Lingo-1結構的製作方法

2024-04-03 06:25:05 3

專利名稱：：Lingo-1結構的製作方法LINGO隱l結構相關申請本申請要求2006年2月3日提交的美國臨時申請號60/765,443的權益，該申請通過引用整體併入本文。
技術領域：
本公開涉及LINGO-l多肽、LINGO-l多肽/配體複合物、LINGO-l多肽的晶體、LINGO-l多肽/配體複合物的晶體以及相關方法和軟體系統。
背景技術：
：LINGO-l(含LRR和fe結構域的Hog^受體相互作用蛋白質)是p75的跨膜共受體。共受體與配體結合Nogo-66受體(NogoR)構成Nogo受體複合物，其通常位於神經元上。使得其中有LINGO-l的Nogo受體複合體失去作用能夠誘導髓磷脂和神經纖維的生長。LINGO-l已經顯示在已知稱為少突膠質細胞的髓磷脂產生細胞中具有活性，並且，對LINGO-l的抑制也已顯示能誘導髓磷脂形成。因此，人們預測LINGO-l信號傳導是髓磷脂產生的負調節劑。
發明內容在一個方面，本發明涉及結晶的LINGO-l多肽。在另一個方面，本發明涉及結晶的多肽-配體複合物，其包括LINGO-l多肽和配體，所述配體是LINGO-l多肽的激動劑或拮抗劑。在又一個方面，本發明涉及一種方法，其包括使用LINGO-l多肽的三維模型來設計與LINGO-l多肽結合的物質。在另一個方面，本發明涉及一種方法，其包括使用LINGO-l多肽-配體複合物的三維模型來設計與LINGO-l多肽結合的物質。在另一個方面，本發明涉及一種方法，其包括使用包括LINGO-l多肽的複合物的三維模型來設計與LINGO-l多肽結合的物質。在另一個方面，本發明涉及一種方法，其包括通過例如用LINGO-l多肽或LINGO-l多肽-配體複合物的三維結構，進行合理的藥物設計，來選擇物質；將所述物質與LINGO-l多肽接觸；以及，檢測所述物質與LINGO-l多肽結合的能力。在一些實施方案中，所述方法還包括下迷步驟中的一種或多種獲得包括LINGO-l多肽和所述物質的補充晶體複合物；測定補充晶體複合物的單位結構；通過，例如，用所述補充晶體複合物的三維結構進行合理的藥物設計，來選出第二物質；將所述笫二物質與LINGO-l多肽相接觸；和/或檢測所述第二物質與LINGO-l多肽結合的能力。所述方法還可包括下述步驟中的一種或多種合成第二物質；檢測所述第二物質抑制LINGO-l活性的能力；和/或檢測所述第二物質增加體外或體內髓磷脂水平的能力。在一些實施方案中，本文公開的組合物和方法中的LINGO-l多肽包括富含亮氨酸的重複(LRR)結構域、免疫球蛋白樣(Ig樣)結構域和/或莖結構域或其組合(或主要由它們組成)。在其它實施方案中，LINGO-l多肽包括來自哺乳動物(例如人)或非哺乳動物來源的胺基酸序列(或主要由它們組成)；例如，LINGO-l多肽可包括SEQIDNO:1的氨基紗列或其變體(例如，其保守取代)(或由它們組成)。在其它實施方案中，LINGO-l多肽是結晶的，例如，其能將X-射線衍射為至少大約3.7A的解析度。在一些實施方案中，結晶的LINGO-l多肽具有空間群(spacegroup)P2"J或1222。在其它實施方案中，結晶的LINGO-l多肽具有選自下述一種或多種的晶胞尺寸a=201.5A、b=149.7A、c=157.5A和a=p=y=90。、a=148.7A、b=158.6A、c-200.0A和a-p，卯0，和a-149.6A、b=157.3A、c=200.3A和/或a=p=y=90°。在又一實施方案中、結晶的LINGO-l多肽具有下述三維結構，其中包括根據表2的結構坐標，01碳原子的+/-均方根偏差不超過1.5A。在另一實施方案中，結晶的LINGO-l多肽具有下述三維結構，其包括選自SEQIDNO:1所示的LINGO-l多肽的胺基酸Aspl3、Arg20、Arg22、Arg43、Glu60、Glu62、Leu94、Leul20、Metl23、Hisl76、Tyrl42、Hisl45、Hisl85、His209、His233、Ala238、Trp346、Arg347、Asn349、Asn351、Arg352、Gln353、Phe396、Arg408、Leu420、Leu426、Phe438、Asp440、Arg446、Tyr447和/或Ile459的一個或多個原子的原子結構坐標。在其它實施方案中，使用本文公開的方法設計或篩選的物質能抑制LINGO-l活性。例如，所述物質可在配體結合位點與LINGO-l結合和/或幹擾LINGO-l與配體之間的相互作用。在一些實施方案中，配體結合位點位於LRR結構域的凹面表面，例如，下述LRR結構域表面，其包括根據SEQIDNO:1的Trp346和Arg352;Hisl85、His209和His233;Aspl3;Glu60和Glu62;或Arg20、Arg22和Arg43中的一處或多處。在其它實施方案中，配體結合位點位於LRR結構域的凸面表面，例如，下述LRR結構域表面，其包括才艮據SEQIDNO:1的Tyrl42和Hisl45;Leu94、Leul20和Metl23;Hisl76;或Ala238中的一處或多處。在其它實施方案中，配體結合位點位於Ig結構域上，例如，這樣的結構域，其包括才艮據SEQIDNO:1的Arg446和Tyr447;Arg408、Phe438和Asp440;Phe396;或Leu420、Leu426和Ile459中的一處或多處。在一些實施方案中，本文公開的方法包括提供包括LINGO-l多肽或LINGO-l多肽-配體複合物的組合物，和/或使所述組合物結晶，以形成包括LINGO-l多肽或LINGO-l多肽-配體複合物的結晶複合物。結晶複合物可將X-射線衍射為至少大約3.7A的解析度。本文公開的方法可額外包括下述步驟中的一個或多個計算LINGO-l多肽的原子與該物質的原子之間的距離；測定該物質與LINGO-l多肽的相互作用；將該物質與LINGO-l多肽的相互作用與第二物質與LINGO-l多肽之間的相互作用加以比較；通過計算機建模選擇該物質；合成該物質；檢測該物質抑制LINGO-l活性的能力；和/或檢測該物質體外或體內增加髓磷脂形成的能力。在另一個方面，本發明涉及使用本文公開的方法設計或選擇的物質。在另一個方面，本發明涉及軟體系統，其包括用於使計算機系統接受與LINGO-l多肽的結構相關的信息，接受與候選物質相關的信息，以及確定候選物質與LINGO-l多肽的結合特點的指令。對結合特性的確定可基於與LINGO-l多肽結構相關的信息和與候選物質相關的信息來進行。在又一方面，本發明涉及存在於計算機可讀介質上的電腦程式，其具有儲存於其上的多個指令，當被一個或多個處理器執行時，所述指令導致一個或多個處理器接受與包含LINGO-l多肽的複合物結構相關的信息，接受與候選物質相關的信息，以及確定候選物質與LINGO-l多肽的結合特點。對結合特性的確定可基於與LINGO-l多肽結構相關的信息和與候選物質相關的信息來進行。在另一方面，本發明涉及一種方法，其包括接受與LINGO-l多肽的結構相關的信息，以及對LINGO-l多肽與候選物質的結合特點加以建模。所述方法可通過軟體系統實現。在又一方面，本發明涉及存在於計算機可讀介質上的電腦程式，其具有儲存於其上的多個指令，當被一個或多個處理器執行時，所述指令導致一個或多個處理器接受與LINGO-l多肽的結構相關的信息，以及對LINGO-l多肽與候選物質的結合特點加以建模。在另一個方面，本發明涉及軟體系統，其中包括下述指令，用於使得計算機系統接受與LINGO-l多肽的結構相關的信息以及對LINGO-l多肽與候選物質的結合特點加以建模。在另一個方面，本發明涉及調節受試者中LINGO-l活性的方法，所述方法包括例如使用本文描述的方法(例如，通過合理的藥物設計)，選擇能調節LINGO-l活性的物質，將有效量的所述物質施用給受試者，使得LINGO-l活性被調節。在另一個方面，本發明涉及治療具有與LINGO-l活性相關的病況的受試者的方法，所述方法包括例如使用本文描述的方法(例如，通過合理的藥物設計)，選擇能影響LINGO-l活性的物質，將治療有效量的所述物質施用給需要其的受試者。在又一個方面，本發明涉及對與LINGO-l活性相關的病況易感的受試者進行預防性治療的方法，所述方法包括確定所述受試者是否對與UNGO-l活性相關的病況易感，例如使用本文描述的方法(例如，通過合理的藥物設計)，選擇能影響LINGO-l活性的物質，以及將治療有效量的物質施用給受試者。在一些實施方案中，本文公開的方法(例如本文公開的治療和預防方法)中所用的物質能抑制LINGO-l活性和/或增加體內髓磷脂水平。在一些實施方案中，所述病況是脫髓鞘疾病，例如，多發性硬化。本發明的其它特徵和優點將從說明書、附圖和權利要求中顯而易見。圖1是經組氨酸標籤化的LINGO-l多肽(胺基酸1-516加6個His標籤)的氨基i^列(SEQIDNO:1)。用於結晶的片段被下劃線示出。圖2是針對精確修正過的2.7A解析度的LINGO-l結構的2fo-fc電子密度圖(也見表1)。圖3是LINGO-l單體的帶狀圖(ribbondiagram)。圖4是LINGO-l單體的空間填充模型。被編號的殘基指糖基化的天冬醯胺殘基。圖5A-5C是結構圖，其說明LINGO-l晶體結構的四聚體組織。圖5A是四聚體結構的頂視圖；圖5B是兩個單體間相互作用表面的視圖；圖5C是四聚體結構的側視圖。圖6是pSMEG質粒的圖鐠。圖7A-1至7A-3展示了pSMEG質粒的序列(SEQIDNO:2)。圖8A-8B描繪了人LINGO-l的全長胺基酸和核苷酸序列(分別是SEQIDNO:3和4)。編碼序列由SEQIDNO:4的核苷酸53至1915編碼。發明詳述一般而言，本公開涉及LINGO-l多肽、LINGO-l多肽/配體複合物、LINGO-l多肽的晶體、LINGO-l多肽/配體複合物的晶體以及相關方法和軟體系統。不希望被理論束溥，我們相信，LINGO-l多肽的晶體結構和LINGO-l多肽/配體複合物的晶體結構可用於設計或鑑定能與LINGO-l多肽相互作用的配體。能與LINGO-l多肽相互作用的配體能抑制或增加LINGO-l活性。例如，LINGO-l抑制已顯示能誘導髓磷脂形成。因此，我們相信，對LINGO-l抑制劑的鑑定可用於治療特徵為髓磷脂缺乏的病症，例如多發性硬化、佩，梅病(Pelizaeus-Merzbacher)、中樞神經系統損傷、腦白質營養不良(例如Krabbe病或Canavan病)或維生素B12缺乏。圖l是人LINGO-l多肽的片段(LINGO-lK549his6)的氨基餅列(SEQIDNO:1)，其包括富含亮氨酸的重複的結構域(胺基酸1-382)、免疫球蛋白樣(Ig樣)結構域(殘基383-477)、莖區域(胺基酸478-516)以及與莖區域的C末端融合的六組氨酸標籤。六組氨酸標籤能有利於純化。在全長人LINGO-l的N末端發現的33個胺基酸的信號序列在LINGO-lK549his6多肽中不存在。野生型序列還包括跨膜結構域和蛋白質C末端的短的胞質尾(Mi等人，7V^A^i/y^c/.2:221-228,2004)。圖2是LINGO-lK549his6結構被解析至2.7A解析度的電子密度圖(見表1)。圖3是展示了LINGO-lK549bis6多肽的結構的帶狀圖。LINGO-lK549his6多肽晶體結構的坐標提供於表2中。為測定LINGO-l的結構，可製備人LINGO-l多肽，按照下文所述對其進行結晶。一般而言，可以按照需要製備人LINGO-l多肽。例如，在一些實施方案中，人LINGO-l多肽是從DNA質粒表達的。表達可由啟動子來驅動，所述啟動子例如誘導型啟動子或組成型啟動子，例如，巨細胞病毒啟動子。人LINGO-l多肽可作為融合蛋白與合適的標籤一起表達，所述標籤例如多聚組氨酸(例如六組氨酸)、穀胱甘肽-S-轉移酶(GST)、myc、HA、Strep或FLAG標籤。標籤可協助將人LINGO-l多肽與細胞分離，例如，與細菌細月包或與哺乳動物細胞系分離。例如，人LINGO-l多肽可在中國倉鼠卵巢(CHO)細胞中表達，並從中^f皮分離。例如，人LINGO-l多肽可與六組氨酸標籤融合，並這樣來分離將細胞提取物與鎳樹脂(例如，次氮基三乙酸鎳(Ni-NTA)樹脂)接觸，以結合六組氨酸標籤，然後通過用含咪唑的緩衝液洗樹脂來釋放多肽。此外，可在設計加入融合蛋白的蛋白酶位點(例如，在多肽與標籤之間的融合位點或附近)，將融合LINGO-l多肽切割下來。人LINGO-l多肽可被放置於溶液中，以收集鐠數據、NMR數據，或者用於生長晶體。例如，人LINGO-l多肽可在鹽(例如，鈉鹽和/或銨鹽)存在下結晶。晶體可通過多種方法生長，例如，沉滴或懸滴蒸汽擴散法。一般而言，結晶可在從大約4°C至大約60°C的溫度(例如，從大約10°C至大約45。C，例如大約12°C、大約15°C、大約18°C、大約20°C、大約25°C、大約30。C、大約32。C、大約35°C、大約37。C)下進行。一般而言，人LINGO-l多肽可將X射線衍射至大約3.7A或更小的解析度(例如，大約3.6A或更小、大約3.5A或更小、大約3，2A或更小、大約3.0A或更小、大約2.7A或更小、大約2.4A或更小、大約2.3入或更小、大約2JA或更小、大約2.lA或更小、大約2.0A或更小、大約1.9人或更小、大約1,8A或更小、大約1.7A或更小、大約1.6A或更小、大約1.5A或更小、或者大約1.4A或更小)。在一些實施方案中，人LINGO-l多肽的晶體可將X射線衍射至從大約1.7A至大約3.7A的解析度(例如，人LINGO-l多肽的晶體可將X射線衍射至大約2.7A、大約3.5A或大約3.6A)。在某些實施方案中，人LINGO-l多肽的晶體屬於空間群I222，具有下述晶胞參數a=148.7A、b=158.6A、c=200.0A以及a-卩，-卯。。在其它實施方案中，人LINGO-l多肽的晶體屬於空間群1222,具有下述晶胞參數a=149.6A、b=157.3A、c=200.3人以及01=卩=7=卯°。在其它實施方案中，人LINGO-l多肽的晶體屬於空間群P2^2，具有下述晶胞參數a=201.5A、b=149.7A、c=157.5人以及a=P=y=90°。空間群指晶體的總體對稱，其包括點對稱和空間對稱。在某些實施方案中，人LINGO-l多肽的晶體屬於空間群1222，在其不對稱單位中含有兩個分子的人LINGO-l多肽。在其它實施方案中，人LINGO-l多肽的晶體屬於空間群P2JJ,其在不對稱單位中含有四個分子的人LINGO-l多肽。不對稱單位是可使用空間群的對稱操作來由其產生晶體結構的最小單位。晶體通常由不對稱單位上的空間群對稱操作所界定的基序以及經由晶格對該基序的平移(translation)構成。可以例如通過X射線衍射獲得描述晶體的結構數據，。可通過多種來源、x射線波長和檢測器收集x射線衍射數據。在一些實施方案中，可使用旋轉陽極和同步加速器源(例如，AdvancedLightSource(ALS),Berkeley,California或AdvancedPhotonSource(APS),Argonne，Illinois)作為X射線源。在某些實施方案中，用於產生衍射數據的X射線可具有從大約0.5A至大約1.6A的波長(例如，大約0.7A、大約0.9A、大約l.oA、大約l.iA、大約L3A、大約1.4A、大約1.5A或者大約1.6A)。在一些實施方案中，平面檢測器和/或電荷耦合器件(CCD)可用作檢測器。人LINGO-l多肽晶體的X射線衍射數據可用於獲得複合物中原子的結構坐標。結構坐標是笛卡爾(Cartesian)坐標，其描述了三維空間中的原子相對於複合物中其它原子的位置。例如，表中列出的結構坐標是結晶人LINGO-l多肽的結構坐標。表2的結構坐標描述了人LINGO-l多肽(SEQIDNO:5)、(SEQIDNO:6)、(SEQIDNO:7)和(SEQIDNO:8)的原子互相之間的相對位置。可通過數學處理來修改結構坐標，例如通過倒數或整數加減來進行。因此，結構坐標是相對坐標。例如，描述人LINGO-l多肽中原子位置的結構坐標並不被表2中實際的x、y和z坐標特定地限制。人LINGO-l多肽的結構坐標可用於得到對多肽或多肽片段的表示(representation)(例如，二維表示或三維表示)。此類表示可用於多種應用，包括，例如，對多肽活性位點的觀察、鑑定和分析。在某些實施方案中，三維表示可包括根據表2的人LINGO-l多肽結構坐標，±不超過大約1.5A(例如，不超過大約1.0A,不超過大約0.5A)的來自胺基酸a碳原子的均方根(rms)偏差。RMS偏差是與均值偏差的平方的算術均值的方根，其是表示與結構坐標的偏差或變化的方式。胺基酸的保守取代(見下文討論)可產生具有處於指定的rms偏差內的結構坐標的分子表示。例如，由於保守胺基酸取代而相互有所不同的兩個多肽分子模型具有的主鏈原子坐標可處於指定的rms偏差內，例如小於約1.5A(例如小於約l.O人、小於約0.5A)。多肽的主鏈原子包括a碳(Ca或CA)原子、羰基碳(C)原子和醯胺氮(N)原子。多種軟體程序允許對一套結構坐標進行圖形表示，以獲得對LINGO-l多肽或多肽片段的表示。通常，此類表示應當精確反映(相對和/或絕對)結構坐標或源自結構坐標的信息，例如特徵之間的距離或角度。在一些實施方案中，表示是交互式二維顯示，例如交互式立體二維顯示。交互式二維顯示可以是，例如，可旋轉以展示多肽或多肽片段的不同面的計算機顯示。在一些實施方案中，表示是三維表示。例如，三維表示可以是分子結構的物理模型(例如，球和棒模型)。還例如，三維表示可以是分子結構的圖形表示(例如，計算顯示上呈現的圖畫或圖)。當二維表示反映了三維信息時，例如，通過用與觀察者較近的特徵對與觀察者較遠的特徵加以透視、陰影或障礙時，二維圖形表示(例如圖畫)可對應於三維表示。在一些實施方案中，可在超過一個水平上針對表示建模。例如，當三維表示包括多肽，例如人LINGO-l多肽時，可在一個或多個不同的結構水平來表示該多肽，例如，在一級結構(胺基酸序列)、二級結構(例如a-螺旋和p-片)、三級結構(整體摺疊)和四級結構(寡聚狀態)上來進行。該表示可包括不同水平的細節。例如，該表示可包括蛋白質二級結構特徵的相對位置，而不特別指出原子位置。更詳細的該表示可例如包括原子位置。在一些實施方案中，該表示可還包括除了人LINGO-l多肽中原子的結構坐標之外的信息。例如，該表示可提供關於溶劑可達的表面的形狀、模型的原子的範德華半徑和溶劑(例如，水)的範德華半徑。可從該表示中獲得的其它特徵包括，例如，靜電勢、大分子結構中的空隙或口袋的位置以及氫鍵和鹽橋的位置。可通過下述方法來鑑定或設計與人LINGO-l多肽相互作用(例如結合)的物質，所述方法包括使用對多肽或多肽片段的表示。表示的示例性類型包括上文所討論的表示。在一些實施方案中，該表示可以是類似物多肽或多肽片段的。可通過進行對候選物質與表示的計算機擬合(fitting)分析，來鑑定或設計與該表示相互作用的候選物質。通常，該物質是分子。該物質的例子包括多肽、核酸(包括DNA或RNA)、甾類和非甾類有機化合物。與多肽(例如人LINGO-l多肽)相互作用的物質能與多肽暫時或穩定地相互作用。相互作用可被本文提到的任何力介導，所述力包括，例如，氫鍵、靜電力、疏水相互作用和範德華相互作用。如上文所述，可使用X射線晶體圖來獲得人LINGO-l多肽的結構坐標。但是，可使用其它技術，包括NMR技術，來獲得此類結構坐標。可從光鐠技術(例如，旋光色散(ORD)、圓二色鐠(CD))同源性建模和計算方法(例如，可包括來自分子力學的數據的計算方法、可包括來自動力學檢驗的數據的計算方法)來獲得其它結構信息。在一些實施方案中，可使用X射線衍射來構建人LINGO-l多肽或多肽片段的電子密度圖，可使用電子密度圖來獲得對人LINGO-l多肽的表示(例如，二維表示、三維表示)。典型地，電子密度圖的產生涉及到使用關於X射線散射相位的信息。相位信息可例如提取自衍射數據或用於完成對電子密度圖構建的補充性衍射實驗。用於計算來自X射線衍射數據的相位的方法包括，例如，多波長反常散射法(MAD)、多重同晶型取代法(MIR)、具反常散射的多重同晶型取代法(MIRAS)、具反常散射的單同晶型取代法(SIRAS)、倒易空間溶劑扁平化(reciprocalspacesolventflattening),分子置換(molecularreplacement)或其任何組合。這些方法通過製造天然蛋白質的同晶型(isomorphous)結構修飾(例如通過包括重原子或改變已經存在的重原子的散射強度)，然後測量天然蛋白質和每種經修飾情況的衍射幅度來產生相位信息。如果額外的重原子的位置或其^L射強度的改變是已知的，電腦程式來鑑定重原子位點的位置，所述程序例如，SHELXD(Bruker隱AXS，Madison,WI)或SHELXS(Sheldrick，InstitutAnorg.Chemie，G6ttingen,Germany)和XPREP(Bruker-AXS，Madison，WI);可使用電腦程式來加工衍射數據，所述程序例如MOSFLM、SCALA、SOLOMON和SHARP("TheCCP4Suite:ProgramsforProteinCrystallography,"爿c似O^toWogr.Sect.D,54:905-921,1997;deLaFortelleandBrigogne，Me仇五"g;附.276:472-494,1997)。4十對結晶人LINGO-l多肽的X射線散射的相位例如可通過SIRAS,使用LINGO-l多肽鉑衍生物的晶體來測定。為製造結晶LINGO-l多肽的鉑衍生物，可將結晶LINGO-l多肽浸泡於含鉑的溶液中。然後可在電腦程式(例如DM(CowtanandMain,J"flOj;".3^2:148-157，1993))中使用例如非晶體學對稱性(NCS)平均和相位延伸，來精確修正通過SIRAS從鉑衍生物獲得的相位。還可通過用第二數據組進行分子置換，來進一步衍生獲得的模型。例如，可用來自具有空間群P2"J的結晶LINGO-l多肽的數據組進行分子置換，對源自具有空間群1222的結晶LINGO-l多肽的模型進行精確修正。然後，可使用通過SIRAS從天然結晶多肽和鉑衍生物的晶體獲得的相位，來產生LINGO-l多肽的電子密度圖。可使用電子密度圖來獲得多肽或多肽片段的表示，這通過將多肽的三維模型與電子密度圖進行比對來實現。例如，可以將對應於天然結晶人LINGO-l多肽的電子密度圖與對應於結晶人LINGO-l多肽複合物的鉑衍生物(通過同晶型取代方法獲得的)的電子密度圖加以比對。比對過程產生了比較模型，其展示出計算出的電子密度圖與以前已知的多肽或以前已知的複合物相比變化的程度。然後可對比較模型進行一輪或數輪(例如兩輪、三輪、四輪、五輪、六輪、七輪、八輪、九輪、十輪)的精確修正，以產生與電子密度圖的更好的擬合。可使用軟體程序，例如CNS(Brunger等人，爿""Co^a/togr.^:905-921,1998)和REFMAC(CollaborativeComputationalProject,Number4.TheCCP4suite:ProgramsforProteinCrystallography,爿c似Oy1yto//og/%D50:760-776,1994)，來對模型加以精確修正。可例如通過Rfaet。r或Rfree值來測量比較才莫型中的擬合質量。通常，Rfact。r或Rfree的值越小就表明越好的擬合。可對比較模型中的不重合加以調整，以提供經修改的比較模型和較低的Rfact。r或Rfree值。調整可基於與人LINGO-l多肽的變化相關的信息(例如，序列變化信息、備選結構信息、重原子衍生物信息)來適當地進行。例如，在使用結晶LINGO-l多肽的重原子衍生物模型的實施方案中，調整可包括在重原子衍生物^t型上擬合天然LINGO-l多肽的大致模型。還例如，在某些實施方案中，調整可包括用具有相似結構的胺基酸替換以前已知的LINGO-l多肽中的胺基酸(保守胺基酸改變)。當對經修正的比較模型的調整滿足對電子密度圖的最佳擬合時，得到的模型就是被確定用來描述從其中獲得X射線數據的多肽或複合物的模型。此類過程的方法被公開於，例如，Carter和Sweet，編輯，"MacromolecularCrystallography"在MethodsinEnzvmologv,第277巻，B部分，NewYork:AcademicPress,1997及其中的文章，例如,Jones和Kjeldgaard,"Electron-DensityMapInterpretation,"第173頁和Kleywegt和Jones,"ModelBuildingandRefinementPractice,"第208頁中。機器，例如，計算機可按程序工作，在內存中使用人LINGO-l多肽的結構坐標連同程序能夠在機器相連的顯示器上產生對結構坐標的圖形表示。還可設計和/或利用軟體系統來接受或存儲結構坐標。軟體系統也能夠產生結構坐標的圖形表示。軟體系統還可能進入外部資料庫，以鑑定出一種或多種可能與人LINGO-l多肽相互作用的候選物質。具有含結構數據的內存或含此類數據的軟體系統的機器可協助對人LINGO-l多肽拮抗劑的人LINGO-l多肽激動劑的合理設計或選擇。例如，此類機器或軟體系統可協助對該物質與人LINGO-l多肽結合的能力加以評估，或者可協助通過與人LINGO-l多肽的結構或序列同源性來對相關化合物或蛋白質加以建模。在本文中使用時，激動劑指增強人LINGO-l多肽的至少一種活性的化合物，拮抗劑指抑制或抵消人LINGO-l多肽的至少一種活性的化合物。例如，化合物可通過，例如，增加神經細胞髓磷脂生產的速率，或者通過抑制人LINGO-l多肽與Nogo受體複合物的相互作用，來作為人LINGO-l多肽的拮抗劑發揮功能。機器可產生對人LINGO-l多肽或多肽片段的表示(例如，二維表示、三維表示)。軟體系統例如可使得機器產生此類信息。機器可包括機器可讀的存儲介質，其中包括用機器可讀的數據編碼的數據存儲材料。機器可讀的數據包括人LINGO-l多肽的原子的結構坐標。機器可讀的存儲介質(例如，數據存儲材料)包括，例如，傳統的計算機硬碟、軟盤、DAP磁帶、CD-ROM、DVD和其它磁性、磁光、光和可適於與機器(例如計算機)一起使用的其它介質。機器還可具有工作內存，以存儲用於處理機器可讀的數據的指令，以及具有與工作內存和機器可讀的數據存儲介質相耦合的中央處理單元(CPU)，用於將機器可讀的數據處理為想要的三維表示的目的。顯示器可與CPU相連，使得三維表示可被使用者看到。因此，當使用編程有使用數據的指令的機器(例如，裝有本文所述的種類的一種或多種程序的計算機)時，所述及其能顯示本文所述的多肽、多肽片段、複合物或複合物片段中任何的圖形表示(例如，二維圖形表示、三維圖形表示)。顯示器(例如計算機顯示器)可展示人LINGO-l多肽或人LINGO-l多肽片段的表示。使用者可觀察所述表示，以及，使用從所述表示獲得的信息，產生人LINGO-l多肽或與配體結合的多肽片段的模型。可例如通過改造已有的人LINGO-l多肽的表示來產生模型。任選地，使用者可將該物質的三維模型疊加到人LINGO-l多肽的表示上。該物質可以是人LINGO-l多肽的激動劑(例如候選激動劑)。在一些實施方案中，該物質可以是已知化合物或已知化合物的片段。在某些實施方案中，該物質可以是以前未知的化合物或以前未知的化合物的片段。其形狀能補足活性位點形狀的該物質可能是人們想要的。在該物質的原子和人LINGO-l多肽的原子間可以有優選的距離或距離範圍。比優選距離更長的距離可能與該物質和活性位點(例如，人LINGO-l多肽的活性位點)之間的弱相互作用相關聯。比優選距離更短的距離可能與能削弱該物質和多肽之間達到相互作用的斥力相關聯。當原子間距離過短時可能產生空間位阻。當兩個原子的位置不合理地接近時，例如，當兩個原子之間分開的距離要與它們的範德華半徑之和更小時，就可能產生空間位阻。如果存在空間位阻，使用者可調節該物質相對於人LINGO-l多肽的位置(例如，剛體平移或該物質的旋轉)，直到空間位阻減輕。使用者可調節該物質或物質附近人LINGO-l多肽的構象，以減輕空間位阻。還可通過改造該物質的結構，例如，通過將"大塊的基團"(例如芳香族環)改變為較小的基團，例如甲基或羥基，或通過將剛性基團改變為能成為不產生空間位阻的構象的柔性基團，來移除空間位阻。靜電力也可能影響該物質和配體結合結構域之間的相互作用。例如，靜電性質可與能削弱該物質與人LINGO-l多肽間相互作用的斥力相關聯。可通過改變該物質的電荷，例如通過用中性基團替換帶正電荷的基團來減輕靜電斥力。可在多肽/該物質模型中評估影響各候選物質與人LINGO-l多肽間結合強度的力。它們可包括，例如，氫鍵、靜電力、疏7jC相互作用、範德華相互作用、偶極-偶極相互作用、7T-堆集力和陽離子-7C相互作用。使用者可視覺評估這些力，例如通過觀察以適於氫鍵的距離和角度排列的氫鍵供體/受體對來實現。基於這種評估，使用者可對模型加以改造，以發現人LINGO-l多肽和該物質間的更有利的相互作用。對模型的改造可包括改變多肽的三維結構，而不改變其化學結構，這例如通過改變胺基酸側鏈或主鏈兩面角的構象來實現。對模型的改造可包括按照上文所述改變該物質的位置或構象。對模型的改造還可包括改變該物質的化學結構，例如通過取代、添加或去除基團來實現。例如，如果人LINGO-l多肽上的氫鍵供體位於該物質上的氫鍵供體附近，使用者可以用氫鍵受體替換該物質上的氫鍵供體。可以調節該物質和人LINGO-l多肽的相對位置或者它們的構象，以找到特定物質與人LINGO-l多肽的最優結合幾何條件。最優結合幾何條件特徵在於，例如，有利的氬鍵距離和角度、最大的靜電吸引、最小的靜電排斥、疏水部分從水環境的分隔、以及不存在空間碰撞。最優幾何條件計算出來的能量可能是人LINGO-l多肽/物質複合物的可能的幾何條件家族中最低的。可例如通過分子力學或分子動力學計算來確定最優的幾何條件。可以產生針對具有不同結合的該物質的人LINGO-l多肽的一系列表示。可以針對每種表示計算出分數。分數可以描述，例如，人LINGO-l多肽和該物質間相互作用的預期強度。分數可反映上文所述的影響結合強度的因素之一。分數可以是影響超過一種因素的累積分數。可根據其分數對不同的物質加以排序。設計物質的步驟可以通過機器以自動方式進行。例如，可在機器中對人LINGO-l多肽的表示和候選物質的表示一起編程。機器可找到對於每種候選物質與活性位點的最優結合幾何條件，並且計算出分數，以確定系列中的何種物質可能與人LINGO-l多肽最強烈地相互作用。可以設計和/或實現軟體系統，以協助這些步驟。用於產生表示或用於進行擬合分析的軟體系統(例如電腦程式)包括，例如MCSS、Ludi、QUANTA⑧(大分子X射線晶體學軟體)、Insight11@(生物化合物建模和模擬軟體)、Cerius^(建模和模擬軟體)、CHARMm⑧(用於模擬生物學大分子的軟體)、CHARMm斷用於模擬生物學大分子的軟體)和來自Accdrys，Inc.(SanDiego，CA)的Modeler;SYBYL⑧(分子建才莫軟體)、來自TRIPOS，Inc.(St.Louis，MO)的Unity、FleXX和LEAPFROG;AUTODOCK(ScrippsResearchInstitute,LaJolla，CA);GRID(OxfordUniversity,Oxford,UK);DOCK(UniversityofCalifornia,SanFrancisco,CA)和Flo+和Flo99(Thistlesoft,MorrisTownship,NJ)。其它有用的程序包括來自OpeneyeScientificSoftware(SantaFe，NM)的ROCS、ZAP、FRED、Vida和Szybki;來自Schrodinger，LLC(Portland，OR)的Maestro、Macromodel和Glide;MOE(ChemicalComputingGroup,Montreal,Quebec)、Allegrow(BostonDeNovo,Boston,MA)、CNS(Brunger，等人.,JctoOjW"//.Sect.D54:卯5-921,1997)和GOLD(Jones等人，丄Afo/.1^:43-53,1995)。還可使用MOLSCRIPT、RASTER3D或PYMOL(Kraulis/C，to//，946-950，1991;Bacon和Anderson,/楊/.219-220，1998;DeLano，ThePYMOLMolecularGraphicsSystem(2002)DeLanoScientific,SanCarlos,CA)，用結構坐標來觀察人LINGO-l多肽的三維結構。可以例如通過篩選合適的資料庫來選擇物質，可通過在合適的軟體系統協助下分析人LINGO-l多肽的立體構型和電荷勢能來對物質加以從頭設計，和/或可使用已知配體(例如神經營養因子受體p75和Nogo受體(NogoR))的特點來對物質加以設計。所述方法可用於設計或選擇人LINGO-l多肽的激動劑或拮抗劑。可設計和/或實現軟體系統，以協助資料庫搜索和/或物質的選擇和設計。一旦已經設計或鑑定了物質，其就可被獲得或合成，並且針對其對於人LINGO-l多肽活性的影響對其加以評估。例如，可通過將其與人LINGO-l多肽相接觸以及測量物質對於多肽活性的影響來對物質加以評估。用於評估物質的方法可包括體外或體內進行的活性測定。活性測定例如可以是基於細胞的測定。基於細胞的測定可包括監測候選物質對於髓磷脂生產的效果。針對人LINGO-l多肽抑制劑的此類測定可包括將候選抑制劑與表達人LINGO-l多肽的細胞相接觸，測定對於細胞形態的影響。例如，可將神經細胞系與候選物質接觸，就對於少突膠質細胞分化的影響對細胞加以監測。LINGO-l活性的減少已顯示能增加細胞向成熟少突膠質細胞的分化，這由細胞突長度的增加所證實(Mi等人，7VfltA^w仍de"ce2:745-751，2005)。還可通過測量髓磷脂產生所涉及的蛋白質的水平來檢驗LINGO-l活性，所述蛋白質例如髓磷脂相關糖蛋白(MAG)，這是在髓鞘形成開始時表達的蛋白質；髓磷脂鹼性蛋白(MBP)，這是髓磷脂的主要蛋白質組分；以及其它髓磷脂組分，包括少突膠質細胞-髓磷脂糖蛋白(OMpg)、髓磷脂少突膠質細胞糖蛋白(MOG)和環狀核苷酸磷酸二酯酶(CNPase)。LINGO-l抑制劑已顯示能促進對這些蛋白質各自表達的上調(Mi等人，？VM7Ve"fwde"ce5:745-751，2005)。可通過標準的蛋白質檢測技術，例如通過蛋白質印跡分析或通過在培養的細胞或全組織切片中的原位雜交進行的免疫組織化學方法，來檢驗蛋白質水平。取決於物質對於人LINGO-l多肽的作用，物質可作為人LINGO-l多肽活性的激動劑或拮抗劑發揮作用。激動劑例如可減少髓磷脂產生的速率，或者增加人LINGO-l多肽與Nogo受體複合物的結合親和性。相反，拮抗劑可增加髓磷脂產生的速率，或者減少人LINGO-l多肽與Nogo受體複合物的結合親和性。可在存在Nogo受體複合物的一種或多種組分(例如p75或Nogo-66)的情況下，將物質與人LINGO-l多肽相接觸，以確定物質是否能抑制人LINGO-1多肽與Nogo受體複合物結合。含有與鑑定出的物質結合的人LINGO-l多肽的晶體可生長，並通過X射線晶體學對其加以結構分析。可基於第一物質與人LINGO-1多肽的相互作用，來設計或鑑定第二物質。多種分子分析和合理的藥物設計技術還公開於，例如，美國專利號5,834,228、5,939,528和5,856,116中，以及PCT申請號PCT/US98/16879(公開為WO99/09148)中。雖然已經描述了某些實施方案，但是其它實施方案也包括在本發明內。例如，雖然已經描述了涉及人LINGO-1多肽的實施方案，但本文中的描述更為一般性地針對任何LINGO-1多肽。LINGO-1多肽可以是全長的成熟多肽，包括LINGO-1多肽的任何同種型的全長胺基酸序列。同種型是初級結構有所不同的幾種形式中的任何形式。人LINGO-l多肽的全長胺基酸和核苷酸序列公開於圖8A-8B中。LINGO-1多肽可以是人LINGO-1多肽的片段，例如，信號序列、LRR型結構域、Ig樣結構域、跨膜結構域、胞質結構域或其組合。LINGO-1多肽的片段可包括LINGO-1多肽序列(例如SEQIDNO:l)的超過40%、50%、60%、80%、90%或更多。例如，LINGO-1多肽可包括下述結構域中的一種或多種LRR型結構域(例如，SEQIDNO:l的大約1-382號胺基酸)或其片段或選定的殘基(例如，SEQIDNO:1的胺基酸Aspl3、Arg20、Arg22、Arg43、Glu60、Glu62、Leu94、Leul20、Metl23、Hisl76、Tyrl42、Hisl45、Hisl85、His209、His233、Ala238、Trp346、Arg347、Asn349、Asn351、Arg352和/或Gln353中的一個或多個)；Ig樣結構域(例如，SEQIDNO:1的大約383-477號胺基酸)或其片段或選定的殘基(例如，SEQIDNO:l的胺基酸Phe396、Arg408、Leu420、Leu426、Phe438、Asp440、Arg446、Tyr447和/或Ile459中的一個或多個)；和/或莖區域(例如，SEQIDNO:l的大約478-516號胺基酸)或其片段或選定的殘基。在其它實施方案中，LINGO-l多肽可含有本文所述的活性位點和/或結構摺疊中的一種或多種。LINGO-l多肽可含有一處或多處保守胺基酸取代，所述取代產生相似的三維結構，如本文所述。例如，在一些實施方案中，LINGO-l多肽(或其片段)包括對預定序列(例如人LINGO-l氨基*歹ij(例如SEQIDNO:1))的多至5、10、20、30、50、75、100、150或200或更多處保守取代。LINGO-l多肽可具有活性位點。例如，LRR樣結構域包括LINGO-l多肽的可能的活性位點。通常，活性位點包括配體結合位點或磷酸化、糖基化、烷基化、醯化或其它共價修飾位點。配體結合位點可以是Nogo受體複合物的組分或LINGO-l活性的激動劑或拮抗劑的結合位點。活性位點可包括糖基化位點。配體結合位點可包括與可能影響與配體相互作用的活性的實際結合位點接近或鄰近的附加結合位點。可通過將LINGO-l多肽的結構與其它已知多肽的同源結構加以比較，來鑑定人LINGO-l多肽的候選活性位點。例如，可通過將LINGO-l多肽的結構與血小板膜糖蛋白Gplba的結構加以比較，來鑑定人LINGO-l多肽的一個或多個活性位點。LINGO-l上包括Trp346和Arg352的候選活性位點是通過其與Gplba上的配體結合位點結構的相似性鑑定出來的。位於人LINGO-l多肽表面上的腔(cavities)也代表候選的配體結合位點。人LINGO-l多肽的活性位點可包括SEQIDNO:1的胺基酸(圖1)。例如，人LINGO-l多肽的活性位點可包括SEQIDNO:1胺基酸位置中示出的胺基酸Aspl3、Arg20、Arg22、Arg43、Glu60、Glu62、Leu94、Leul20、Metl23、Hisl76、Tyrl42、Hisl45、Hisl85、His209、His233、Ala238、Trp346、Arg347、Asn349、Asn351、Arg352、Gln353、Phe396、Arg408、Leu420、Leu426、Phe438、Asp440、Arg446、Tyr447和Ile459中的一處或多處。活性位點可包括位於人LINGO-l多肽特定區域的胺基酸的亞組。例如，活性位點可以位於LRR結構域的凹面，其包括SEQIDNO:1的Trp346和Arg352;His185、His209和His233;Aspl3;Glu60和Glu62;或Arg20、Arg22和Arg43。在另一實施例中，活性位點可位於LRR結構域的凸面，其包括SEQIDNO:1的Tryl42和Hisl45;Leu94、Leul20和Metl23;Hisl76;或Ala238。在另一實施例中，活性位點可位於Ig結構域，其包括SEQIDNO:1的Arg446和Tyr447;Arg408、Phe438和Asp440;Phe396;或Leu420、Leu426和Ile459。人LINGO-l多肽的胺基酸的編號可與本文所示的不同，人LINGO-l多肽的序列可含有保守胺基酸取代，其產生相同的三維結構。例如，人LINGO-l多肽的編號可不同於圖1所示，並且人LINGO-l多肽的序列可含有保守胺基酸取代，但是產生與表2的坐標定義的以及圖2-4和圖5A-5C闡述的結構相同的結構。通過對相關胺基酸序列的視覺觀察，或通過使用商業可獲得的同源性軟體程序(例如，MODELLAR，MSIManagementSimulations,Inc.,SanDiego,CA)，可容易地鑑定出其它同種型或類似物中對應的胺基酸和保守取代。表2所示的晶體結構坐標是從具有空間群P2,2-口的晶體測定的，但是相同的坐標+/-針對a碳原子而言不超過1.5A的均方根偏差可對應於具有不同空間群(例如1222)的結晶LINGO-l多肽。類似物是具有保守胺基酸取代的多肽。保守取代可包括用具有相似極性、立體排列或屬於同一類(例如，疏水、酸性或鹼性)的另一胺基酸來交換一個胺基酸，保守取代包括在對與多肽相互作用的物質的鑑定和設計方面，以及對分子置換研究和/或對同源性建模方面對於人LINGO-l多肽的三維結構具有不重要影響的取代。LINGO-l多肽的變體或突變體可用於本文7>開的方法、組合物和三維模型中。LINGO-l多肽或其片段的變體或突變體包括嵌合或融合蛋白、標記蛋白(例如放射性標記的蛋白質)、融合蛋白、突變體蛋白、具有相似(例如，高度相似)序列的蛋白質(例如，具有胺基酸取代(例如保守胺基酸取代)、缺失、插入的蛋白質)、蛋白質片段、模擬物，只要所述變體具有天然蛋白質的氨基#列的至少一部分或者具有與天然蛋白質序列高度相同的胺基酸序列的至少一部分即可。在一些實施方案中，突變體LINGO-l與SEQIDNO:l或其片段的氨基紗列具有多至5、10、20、30、50、75、100、150或200或更多個胺基酸殘基的不同。在其它實施方案中，突變體LINGO-l與LINGO-l多肽序列，例如，人LINGO-l多肽(例如SEQIDNO:l)具有至少大約70%、80%、卯％、95%或更高的同一性。"嵌合蛋白"或"融合蛋白，，是編碼多肽的第一胺基酸序列與第二胺基酸序列的融合，其中，所述第一和第二胺基酸序列天然狀態下並不作為單個多肽鏈的一部分存在。在本文中使用時，術語"高度相似"(或"高度"或"充分""同源"或"相同")在本文中用於指含有足夠數量的與笫二胺基酸或核苷酸序列相同或等同(例如，具有相似側鏈，例如，保守胺基酸取代)的胺基酸殘基或核苷酸的第一胺基酸或核苷酸序列。與本文公開的序列相似或同源(例如至少大約85。/。的序列同一性)的序列也是本申請的一部分。在一些實施方案中，序列同一性可以是大約90%、91%、92%、93%、94%、95%、96%、97%、98%、99%或更高。對兩條序列間"同源性"或"序列同一性"的計算按照下文所述來進行。就最優比較的目的對序列加以比對(例如，可向第一和第二胺基酸或核^列之一或兩條中都引入缺口，以進行最優比對，為了比較目的而言，非同源序列可不予考慮)。典型地，就比較目的而言被比對的參照序列的長度為參照序列長度的至少30%、優選至少40%、更優選至少50%、進一步更優選至少60%以及進一步最優選至少70%、80%、卯％、100%。然後對相應胺基酸位置或核苷酸位置上的胺基酸殘基或核苷酸加以比較。當第一序列中的位置被第二序列中相應位置上相同的胺基酸殘基或核苷酸所佔據時，那麼所述分子在該位置上就是相同的(在本文中使用時，胺基酸或核酸"同一性"與胺基酸或核酸"同源性"等同)。兩條序列間的百分比同一性是序列所共享的相同位置的數量的函數，其中要考慮到為對兩條序列進行最優比對需要引入的缺口的數量以及每個所述缺口的長度。對兩條序列間百分比同一性的測定和對序列的比較可以使用數學算法來完成。在一個實施方案中，使用Needleman和Wunsch((1970)/Mo/.5,V/.48:444-453)算法(已被併入商業可獲得的GCG軟體包中的GAP程序中)來測定兩條胺基酸序列間的百分比同一性，其中使用Blossum62矩陣或PAM250矩陣以及16、14、12、10、8、6或4的缺口權重以及1、2、3、4、5或6的長度權重。在另一實施方案中，使用GCG軟體包中的商業可獲得的GAP程序來測定兩條核苷酸序列間的百分比同一性，其中使用NWSgapdna.CMP矩陣和40、50、60、3070或80的缺口權重以及1、2、3、4、5或6的長度權重。典型用於測定百分比同源性的參數是Blossum62計分矩陣，缺口懲罰為12，缺口延伸懲罰為4，框移缺口懲罰為5。還可使用E.Meyers和W.Miller((1989)CM5/OS14:11-17)的算法(其已被併入AUGN程序(版本2.0)中)來測定兩條胺基酸或核苷酸序列的百分比同一性，其中使用PAM120權重殘基表，缺口長度懲罰為12和缺口懲罰為4。LINGO-l多肽可來源於非哺乳動物或哺乳動物物種。哺乳動物LINGO-l多肽可來源於例如人。示例性的非人類哺乳動物包括非人靈長類(例如猴或猿)、小鼠、大鼠、山羊、母牛、公牛、豬、馬、綿羊、野豬、海獺、貓和狗。示例性的非哺乳動物物種包括雞、火雞、壞、短吻鱘和魚。來自數種哺乳動物和非哺乳動物物種(包括，例如，人、小鼠、大鼠、狗、黑猩猩和雞)的LINGO-l胺基酸和核苷酸序列是本領域已知的(見，例如，Mi等人(2005)7VW7Ve"/wc/e"ce8:745-751;Carim國Todd，L.等人(2003)/7Ve"msc/.18(12):3167-3182和Okafuji等人(2005)6(1):57-62)物質可以是，例如，化學化合物(例如多肽、核酸、肽模擬物)。肽模擬物是能模擬肽識別某些生理分子(例如蛋白質和核酸)的能力的化學化合物。在一些情況下，肽模擬物包括能模擬或對抗天然親本肽的生物學作用的非肽性結構元件。例如，易斷開的肽鍵可被一個或多個不易斷開的二肽等排物(isostere)替換。下述實施例意在說明，並非作為限制。實施例對LINGO-l結晶，和測定其結構。人LINGO-l是614個胺基酸的蛋白質，其含有信號序列、富含亮氨酸的重複樣結構域、免疫球蛋白樣結構域、莖結構域、跨膜結構域和短胞質尾(Mi等人，7V"tiVewwd.2:221-228，2004)。人LINGO-l的細胞外區域(包括LRR基序、Ig樣結構域和莖區域，不包括信號序歹'J)在其C末端與六組氨酸標籤融合(圖1)。將得到的LINGO-lK549his6構建體亞克隆進pSMEG載體(SEQIDNO:2)(圖6和7A-1至7A-3)的鼠巨細胞病毒(CMV)啟動子之後(K549指位於全長人LINGO-l構建體的第249位胺基酸上的賴氨酸，其包括33個胺基酸的信號序列。信號序列在LINGO-lK549his6多肽中不存在)。通過測序對構建體加以驗證。在5%C02和37°C下，在溼潤的培養箱中生長和維持哺乳動物中國倉鼠卵巢(CHO)細胞。對Lec3.2.8.1的細胞培養和DNA轉染描述於Zhong等人祝0/^j^.12^:143-150，2005)中。通過用抗his4抗體加以篩選，在Lec3.2.8.1(1042-5)中建立LINGO-lK549his6構建體的穩定克隆。大規模生產LINGO-lK549his6的條件培養基的流程以前有過描述(Zhong等人，祝ocA/肌5,V//^s.1723:143-150,2005)。為純化LINGO-lK549his6，將表達融合蛋白的條件CHO培養基(圖1)換為pH8.0的50mMTris、100mMNaCl的緩沖液，向其中加入蛋白酶抑制劑混合物(來自Roche，Nutley，NJ的完全抑制劑)。為捕獲融合蛋白，在50mMTris,pH8.0，100mMNaCl中對Ni-NTA樹脂加以平衡，然後加入培養基中，用於分批結合(顛倒)2小時。除去培養基之後，將Ni-NTA樹脂裝入柱中。將柱與AKTAExplorere(HPLC)相連，用4-5倍柱體積的50mMTris,pH8.0，100mMNaCl來洗。用12倍柱體積的、從0%至100%的50mMTris，pH8.0;100mMNaCl，300mM咪唑的梯度洗脫蛋白質。將收集的蛋白質級分滲析進50mMTris，pH8.0;500mMNaCl。為進行結晶，將蛋白質與羧肽酶A(Sigma，St.Louis,MO)—起在250C孵育14-16小時，然後滲析進50mMMES，pH6.1;50mMNaCl。滲析後，將蛋白質上樣到SP瓊脂糖凝膠柱(GEHealthcare)上，用4-5倍柱體積的50mMMES,pH6.1;50mMNaCl洗。用從0%至100%的50mMMES,pH6.1;750mMNaCl的梯度洗脫蛋白質。收集蛋白質峰級分，濃縮至5-8mg/ml，然後上樣到用TBS平衡過的凝膠過濾Superdex200柱上。將蛋白質峰級分合併起來，濃縮至4-5mg/ml，用於結晶。純化的蛋白質是完全糖基化的。在18。C使用懸滴蒸汽擴散法來獲得LINGO-lK549his6晶體。從含4mg/mL蛋白質的蛋白質溶液和1.2-1.4M(NH4)2S04、O.IM檸檬酸鈉，pH5.0的沉澱溶液來生長衍射質量晶體(diffractionqualitycrystal)。蛋白質在相同條件下以兩種形式結晶，兩種形式都在同樣的結晶液滴中被發現1222，其每個不對稱單位具有2個分子，74%的溶劑含量；以及P2J"，其每個不對稱單位具有4個分子，73%的溶劑含量。為收集數據，將晶體逐漸從母液轉至含2.9M丙二酸鈉，pH5.2的穩定冷凍保護溶液(Holyoak等人,祝otog/c"/^9:2356-2358，2003)。該溶液(其中發現晶體在pH5-7的範圍內在數天的時間內穩定)被用於晶體衍生。從鈿衍生物獲得允許通過具反常散射的單同晶型取代方法(SIRAS)進行結構測定的單衍生物，所述鉑4汙生物是通過於pH7.0將晶體浸泡於50mMK2PtCl6和2.9M丙二酸鈉中24小時來製造的。在數據收集之前，所有晶體都在氮氣流下於IOOK糹皮沖冷。用從空間群1222的晶體獲得的兩組數據來進行相位測定3.5A天然資料庫和3.6A數據組用於鉑衍生物，兩組都是在室內用安裝於FR-ECuKa旋轉陽極源(Rigaku，Japan)上的Saturn92CCD測量的。在先進光子源(APS)(Argonne，Illinois)上，用來自屬於P2A2空間群晶體的SER-CAT的22-ID光束，將較高解析度的天然數據組收集至2.7A。所有數據都^f皮整合，用HKL2000進4亍度量(scale)(Otwinowski和Minor,五"g;附o/.276:307-326,1997)。使用Pt原子在CuKa-邊緣的反常差異，用SHELXD(2001,Bruker畫AXS，XM，Ver.6.12;Bruker畫AXS,Madison，WI)，對衍生晶體中柏(Pt)原子最初的位置加以定位。用XPREP(2001Bruker-AXS，Ver.6.12;Bruker-AXS，Madison，WI)來產生輸入SAS係數。使用來自天然和衍生資料庫的反常和同晶型差異，以20-3.6A的解析度，用SHARP(deLaFortelle和Bricogne，Me^oA^:472-494，1997)來進行對重原子參數的精確修正、相位計算和密度修改。用SHARP產生的最終的3.6A的、具反常散射的單同晶型取代(SIRAS)圖i普具有可供判斷的質量，其揭示了不對稱單位中的兩個LINGO-l分子。通過兩倍的非晶體學對稱(NCS)平均和在DM中將相位延伸至3.5A來進一步改善SHARP相位(Cowtan和Main,^"flOyW.^[2:148-157，1993)。得到的圖i普令我們可以用QUANTA(Accelrys，Inc.,SanDiego,CA)建立初始的、卯％完成的(大約855個殘基)模型。然後使用該^t型，用P2,2J數據組進行分子置換，以利用更高的2.7人的解析度數據。用PHASER(McCoy等人，j^l:458誦464，2005)來鑑定不對稱單元中四個分子的清澈溶液。1222和P2JJ晶體形式共享相同的四聚體填裝，其中，四聚體可通過圍繞兩倍軸複製二聚體來構建。用(結晶目標)-定向的工具包(COOT)(Emsley和Cowtan,^ctoO^s.D^:2126-2132，2004)和REFMAC(Murshudov等人，爿c似OjW"//ogr.Z)fl:240-255，1997)針對2.7A的數據組進行後續數輪的重構和精確4務正。最後的模型含有四個蛋白質分子(殘基Al-477、B3-475、C2-477和D3-476)、39個N-乙醯葡糖胺和12個甘露糖殘基以及310個水分子。B、C和D的N末端的殘基1-2;B和D的C-末端的476-477和殘基D32-34沒有被建模進入結構，因為缺少足夠的電子密度，這被假設是因為無序(disordering)造成的。用MolProbity進行的對經過最終精確修正的結構的幾何分析將所有殘基中的94%放進了有利的區域中，0.16%是外露的。表1中概括了針對數據收集、定相和精確修正的統計學分析。表2列出了從空間群P2^2的晶體推導出的晶體結構坐標(見表1)。具有空間群I222的天然和衍生結構揭示了高度相同的結構，它們被用於協助定相。在表2中，"#"欄向被給予坐標的每個原子指定指數。"名稱"欄則表明原子的類型，"res，，欄表明原子屬於何種類型的殘基。"鏈"表示原子所述的是何種多肽。"Resr，給出了原子的殘基號。例如，原子號1(表2中的第一列)是Thrl的氮(N)(根據SEQIDNO:1的序列)。在X、Y和Z欄中分別給出其x、y和z結構坐標。標題為"occ"的欄描述了被指定原子的佔據率(l.OO=完全佔據)，"B"欄提供了12單位的B因子(或溫度因子)。標有"元素，，的欄列出了原子的元素符號。水用"HOH"表示。"NAG"和"MAN"分別表示N-乙醯葡糖胺和甘露糖殘基。表l.數據收集、定相和精確修正的統計學分析數據收集天然lK2PtCl6天然2空間群12221222P2^2晶胞尺寸148.7149.6201.5b(A)158.6157.3149.7"A)200.0200.3157.5p=p=Y(度)909090源FR畫ECuKaFR國ECuKaAPSID22最大解析度(A)3.53.62.7反射(總的/獨特的)251,385/29,544201,963/27,406915,151/129,631完成率(％)97.1(98.8)99.1(99.8)98.9(94.7)Rsyma(%)11.7(50.2)10.5(45.9)9.0(61.2)IM(I)16.1(3.6)15.3(3.4)20.6(1.2)定相SIRASAnom.I/o(I)(4.5A/3.6人)2.3/1.2Risob(%)43.6Ranob(%)8.6Pt位點的數量15定相力e(4.5A/3.6A)反常同晶型1.13/0.61.1/0.73晶體品質因素均值d(4.5A/3.6A)0.45/0.25模型精確修真天然2解析度(A)50.0-2.7反射的數量122,982完成率(％)98.7(91.3)Rfacto鳥ee*(%)21.5/25.5蛋白質原子的數量15,114碳水化合物原子的數量700水的數量310與理想幾何條件的r.m.s偏差鍵(人)角(deg)0.0091.25aRsym-HillOOi_I/ZI(h)i，其中是平均強度。括號中的數字反映了對最高解析度外形(shell)的統計學分析。bRis。=i:IFnat(h)—FPt(h)I/ZFnat(h)，Ran。是針對Bijvoet對的陽性和陰性副本的幅度來計算的。c定相力被定義為叫FHlW〈(缺少封閉(lack-of-closure))、其中'H，代表重原子。d晶體品質因素均值是估計的相位錯誤的平均餘弦。、free是用數據的5%計算的。LINGO-l的兩種晶體結構(1222和P2JJ)揭示了與凝膠過濾數據和動力學光散射測量相一致的四聚體結構，這表明，LINGO-l作為四聚體存在於溶液中，分子量為大約240kDa。圖2顯示了針對經精確修正的2.7A解析度結構的電子密度的片段。圖3中顯示了單體LINGO-l結構的總視圖。每個單體都是由兩個不同的結構域形成的殘基1-382組成了N末端LRR結構域，殘基383-477形成了C末端的Ig樣結構域。兩種組分結構域之間的相對定向賦予單體高難度結構的形狀(questionmarkshape)。LRR結構域(殘基l-382)採用延長的弧形，其具有在凹內面上平行的15鏈p-片，還具有凸外面上的高度反常的二級結構(圖3)。總而言之，有12個LRR，每個23至25個殘基，它們一起產生連續的右手超螺旋集合。每個LRR都從p-鏈開始，其具有24個殘基的序列重複基序xL2xxL5xL7xxN10xL12xxLlsxxxxF20xxL23x(SEQIDNO:9)，其中，x可以是任何胺基酸；L是疏水殘基，優選是L但也可以是Ile、Val、Met、Phe或Thr;N是天然較不保守的，其包括主要是Asn，但也可以是Cys、Asp、Leu或Trp;F代表疏水殘基Phe或Leu。指出的位置上的共有殘基構成了LRR結構域的內部。與數種其它LRR蛋白質中一樣，兩種LRR帽("N帽"和"C帽，，)使得LRR疏水核心的N和C末端針對溶劑而言被遮蔽(圖3)。"N帽"具有兩條反平行的P-鏈，其在底部(base)具有兩個二石克鍵(Cys-Cys9和Cys7-Cys18)，這是與NogoR結構上非常接近的排列(He，等人，A^w/wi^:177-185，2003)。"C帽"還被兩個二硫鍵(Cys334-Cys357和Cys336-Cys382)支持，並且，與NogoR類似，具有由一個a-螺旋和三個短310-螺旋構成的特徵性基序。但與NogoR不同，LINGO-l中"C帽，，的內部基本全部填充苯丙氨酸蔟(來自Phe342、Phe350、Phe362、Phe368、Phe371、Phe380的六個芳香族環和來自Tyr379的一個芳香族環)。此外，a-螺4t之後的短環片斷(殘基349-353)以與NogoR中略有不同的方式整合進規範的LRR結構。這導致5個殘基環的頂部離開P-片凸出進凹面空間至少7.5A，因此展示出比NogoR中同樣長度的相應片斷更突起的特點。凸出環的位置(圖3)(對應於血小板膜糖蛋白Gplba中配體結合Ji-開關環(Huizinga等人，Sdewce122:1176-1179，2002))與表面暴露和突起側鏈(Trp346、Arg347和Asn349、Asn351、Gln353和Arg352，位於環尖)的特點組合，暗示其可能是與配體相互作用的候選者。分子的靜電錶面(圖4)揭示了在LRR結構域的所有側面上的正電和負電補片(patch)，只除了在N末端凸側發現的一個相對較大的疏水補片之外。基於四聚體複合物的結構，位於LRR結構域凹面上的五個胺基酸亞組被確定為候選的配體結合位點(1)Trp346和Arg352;(2)Hisl85、His209和His233;(3)Aspl3;(4)Glu60和Glu62;和(5)Arg20、Arg22和Arg43。類似地，位於LRR結構域凸面上的四個胺基酸亞組被確定為候選的配體結合位點(1)Tryl42和Hisl45;(2)Leu94、Leul20和Metl23;(8)Hisl76;和(9)Ala238。完成LRR結構域後，多肽鏈進入壓縮的Ig樣摺疊(殘基383-477)，其代表經典的、由一個二硫鍵(Cys407-Cys458)交聯的兩個p-片的卩-三明治。來自一個P-片的四條鏈(A、B、D和E)和五條鏈(A'、C、C'、F和G)構成了第二P-片。有一個310a-轉角連接E和F鏈。與其它Ig樣結構的比較表明，LINGO-lIg樣結構域的最接近的結構的神經細胞粘附分子NCAM的Ig3模塊(Soroka等人，5^""""!￡:1291-1301，2003)，計算出的兩條序列的同一性為約30%。並不出人意料地，胺基酸替換的絕大多數都發生於Ig結構域表面，這改變了側鏈體積和/或側鏈極性，而保守胺基酸中的大多數都定位於結構的核心，並且具有等同的構象，以滿足摺疊。表面靜電勢是ABDE-表面上負和正補片的組合。相反，反向的A，CC'FG-表面則高度富含疏水殘基(Ala416、Leu418、Leu420、Leu426、Leu457、Ile459、Ala461、Ala463)，它們被大量的極性和帶正電荷的殘基環繞。Ig結構域定向使得其遠離凸LRR弧而突出，在LRR結構域的背面產生寬廣的暴露給溶劑的裂縫，並且具有大約90度的急彎(圖4)。裂縫的壁是由一側的LRRC-末端凸面(重複10-12和C帽)和另一側的Ig結構域的A，CC，FGp-片形成的。反面則相對遠離，並且具有不同的性質。凸面主要由極性和帶電荷殘基構成，而反面的Ig面則相當平，排列有主要疏水的胺基酸(如上文所述)。在急彎的尖上發生小的結構域間相互作用，這涉及FG環上的殘基(Ala463、Gly464)和LRR的C末端部分(Cys336、Arg337和Cys382)的範德華接觸。需要注意的是急彎尖上的二硫鍵——Cys336-Cys382以及結構域間不存在接頭(因為Arg383是第一P-鏈的第一個殘基以及ABDEp-片的組分)。結構域間的此類聯結限制了它們兩個互相之間的定位。基於四聚體複合物的結構，位於lg結構域凹面上的五個胺基酸亞組被確定為候選的配體結合位點(1)Arg446和Tyr447;(2)Arg408、Phe438和Asp440;(3)Phe396;和(4)Leu420、Leu426和Ile459。我們預計，CHO受限細胞中LINGO-l的糖形式主要是高甘露糖形式的多糖，例如MansGlcNAc2,這與我們的質譜數據一致。結晶的糖蛋白含有八個典型的N-糖基化共有位點。其中六個位於LRR結構域中(Asn105、Asnl63、Asn225、Asn235、Asn254和Asn302),兩個位於Ig樣結構域中(Asn466和Asn453)。所有這些位點都位於結構域表面。可對所有這些位置上的碳7JC化合物基序給予電子密度，只除了Asn466位點。後者雖然也位於表面，但卻被對稱性相關LINGO-l伴侶緊密包裹，如下文所述和圖5所示。因為蛋白質包裹沒有給Asn466留存糖基化的空間，因此與Asn466相連的N-多糖將阻止在晶體中觀察到的LINGO-l四聚化。剩下的七個位點上的寡糖在如圖4的被編號的殘基所示的結構上鋪展，其中，#1對應於Asnl05，^2對應於Asn163，#3對應於Asn225，弁4對應於Asn235,#5對應於Asn254，糾對應於Asn302,#7對應於Asn453。在LRR結構域的四個面外，僅凸外面完全沒有碳水化合物，此發現與其在自聯作用中的作用一致。凹面和兩個側面(每個都具有兩個N-多糖結合位點)被碳7jC化合物大大覆蓋。最後的碳水化合物部分定位到Ig-面A，CC，FG上，接近C末端，並且遠離分子間界面(圖4)。一般而言，在糖蛋白表面上大量的糖基化的存在會限制它們與配體相互作用發生的可及性，在大多數情況下，沒有被糖覆蓋的表面是配體預計會結合之處(Rudd等人，/Af必293:351-366，1999)。因此，LINGO-l的凹LRR面(在弧中心具有兩個糖部分)看起來不可能在容納此類大的蛋白質伴倡(如NogoR或p75)中扮演主要角色。這與頻繁使用凹面與它們的配體發生相互作用的其它含LRR受體相反(Bell等人，7>wi*/附附wto/.2^:528，2003)。因為沒有證據表明與Asn相連的N-多糖直接與配體結合相關，因此也有可能是LINGO-l糖基化協助阻止非特異性蛋白質-蛋白質相互作用或者協助保持正確的骨架用於隨後的配體結合。結晶、體積排阻色譜和動力學光散射都表明，LINGO-l在晶體和溶液中都採用四聚體形式。在晶體中，LINGO-l的四個獨立的拷貝相互作用，構成被壓緊的四聚體結構。旋轉的假四倍軸將環樣結構中的四個分子與中心的大洞(直徑大約40A，外環直徑大約95A;圖5A)關聯起來。這種排列將每個LRR結構域的N末端凸側放置於鄰近分子的結構域間的急彎上(圖5B)，令人聯想到細胞因子/受體結合模式。在後一種情況下，兩個分子間的連結點是三個表面提供的N末端彎曲重複l-6形成的一個、如上文所述分別通過C末端彎曲重複11-12、"C帽"和A，CC，FGp-鏈形成的兩個急彎表面。因此，四個LRR結構域頭尾聯鎖成環，相應的Ig樣模塊從環的周界以起落架(landinggear)方式延伸(見圖5C)。如果我們將這種幾何條件相對細胞表面來應用的話，那麼蛋白質旋轉軸將以大致垂直於表面，接近膜的C末端將指向同方向，即朝向細胞膜。每個分子間界面都揭示了結合表面間的緊密幾何匹配和相互作用的精確立體化學互補性。在每個格間界面下埋藏著的溶劑可達的表面區域相對較大，來自三種各組分，總共2400A2，這暗示了強烈的關聯。上述證據組合相互作用的多價特點暗示，四聚體內的接觸並不僅是晶體接觸。表2.LINGO-lK549his6多肽的結構坐標(分別為SEOIDNO:5-8)tableseeoriginaldocumentpage43tableseeoriginaldocumentpage44原子86CBASPA1347.45347.69522.8231.0078.35C原子87CGASPA1347.61548.21624.2391.0079.47C原子880D1ASPA1347■48849.45124.44310081,.370原子89OD2ASPA1347.8594739425.15110079,.74〇原子90CASPA1348.20347.85520.4581.0077.63C原子910ASPA1349.05046.98120.2751.0077.600原子92NARGA1447.3214824419.5321.0076.93N原子93CAARGA1447.09547.53018.2751.0076.17C原子94CBARGA1448.25647.74917.3001.0076.39C原子95CGARGA1448.45149.22916.9531.0077.97C原子96CDARGA1449.71449.48016.1481.0080.67C原子97NEARGA1449.92650.90915.9181.0083.36N原子98CZARGA1450.61751.42514.8991.0084.74C原子99麗lARGA1450.73952.7441477510083.73N原子100NH2ARGA1451.17950，62713，9941.0085.78N原子101CARGA1446.81146.05118.5611.0075.25C原子1020ARGA144740845.16317，9711.0075.140原子103NalaA1545.88645.82619.4931.0074.33N原子104CAALAA1545.,48144..50719.,9471.,0073.,70C原子105CBALAA1545.,54644..44621.,4521.,0073..72C原子106ca:laa1544.07244.180is-4801.0073.38c原子1070ALAA1543.24445.069IS.3261.0073.570原子108NVALA1643.80942.90119.2431.0073.08N原子109CAVALA1642.,48342.,43118.,8671..0072.,86C原子110CBVALA1642..35342.■20017..3381..0072.,76c原子111CGIVALA1641.10841.38217.0121.0072.82c原子112CG2VALA1642.30943.52716.5941.0072.51c原子113Cvala164221141.146IS-6281.0072.88c原子1140VALA1642.■97640.199IS.5501.0072710原子115NLEUA1741.11141.12620.3631.0073.25N原子116CALEUA1740,.79540..02321,.2371,.0073,.61C原子117CBLEUA1740,.95740..50322.6751.0073,.93C原子118CGLEUA1740,.83439,.52223,.83510075,.24C原子119CD1LEUA1741.87539.870248851，0077.28C原子120CD2LEUA173941939.525244401.0076.11C原子121CLEUA1739.,38439.50020.,9551.,0073..77c原子1220LEUA1738.,40840..21821■.1181.,0073..270原子123NCYSA1839.,29138.,24620.,5201.,0074.,57N原子124CACYSA1838.01537.638201281.007547C原子125CBCYSA1837.94437,50018.6081.007544C原子126SGCYSA1838.02539,.05917.7411.0076,.95S原子127CCYSA1837.82136.■26220.,7401.,0076.04C原子1280CYSA1838■,23335..26220.,1561.■0076..18〇原子129NHISA1937.,18736.,19921.,9071.,0076..81原子130CAHISA1936.95934.90822.5511.0077，38C原子131CBHISA1937.36834.95924.0181.0077.93C原子132CGHISA1938.83835.13524.2201.0079.99C原子133ND1HISA1939.41036.357244931.0081.52N原子134CE1HISA1940.71836.21024.6131.0083.13C原子135NE2HISA1941.01534.938244141，0083.73N原子136CD2HISA1939.85634,24324.17110082.59C原子137CHISA1935.51534.46722.4311.0077，21C原子1380HISA1934.60935.29422.4621.0077,010原子139NARGA2035.32333.15822.2791.0077.16N原子140CAARGA2034.00232.52122.3411.0077.64C原子141CBARGA2033.41932.63823.7571.0077.35C原子142CGARGA203412531.770247841.0078.80C原子143CDARGA2033.60232.02226.1931.0080.18C原子144NEARGA2033.97233.35426.6861.0086,15N原子145CZARGA2035.08033.62927.3821.0088.16C原子146NH1ARGA2035.95732.66827.6951.0087.59N原子147NH2ARGA2035.30834.88227.7671.0089.44N原子148CARGA2033.00033.02821.3071.0076.83C原子1490ARGA2031.81333.15721.6051.0076.960原子150NLYSA2133.47033.29420.0901.0076.32N原子151CALYSA2132.62433.92319.07510075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