![]() A list of highly toxic proteins or peptides would also include the venoms of many snakes, and ricin, the toxic protein found in castor beans.ĭespite the variety of their physiological function and differences in physical properties-silk is a flexible fiber, horn a tough rigid solid, and the enzyme pepsin water soluble crystals-proteins are sufficiently similar in molecular structure to warrant treating them as a single chemical family. The toxins produced by tetanus and diphtheria microorganisms are nearly as poisonous. Based on toxicology studies, a teaspoon of this toxin would be sufficient to kill a fifth of the world's population. Botulinum toxin A, from Clostridium botulinum, is regarded as the most powerful poison known. The deadly properties of protein toxins and venoms is less widely appreciated. Protein based antibiotics and vaccines help to fight disease, and we warm and protect our bodies with clothing and shoes that are often protein in nature (e.g. Humans can become seriously ill if they do not eat enough suitable protein, the disease kwashiorkor being an extreme form of protein deficiency. Proteins are generally regarded as beneficial, and are a necessary part of the diet of all animals. In the form of hemoglobin, myoglobin and various lipoproteins, they effect the transport of oxygen and other substances within an organism. ![]() In the form of enzymes, hormones, antibodies, and globulins, they catalyze, regulate, and protect the body chemistry. In the form of skin, hair, callus, cartilage, muscles, tendons and ligaments, proteins hold together, protect, and provide structure to the body of a multi-celled organism. Proteins, from the Greek proteios, meaning first, are a class of organic compounds which are present in and vital to every living cell. Rapiddevelopmentsforsemiempiricalforce elds,such1,31 35andReferenceInteractionSiteModels(RISM).Inbothcases,molecularsimulationisexactandcapableofmolecular molecularcorrelationfunctions,however,BecausethecorrelationbetweenatomicsitescanbedescribedbycalculationofSFEusingmolecularsimulationmethodsisathree-dimensionalfunctionwhilethatbetweenmoleculescomputationallydemanding,inparticularforstudyingtheinvolvesmuchhigherdimensionality,applicationsofRISMtosolvationoflargebiomacromolecules.Toavoidextensivesolvation,pioneeredb圜handler31,36andthereaftergreatlynumericalwork,onemayfollowphenomenologicalmethodsextendedbyHirataandothers,32,33,35haveattractedmuchmoresuchasvariousmodi cationsoftheBornmodel2,3,15,16ortheLangevin Debyemodel.Proteins Proteins, Peptides & Amino Acids 1. Statetheories.1,17,18MolecularsimulationofSFEismostlybasedsolventcon guration,theintegral-equationtheoriescanbeonthermodynamicfurtherclassi edintomolecularOrnstein Zernike(MOZ)ġ1integration19,20andfree-energyperturba-tioncalculations.Withtheadventofmoderncomputersandtheories6,24,30 Inwaterremainsadauntingchallenge.6 116,17,24,25Overthepastdecades,boththeintegral-equationtheoriesandtheclassicaldensityfunctionaltheories26 29Fromatheoreticalperspective,computationalmethodstohavebeenevolvedintorobustcomputationaltoolsforpredictingstudysolvationdiversepropertiesofhomogeneousandinhomogeneousliquid-ġ2 14maybeclassi edintothreecategories:molecularsimulation,phenomenologicalmethods,2,15,16andliquid-statesystems.Onthebasisofthedi erentdescriptionsofthe Historyoftheoreticaldevelopments,accuratepredictionofSFEmethods. ![]() Liquidsolubilitybutalsoforunderstandingvirtuallyallchemical23parametersvalidonlyforanarrowrangeofconditions.ĪndbiochemicalprocessesinanaqueousenvironmentToacertaindegree,liquid-statetheoriesrepresentaġ 5includingmolecularrecognitionandbindinga nity.Despitealongcompromisebetweensimulationsandphenomenological I.INTRODUCTIONsurface,andneglectingthemicroscopicdetailsmakestheInsolutionthermodynamics,solvationfreeenergy(SFE)isphenomenologicalcalculationscomputationallyverye cienttypicallyde nedasthereversibleworktotransferasolutefromaandthusconvenientformanypracticalapplications.Regrettably,vacuumtoapuresolventatagiventemperatureandpressure(orthephenomenologicalmethodsareoftennotaccurateinequivalently,temperatureandthesolventchemicalpotential).comparisonwithsimulationresultsorexperimentaldata.ThethermodynamicconceptisimportantnotonlyforpredictingBesides,theyinvolveempirical StateKeyLaboratoryofChemicalEngineering,EastChinaUniversityofScienceandTechnology,Shanghai,200238,P.R.China*SupportingInformation YuLiu, ShuangliangZhao,*, andJianzhongWu*,ĭepartmentsofChemicalandEnvironmentalEngineeringandMathematics,UniversityofCalifornia,Riverside,California92521,UnitedStates ASiteDensityFunctionalTheoryforWater:ApplicationtoSolvationofAminoAcidSideChains
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