: 241] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Accepted: 05/24/2005] [Indexed: 11/10/2022]
Abstract
Following the interest generated by two previous blind tests of crystal structure prediction (CSP1999 and CSP2001), a third such collaborative project (CSP2004) was hosted by the Cambridge Crystallographic Data Centre. A range of methodologies used in searching for and ranking the likelihood of predicted crystal structures is represented amongst the 18 participating research groups, although most are based on the global minimization of the lattice energy. Initially the participants were given molecular diagrams of three molecules and asked to submit three predictions for the most likely crystal structure of each. Unlike earlier blind tests, no restriction was placed on the possible space group of the target crystal structures. Furthermore, Z′ = 2 structures were allowed. Part-way through the test, a partial structure report was discovered for one of the molecules, which could no longer be considered a blind test. Hence, a second molecule from the same category (small, rigid with common atom types) was offered to the participants as a replacement. Success rates within the three submitted predictions were lower than in the previous tests – there was only one successful prediction for any of the three `blind' molecules. For the `simplest' rigid molecule, this lack of success is partly due to the observed structure crystallizing with two molecules in the asymmetric unit. As in the 2001 blind test, there was no success in predicting the structure of the flexible molecule. The results highlight the necessity for better energy models, capable of simultaneously describing conformational and packing energies with high accuracy. There is also a need for improvements in search procedures for crystals with more than one independent molecule, as well as for molecules with conformational flexibility. These are necessary requirements for the prediction of possible thermodynamically favoured polymorphs. Which of these are actually realised is also influenced by as yet insufficiently understood processes of nucleation and crystal growth.
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Affiliation(s)
- G M Day
- The Pfizer Institute for Pharmaceutical Materials Science, University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, England.
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Cerovský V, Scheraga HA. Combined solid-phase/solution synthesis of large ribonuclease A C-terminal peptides containing a non-natural proline analog. J Pept Res 2005; 65:518-28. [PMID: 15885111 DOI: 10.1111/j.1399-3011.2005.00257.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Three large peptides corresponding to the 65-124 (60-mer), 72-124 (53-mer), and 77-124 (48-mer) sequence of bovine pancreatic ribonuclease A (RNase A) were assembled from either two or three shorter protected peptide fragments by chemical coupling in solution. The fragments were synthesized manually by 9-fluorenylmethyloxycarbonyl (Fmoc)-based solid-phase peptide chemistry in plastic syringes, and subsequently purified by normal-phase high-performance liquid chromatography on a silica gel column. The main aim of this work was to incorporate sterically hindered l-5,5-dimethylproline (dmP) as a substitute for Pro(93) into the sequence of RNase A in order to constrain the -Tyr(92)-Pro(93)- peptide group to a single cis-conformation.
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Affiliation(s)
- V Cerovský
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
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Ołdziej S, Czaplewski C, Liwo A, Chinchio M, Nanias M, Vila JA, Khalili M, Arnautova YA, Jagielska A, Makowski M, Schafroth HD, Kaźmierkiewicz R, Ripoll DR, Pillardy J, Saunders JA, Kang YK, Gibson KD, Scheraga HA. Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc Natl Acad Sci U S A 2005; 102:7547-52. [PMID: 15894609 PMCID: PMC1140449 DOI: 10.1073/pnas.0502655102] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of alpha and alpha+beta proteins [60-70 residues with C(alpha) rms deviation (rmsd) <6 A]. However, for alpha+beta proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two alpha and three alpha+beta, with sizes of 53-235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue alpha+beta protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-A C(alpha) rmsd. So far this protein is the largest alpha+beta protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly alpha-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 A rmsd, except the 32 C-terminal residues, most of which form a beta-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction.
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Affiliation(s)
- S Ołdziej
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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Scheraga HA, Liwo A, Oldziej S, Czaplewski C, Pillardy J, Ripoll DR, Vila JA, Kazmierkiewicz R, Saunders JA, Arnautova YA, Jagielska A, Chinchio M, Nanias M. The protein folding problem: global optimization of the force fields. FRONT BIOSCI-LANDMRK 2004; 9:3296-323. [PMID: 15353359 DOI: 10.2741/1482] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The evolutionary development of a theoretical approach to the protein folding problem, in our laboratory, is traced. The theoretical foundations and the development of a suitable empirical all-atom potential energy function and a global optimization search are examined. Whereas the all-atom approach has thus far succeeded for relatively small molecules and for alpha-helical proteins containing up to 46 residues, it has been necessary to develop a hierarchical approach to treat larger proteins. In the hierarchical approach to single- and multiple-chain proteins, global optimization is carried out for a simplified united residue (UNRES) description of a polypeptide chain to locate the region in which the global minimum lies. Conversion of the UNRES structures in this region to all-atom structures is followed by a local search in this region. The performance of this approach in successive CASP blind tests for predicting protein structure by an ab initio physics-based method is described. Finally, a recent attempt to compute a folding pathway is discussed.
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Affiliation(s)
- H A Scheraga
- Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853, USA.
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Edsall JT, Flory PJ, Kendrew JC, Liquori AM, Némethy G, Ramachandran GN, Scheraga HA. A proposal of standard conventions and nomenclature for the description of polypeptide conformations. Biopolymers 2004. [DOI: 10.1002/bip.1966.360041010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Wójcik J, Altmann KH, Scheraga HA. Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random poly(hydroxybutylglutamine-CO-S-methylthio-L-cysteine). Biopolymers 2004. [DOI: 10.1002/bip.360300113] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Cerovský V, Welker E, Scheraga HA. A convenient incorporation of conformationally constrained 5,5-dimethylproline into the ribonuclease A 89-124 sequence by condensation of synthetic peptide fragments. J Pept Res 2003; 61:140-51. [PMID: 12558949 DOI: 10.1034/j.1399-3011.2003.00041.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The presence of l-5,5-dimethylproline (dmP) within an amino acid sequence results in the formation of an X-dmP peptide bond predominantly locked in a cis conformation. However, the common use of this unnatural amino acid has been hampered by the difficulty of the economical incorporation of the dmP residue into longer peptide segments due to the steric hindrance imposed by the dimethyl moieties. Here, we describe synthesis of the C-terminal 36-residue peptide, corresponding to the 89-124 sequence of bovine pancreatic ribonuclease A (RNase A), in which dmP is incorporated as a substitute for Pro93. The peptide was assembled by condensation of protected 5- and 31-residue peptide fragments, which were synthesized by solid-phase peptide methodology using fluorenylmethyloxycarbonyl chemistry. We focused on optimizing the synthesis of the Fmoc-Ser(tBu)-Ser(tBu)-Lys(Boc)-Tyr(tBu)-dmP-OH pentapeptide (residues 89-93) with efficient acylation of the sterically hindered dmP residue. In a comparative study, the reagent O-(7-azabenzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate was found to be superior to bromo-tris-pyrrolidino-phosphonium hexafluorophosphate and tetramethylfluoroformamidinium hexafluorophosphate for the synthesis of the -Tyr(tBu)-dmP- peptide bond in solution as well as on a resin.
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Affiliation(s)
- V Cerovský
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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Abstract
Our previous methodology for ab initio prediction of protein structure is extended here to treat multiple-chain proteins. This involved modification of our united-residue (UNRES) force field and our Conformational Space Annealing (CSA) Global Optimization procedure. Good results have been obtained for both a four- and a three-helix protein from the CASP3 exercise.
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Affiliation(s)
- J A Saunders
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
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Van Wart HE, Shipman LL, Scheraga HA. Nature of the potential function for internal rotation about carbon-sulfur bonds in disulfides. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100581a017] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Oka M, Montelione GT, Scheraga HA. Chain-folding initiation structures in ribonuclease A: conformational free energy calculations on Ac-Asn-Pro-Tyr-NHMe, Ac-Tyr-Pro-Asn-NHMe, and related peptides. J Am Chem Soc 2002. [DOI: 10.1021/ja00337a051] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vorobjev YN, Grant JA, Scheraga HA. A combined iterative and boundary-element approach for solution of the nonlinear Poisson-Boltzmann equation. J Am Chem Soc 2002. [DOI: 10.1021/ja00035a003] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rice DM, Meinwald YC, Scheraga HA, Griffin RG. Tyrosyl motion in peptides. Deuterium NMR line shapes and spin-lattice relaxation. J Am Chem Soc 2002. [DOI: 10.1021/ja00240a006] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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von Dreele PH, Lotan N, Ananthanarayanan VS, Andreatta RH, Poland D, Scheraga HA. Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. II. Characterization of the Host Polymers and Application of the Host-Guest Technique to Random Poly(hydroxypropylglutamine-co-hydroxybutylglutamine). Macromolecules 2002. [DOI: 10.1021/ma60022a008] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Howard JC, Momany FA, Andreatta RH, Scheraga HA. Investigation of the Cis and Trans Isomers of Sarcosylsarcosine by Nuclear Magnetic Resonance Spectroscopy and Conformational Energy Calculations. Macromolecules 2002. [DOI: 10.1021/ma60034a015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rackovsky S, Scheraga HA. Differential Geometry and Polymer Conformation. 2. Development of a Conformational Distance Function. Macromolecules 2002. [DOI: 10.1021/ma60078a017] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Nagy JA, Powers SP, Zweifel BO, Scheraga HA. Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. 18. Tryptophan Parameters from Random Poly[(hydroxypropyl)glutamine-co-L-tryptophan]. Macromolecules 2002. [DOI: 10.1021/ma60078a016] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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von Dreele PH, Poland D, Scheraga HA. Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. I. Properties of Copolymers and Approximate Theories. Macromolecules 2002. [DOI: 10.1021/ma60022a007] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Winzor DJ, Scheraga HA. Studies of Chemically Reacting Systems on Sephadex. II. Molecular Weights of Monomers in Rapid Association Equilibrium. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100784a022] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Fredrickson RA, Chang MC, Powers SP, Scheraga HA. Helix-coil stability constants for the naturally occurring amino acids in water. 19. Isoleucine parameters from random poly[(hydroxypropyl)glutamine-co-L-isoleucine]. Macromolecules 2002. [DOI: 10.1021/ma50004a034] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ananthanarayanan VS, Andreatta RH, Poland D, Scheraga HA. Helix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. III. Glycine Parameters from Random Poly(hydroxybutylglutamine-co-glycine). Macromolecules 2002. [DOI: 10.1021/ma60022a009] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wojcik J, Kidera A, Leed AR, Nakajima A, Scheraga HA. Helix-coil transition in multicomponent random copolypeptides in water. 3. Inclusion of nearest-neighbor interactions and application to random copolymers of (hydroxybutyl)-L-glutamine, L-alanine, L-phenylalanine, L-lysine, and glycine. Macromolecules 2002. [DOI: 10.1021/ma00217a019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gibson KD, Scheraga HA. Crystal Packing without Symmetry Constraints. 1. Tests of a New Algorithm for Determining Crystal Structures by Energy Minimization. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100011a051] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chang MC, Fredrickson RA, Powers SP, Scheraga HA. Helix-coil stability constants for the naturally occurring amino acids in water. 20. Reinvestigation of valine parameters from random poly[(hydroxypropyl)glutamine-co-L-valine]. Macromolecules 2002. [DOI: 10.1021/ma50004a035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Scheraga HA, Manes M. Apparatus for Fractional Crystallization in Vacuum. Anal Chem 2002. [DOI: 10.1021/ac60036a052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Meirovitch H, Rackovsky S, Scheraga HA. Empirical Studies of Hydrophobicity. 1. Effect of Protein Size on the Hydrophobic Behavior of Amino Acids. Macromolecules 2002. [DOI: 10.1021/ma60078a013] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hermans J, Leach SJ, Scheraga HA. Thermodynamic Data from Difference Spectra.1,2 II. Hydrogen Bonding in Salicylic Acid and its Implications for Proteins. J Am Chem Soc 2002. [DOI: 10.1021/ja00893a007] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Van Wart HE, Scheraga HA. Raman spectra of strained disulfides. Effect of rotation about sulfur-sulfur bonds on sulfur-sulfur stretching frequencies. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100557a016] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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