[
    {
        "id": "authors:r5yak-bwz59",
        "collection": "authors",
        "collection_id": "r5yak-bwz59",
        "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161129-131523601",
        "type": "article",
        "title": "Solvent Effects on the Secondary Structures of Proteins",
        "author": [
            {
                "family_name": "Park",
                "given_name": "Changmoon",
                "clpid": "Park-Changmoon"
            },
            {
                "family_name": "Carlson",
                "given_name": "Matt J.",
                "clpid": "Carlson-M-J"
            },
            {
                "family_name": "Goddard",
                "given_name": "William A., III",
                "orcid": "0000-0003-0097-5716",
                "clpid": "Goddard-W-A-III"
            }
        ],
        "abstract": "We examined the effect of solvation on the conformational preferences (e.g., \u03b1-helix versus \u03b2-sheet) of tripeptides using ab initio quantum mechanics (Hartree\u2212Fock 6-31G**) with solvation in the Poisson\u2212Boltzmann continuum solvent approximation. We find that aqueous solvent preferentially stabilizes the \u03b1-helix conformation over \u03b2-sheet conformations by 3.5 kcal/mol for Ala, 2.4 kcal/mol for Gly, and 2.0 kcal/mol for Pro. We determined the torsional potential surfaces of the tripeptides, Gly-Ala-Gly, Gly-Gly-Gly, and Gly-Pro-Gly using both aqueous solvent and nonpolar solvent conditions. These results were used to determine force-field torsional parameters for the protein main chains.",
        "doi": "10.1021/jp9911189",
        "issn": "1089-5639",
        "publisher": "American Chemical Society",
        "publication": "Journal of Physical Chemistry A",
        "publication_date": "2000-03-23",
        "series_number": "11",
        "volume": "104",
        "issue": "11",
        "pages": "2498-2503"
    },
    {
        "id": "authors:cez9m-6q233",
        "collection": "authors",
        "collection_id": "cez9m-6q233",
        "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20141125-144835029",
        "type": "article",
        "title": "The topomer-sampling model of protein folding",
        "author": [
            {
                "family_name": "Debe",
                "given_name": "Derek A.",
                "clpid": "Debe-D-A"
            },
            {
                "family_name": "Carlson",
                "given_name": "Matt J.",
                "clpid": "Carlson-M-J"
            },
            {
                "family_name": "Goddard",
                "given_name": "William A., III",
                "orcid": "0000-0003-0097-5716",
                "clpid": "Goddard-W-A-III"
            }
        ],
        "abstract": "Clearly, a protein cannot sample all of its conformations (e.g., \u22483^(100) \u2248 10^(48) for a 100 residue protein) on an in vivo folding timescale (<1 s). To investigate how the conformational dynamics of a protein can accommodate subsecond folding time scales, we introduce the concept of the native topomer, which is the set of all structures similar to the native structure (obtainable from the native structure through local backbone coordinate transformations that do not disrupt the covalent bonding of the peptide backbone). We have developed a computational procedure for estimating the number of distinct topomers required to span all conformations (compact and semicompact) for a polypeptide of a given length. For 100 residues, we find \u22483 \u00d7 10^7 distinct topomers. Based on the distance calculated between different topomers, we estimate that a 100-residue polypeptide diffusively samples one topomer every \u22483 ns. Hence, a 100-residue protein can find its native topomer by random sampling in just \u2248100 ms. These results suggest that subsecond folding of modest-sized, single-domain proteins can be accomplished by a two-stage process of (i) topomer diffusion: random, diffusive sampling of the 3 \u00d7 10^7 distinct topomers to find the native topomer (\u22480.1 s), followed by (ii) intratopomer ordering: nonrandom, local conformational rearrangements within the native topomer to settle into the precise native state.",
        "doi": "10.1073/pnas.96.6.2596",
        "pmcid": "PMC15813",
        "issn": "0027-8424",
        "publisher": "National Academy of Sciences",
        "publication": "Proceedings of the National Academy of Sciences of the United States of America",
        "publication_date": "1999-03-16",
        "series_number": "6",
        "volume": "96",
        "issue": "6",
        "pages": "2596-2601"
    },
    {
        "id": "authors:byfdd-cv691",
        "collection": "authors",
        "collection_id": "byfdd-cv691",
        "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180515-133335193",
        "type": "article",
        "title": "Time-Resolved Resonance Raman Spectroscopy at Low Temperature. The Excited-State Metal\u2212Metal Stretching Frequency of Rh_2(TMB)_4^(2+)(TMB = 2,5-Dimethyl-2,5-diisocyanohexane)",
        "author": [
            {
                "family_name": "Dallinger",
                "given_name": "Richard F.",
                "clpid": "Dallinger-R-F"
            },
            {
                "family_name": "Carlson",
                "given_name": "Matt J.",
                "clpid": "Carlson-M-J"
            },
            {
                "family_name": "Miskowski",
                "given_name": "Vincent M.",
                "clpid": "Miskowski-V-M"
            },
            {
                "family_name": "Gray",
                "given_name": "Harry B.",
                "orcid": "0000-0002-7937-7876",
                "clpid": "Gray-H-B"
            }
        ],
        "abstract": "The excited-state metal\u2212metal stretching frequency of the bridged binuclear complex Rh_2(TMB)_4^(2+) (TMB = 2,5-dimethyl-2,5-diisocyanohexane) obtained from time-resolved resonance Raman spectra is 151 cm^(-1), as compared to 50 cm^(-1) in the ground state, indicating a much stronger Rh\u2212Rh bond in the excited state than in the ground state. The key experimental innovation was lowering the solution sample temperature to just above the glass transition to increase the excited triplet state lifetime relative to the laser pulse width.",
        "doi": "10.1021/ic980130x",
        "issn": "0020-1669",
        "publisher": "American Chemical Society",
        "publication": "Inorganic Chemistry",
        "publication_date": "1998-09-21",
        "series_number": "19",
        "volume": "37",
        "issue": "19",
        "pages": "5011-5013"
    }
]